How can I map from PDB-Residues to UniProt-Residues and vice versa? #17

NatureGeorge · 2021-06-02T06:37:37Z

NatureGeorge
Jun 2, 2021
Maintainer

Demo PDB2UNP input

pdb_id	chain_id	Ref	Alt	author_residue_number
1b28	A	M	A	31
1b28	A	Y	A	36
1b28	A	L	A	40
1lve	A	S	N	29
1uw3	A	H	R	155
4fng	A	L	M	364
4fng	A	E	K	530
4fng	A	G	D	554
4z3t	A	R	L	130
4z3t	A	D	G	133
4z3t	B	R	L	130
4z3t	B	D	G	133

click to get csv format

pdb_id,chain_id,Ref,Alt,author_residue_number,author_insertion_code
1b28,A,M,A,31,
1b28,A,Y,A,36,
1b28,A,L,A,40,
1lve,A,S,N,29,
1uw3,A,H,R,155,
4fng,A,L,M,364,
4fng,A,E,K,530,
4fng,A,G,D,554,
4z3t,A,R,L,130,
4z3t,A,D,G,133,
4z3t,B,R,L,130,
4z3t,B,D,G,133,

Demo UNP2PDB input

ftId	Ref	Pos	Alt
P03050	R	31	M
P03050	E	36	Y
P03050	R	40	L
P06312	N	55	S
P23907	Y	158	H
Q25252	M	364	L
Q25252	K	530	E
Q25252	D	554	G
Q6VS32	L	130	R
Q6VS32	G	133	D
Q6VS32	L	130	R
Q6VS32	G	133	D

click to get csv format

ftId,Ref,Pos,Alt
P03050,R,31,M
P03050,E,36,Y
P03050,R,40,L
P06312,N,55,S
P23907,Y,158,H
Q25252,M,364,L
Q25252,K,530,E
Q25252,D,554,G
Q6VS32,L,130,R
Q6VS32,G,133,D
Q6VS32,L,130,R
Q6VS32,G,133,D

Answered by NatureGeorge

Jun 2, 2021

PDB2UNP

pdb_profiling --custom_db task_20210602.db insert-pdb-mutation -i pdb2unp.csv --sep ',' --usecols 'pdb_id,chain_id,Ref,Alt,author_residue_number,author_insertion_code' --auth

pdb_profiling --custom_db task_20210602.db sifts-mapping --func pipe_select_base --autotype from_PDBAuthMutation -o task_20210602_pdb2unp_SIFTS-MAPPING.tsv

pdb_profiling --custom_db task_20210602.db residue-mapping -i task_20210602_pdb2unp_SIFTS-MAPPING.tsv

pdb_profiling --custom_db task_20210602.db export-pdb-mutation-mapping --auth -o task_20210602_pdb2unp_RESIDUE-MAPPING.tsv

click to get final result

UniProt	pdb_id	entity_id	struct_asym_id	chain_id	Ref	Alt	author_residue_number	author_insertion_code	ob…

View full answer

NatureGeorge · 2021-06-02T07:15:36Z

NatureGeorge
Jun 2, 2021
Maintainer Author

PDB2UNP

pdb_profiling --custom_db task_20210602.db insert-pdb-mutation -i pdb2unp.csv --sep ',' --usecols 'pdb_id,chain_id,Ref,Alt,author_residue_number,author_insertion_code' --auth

pdb_profiling --custom_db task_20210602.db sifts-mapping --func pipe_select_base --autotype from_PDBAuthMutation -o task_20210602_pdb2unp_SIFTS-MAPPING.tsv

pdb_profiling --custom_db task_20210602.db residue-mapping -i task_20210602_pdb2unp_SIFTS-MAPPING.tsv

pdb_profiling --custom_db task_20210602.db export-pdb-mutation-mapping --auth -o task_20210602_pdb2unp_RESIDUE-MAPPING.tsv

click to get final result

UniProt	pdb_id	entity_id	struct_asym_id	chain_id	Ref	Alt	author_residue_number	author_insertion_code	observed_ratio	residue_number	unp_residue_number	multiple_conformers	residue_name	pdb_one_letter_code	unp_one_letter_code
P03050	1b28	1	A	A	M	A	31		1.0	31	31		MET	M	R
P03050	1b28	1	A	A	Y	A	36		1.0	36	36		TYR	Y	E
P03050	1b28	1	A	A	L	A	40		1.0	40	40		LEU	L	R
P06312	1lve	1	A	A	S	N	29		1.0	35	55		SER	S	N
P23907	1uw3	1	A	A	H	R	155		1.0	31	158		HIS	H	Y
Q25252	4fng	1	A	A	L	M	364		1.0	364	364		LEU	L	M
Q25252	4fng	1	A	A	E	K	530		1.0	530	530		GLU	E	K
Q25252	4fng	1	A	A	G	D	554		1.0	554	554		GLY	G	D
Q6VS32	4z3t	1	A	A	R	L	130		1.0	135	130		ARG	R	L
Q6VS32	4z3t	1	A	A	D	G	133		1.0	138	133		ASP	D	G
Q6VS32	4z3t	1	B	B	R	L	130		1.0	135	130		ARG	R	L
Q6VS32	4z3t	1	B	B	D	G	133		1.0	138	133		ASP	D	G

