Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1Q9X

Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003676	molecular_function	nucleic acid binding
A	0003677	molecular_function	DNA binding
A	0003824	molecular_function	catalytic activity
A	0003887	molecular_function	DNA-directed DNA polymerase activity
A	0004518	molecular_function	nuclease activity
A	0004527	molecular_function	exonuclease activity
A	0006260	biological_process	DNA replication
A	0006287	biological_process	base-excision repair, gap-filling
A	0006297	biological_process	nucleotide-excision repair, DNA gap filling
A	0008152	biological_process	metabolic process
A	0008296	molecular_function	3'-5'-DNA exonuclease activity
A	0008408	molecular_function	3'-5' exonuclease activity
A	0009432	biological_