UNP2PDB

pdb_profiling --custom_db task_20210602.db insert-mutation -i unp2pdb.csv --sep ',' --usecols 'ftId,Ref,Pos,Alt'

pdb_profiling --custom_db task_20210602.db id-mapping check-muta-conflict

pdb_profiling --custom_db task_20210602.db sifts-mapping --func pipe_select_base -o task_20210602_unp2pdb_SIFTS-MAPPING.tsv residue-mapping -i task_20210602_unp2pdb_SIFTS-MAPPING.tsv

pypath=$(python -c 'from distutils.sysconfig import get_python_lib; print(get_python_lib())')
sqlite3 -header -cmd ".mode tabs" ./local_db/task_20210602.db < $pypath/pdb_profiling/sql/export_mutation_mapping_all.sql > task_20210602_unp2pdb_RESIDUE-MAPPING.tsv

click to get final result

UniProt	Ref	Pos	Alt	residue_number	author_residue_number	author_insertion_code	observed_ratio	pdb_id	entity_id	struct_asym_id	chain_id	observed_ratio	residue_name	unp_one_letter_code	pdb_one_letter_code
P03050	R	31	M	31	31		1.0	1arq	1	A	A	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1arq	1	A	A	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1arq	1	A	A	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1arq	1	B	B	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1arq	1	B	B	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1arq	1	B	B	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1arr	1	A	A	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1arr	1	A	A	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1arr	1	A	A	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1arr	1	B	B	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1arr	1	B	B	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1arr	1	B	B	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1b28	1	A	A	1.0	MET	R	M
P03050	E	36	Y	36	36		1.0	1b28	1	A	A	1.0	TYR	E	Y
P03050	R	40	L	40	40		1.0	1b28	1	A	A	1.0	LEU	R	L
P03050	R	31	M	31	131		1.0	1b28	1	B	B	1.0	MET	R	M
P03050	E	36	Y	36	136		1.0	1b28	1	B	B	1.0	TYR	E	Y
P03050	R	40	L	40	140		1.0	1b28	1	B	B	1.0	LEU	R	L
P03050	R	31	M	31	31		1.0	1baz	1	A	A	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1baz	1	A	A	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1baz	1	A	A	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1baz	1	B	B	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1baz	1	B	B	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1baz	1	B	B	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1baz	1	C	C	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1baz	1	C	C	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1baz	1	C	C	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1baz	1	D	D	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1baz	1	D	D	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1baz	1	D	D	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1bdt	3	C	A	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1bdt	3	C	A	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1bdt	3	C	A	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1bdt	3	D	B	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1bdt	3	D	B	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1bdt	3	D	B	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1bdt	3	E	C	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1bdt	3	E	C	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1bdt	3	E	C	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1bdt	3	F	D	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1bdt	3	F	D	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1bdt	3	F	D	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1bdv	3	C	A	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1bdv	3	C	A	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1bdv	3	C	A	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1bdv	3	D	B	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1bdv	3	D	B	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1bdv	3	D	B	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1bdv	3	E	C	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1bdv	3	E	C	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1bdv	3	E	C	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1bdv	3	F	D	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1bdv	3	F	D	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1bdv	3	F	D	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1myk	1	A	A	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1myk	1	A	A	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1myk	1	A	A	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1myk	1	B	B	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1myk	1	B	B	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1myk	1	B	B	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1myl	1	A	A	1.0	MET	R	M
P03050	E	36	Y	36	36		1.0	1myl	1	A	A	1.0	TYR	E	Y
P03050	R	40	L	40	40		1.0	1myl	1	A	A	1.0	LEU	R	L
P03050	R	31	M	31	31		1.0	1myl	1	B	B	1.0	MET	R	M
P03050	E	36	Y	36	36		1.0	1myl	1	B	B	1.0	TYR	E	Y
P03050	R	40	L	40	40		1.0	1myl	1	B	B	1.0	LEU	R	L
P03050	R	31	M	31	31		1.0	1myl	1	C	C	1.0	MET	R	M
P03050	E	36	Y	36	36		1.0	1myl	1	C	C	1.0	TYR	E	Y
P03050	R	40	L	40	40		1.0	1myl	1	C	C	1.0	LEU	R	L
P03050	R	31	M	31	31		1.0	1myl	1	D	D	1.0	MET	R	M
P03050	E	36	Y	36	36		1.0	1myl	1	D	D	1.0	TYR	E	Y
P03050	R	40	L	40	40		1.0	1myl	1	D	D	1.0	LEU	R	L
P03050	R	31	M	31	31		1.0	1myl	1	E	E	1.0	MET	R	M
P03050	E	36	Y	36	36		1.0	1myl	1	E	E	1.0	TYR	E	Y
P03050	R	40	L	40	40		1.0	1myl	1	E	E	1.0	LEU	R	L
P03050	R	31	M	31	31		1.0	1myl	1	F	F	1.0	MET	R	M
P03050	E	36	Y	36	36		1.0	1myl	1	F	F	1.0	TYR	E	Y
P03050	R	40	L	40	40		1.0	1myl	1	F	F	1.0	LEU	R	L
P03050	R	31	M	31	31		1.0	1nla	1	A	A	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1nla	1	A	A	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1nla	1	A	A	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1nla	1	B	B	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1nla	1	B	B	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1nla	1	B	B	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1par	3	C	A	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1par	3	C	A	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1par	3	C	A	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1par	3	D	B	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1par	3	D	B	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1par	3	D	B	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1par	3	E	C	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1par	3	E	C	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1par	3	E	C	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1par	3	F	D	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1par	3	F	D	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1par	3	F	D	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1qtg	1	A	A	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1qtg	1	A	A	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1qtg	1	A	A	1.0	ARG	R	R
P03050	R	31	M	31	31		1.0	1qtg	1	B	B	1.0	ARG	R	R
P03050	E	36	Y	36	36		1.0	1qtg	1	B	B	1.0	GLU	E	E
P03050	R	40	L	40	40		1.0	1qtg	1	B	B	1.0	ARG	R	R
P23907	Y	158	H	14	14		1.0	1g04	1	A	A	1.0	TYR	Y	Y
P23907	Y	158	H	14	14		1.0	1m25	1	A	A	1.0	TYR	Y	Y
P23907	Y	158	H	21	155		1.0	1s4t	1	A	A	1.0	TYR	Y	Y
P23907	Y	158	H	45	158		1.0	1tpx	1	A	A	1.0	TYR	Y	Y
P23907	Y	158	H	32	158		1.0	1tqb	1	A	A	1.0	TYR	Y	Y
P23907	Y	158	H	32	158		1.0	1tqc	1	A	A	1.0	TYR	Y	Y
P23907	Y	158	H	31	155		1.0	1uw3	1	A	A	1.0	HIS	Y	H
P23907	Y	158	H	35	155		1.0	1xyu	1	A	A	1.0	TYR	Y	Y
P23907	Y	158	H	37	155		1.0	1y2s	1	A	A	1.0	TYR	Y	Y
P23907	Y	158	H	78	158		1.0	2mv8	1	A	A	1.0	TYR	Y	Y
P23907	Y	158	H	78	158		1.0	2mv9	1	A	A	1.0	TYR	Y	Y
P23907	Y	158	H	78	158		1.0	2n53	1	A	A	1.0	TYR	Y	Y
Q6VS32	L	130	R	135	130		1.0	4z3t	1	A	A	1.0	ARG	L	R
Q6VS32	G	133	D	138	133		1.0	4z3t	1	A	A	1.0	ASP	G	D
Q6VS32	L	130	R	135	130		1.0	4z3t	1	B	B	1.0	ARG	L	R
Q6VS32	G	133	D	138	133		1.0	4z3t	1	B	B	1.0	ASP	G	D
Q25252	M	364	L	364	364		1.0	4fng	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	4fng	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	4fng	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	363	364		1.0	4fnm	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	529	530		1.0	4fnm	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	553	554		1.0	4fnm	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	364	364		1.0	4qwm	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	4qwm	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	4qwm	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	364	364		1.0	4ubi	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	4ubi	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	4ubi	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	364	364		1.0	4ubj	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	4ubj	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	4ubj	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	364	364		1.0	4ubk	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	4ubk	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	4ubk	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	364	364		1.0	4ubl	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	4ubl	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	4ubl	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	364	364		1.0	4ubm	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	4ubm	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	4ubm	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	364	364		1.0	4ubn	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	4ubn	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	4ubn	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	364	364		1.0	4ubo	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	4ubo	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	4ubo	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	364	364		1.0	4w1p	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	4w1p	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	4w1p	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	364	364		1.0	4w1q	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	4w1q	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	4w1q	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	364	364		1.0	4w1r	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	4w1r	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	4w1r	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	364	364		1.0	4w1s	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	4w1s	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	4w1s	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	364	364		1.0	5c8v	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	530	530		1.0	5c8v	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	554	554		1.0	5c8v	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5ch3	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5ch3	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5ch3	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5ch5	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5ch5	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5ch5	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5ikx	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5ikx	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5ikx	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5ikx	1	B	B	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5ikx	1	B	B	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5ikx	1	B	B	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5ivd	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5ivd	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5ivd	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5ivh	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5ivh	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5ivh	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5ivi	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5ivi	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5ivi	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5ivk	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5ivk	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5ivk	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5tyj	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5tyj	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5tyj	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5tyk	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5tyk	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5tyk	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5tyl	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5tyl	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5tyl	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5tym	1	A	A	1.0	MET	M	M
Q25252	K	530	E	537	530		1.0	5tym	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5tym	1	A	A	1.0	ASP	D	D
Q25252	M	364	L	371	364		1.0	5tyn	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5tyn	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5tyn	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5tyo	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5tyo	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5tyo	1	A	A	1.0	GLY	D	G
Q25252	M	364	L	371	364		1.0	5typ	1	A	A	1.0	LEU	M	L
Q25252	K	530	E	537	530		1.0	5typ	1	A	A	1.0	GLU	K	E
Q25252	D	554	G	561	554		1.0	5typ	1	A	A	1.0	GLY	D	G
P06312	N	55	S	35	29		1.0	1eeq	1	A	A	1.0	SER	N	S
P06312	N	55	S	35	329		1.0	1eeq	1	B	B	1.0	SER	N	S
P06312	N	55	S	35	29		1.0	1eeu	1	A	A	1.0	SER	N	S
P06312	N	55	S	35	329		1.0	1eeu	1	B	B	1.0	SER	N	S
P06312	N	55	S	35	29		1.0	1efq	1	A	A	1.0	SER	N	S
P06312	N	55	S	35	29		1.0	1ek3	1	A	A	1.0	ASP	N	D
P06312	N	55	S	35	329		1.0	1ek3	1	B	B	1.0	ASP	N	D
P06312	N	55	S	35	29		1.0	1lve	1	A	A	1.0	SER	N	S
P06312	N	55	S	35	29		1.0	1qac	1	A	A	1.0	SER	N	S
P06312	N	55	S	35	329		1.0	1qac	1	B	B	1.0	SER	N	S
P06312	N	55	S	35	29		1.0	2lve	1	A	A	1.0	SER	N	S
P06312	N	55	S	35	29		1.0	3lve	1	A	A	1.0	SER	N	S
P06312	N	55	S	35	29		1.0	4lve	1	A	A	1.0	SER	N	S
P06312	N	55	S	35	329		1.0	4lve	1	B	B	1.0	SER	N	S
P06312	N	55	S	35	29		1.0	5lve	1	A	A	1.0	SER	N	S

1 reply

NatureGeorge Jun 24, 2021
Maintainer Author

Noted above UNP2PDB pipeline provides the full mapping data without any filtering like observed_ratio > 0, identity >= 0.9, leaving users to check sequence conflict between PDB Chain Instance and UniProt according to pdb_one_letter_code and unp_one_letter_code on their own, and more importantly, no selection for a single UniProt position with multiple alternative PDB positions.

If you want curated results of theUNP2PDB pipeline which has performed some filtering, checking on sequence conflicts, and select for a non-redundant PDB position dataset, you can use the following scripts:

pdb_profiling --custom_db task_20210602.db insert-mutation -i unp2pdb.csv --sep ',' --usecols 'ftId,Ref,Pos,Alt'

pdb_profiling --custom_db task_20210602.db id-mapping check-muta-conflict

pdb_profiling --custom_db task_20210602.db sifts-mapping --func pipe_select_mo -o task_20210602_unp2pdb_SIFTS-MAPPING.tsv 

pdb_profiling --custom_db task_20210602.db residue-mapping -i task_20210602_unp2pdb_SIFTS-MAPPING.tsv 

pdb_profiling --custom_db task_20210602.db insert-sele-mapping -i task_20210602_unp2pdb_SIFTS-MAPPING.tsv

pdb_profiling --custom_db task_20210602.db export-mutation-mapping -o rtask_20210602_resmap.tsv --sele # add --with_id if you want the original identifiers

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How can I map from PDB-Residues to UniProt-Residues and vice versa? #17

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How can I map from PDB-Residues to UniProt-Residues and vice versa? #17

NatureGeorge Jun 2, 2021 Maintainer

Demo PDB2UNP input

Demo UNP2PDB input

PDB2UNP

Replies: 1 comment · 1 reply

NatureGeorge Jun 2, 2021 Maintainer Author

PDB2UNP

UNP2PDB

NatureGeorge Jun 24, 2021 Maintainer Author

NatureGeorge
Jun 2, 2021
Maintainer

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NatureGeorge
Jun 2, 2021
Maintainer Author

NatureGeorge Jun 24, 2021
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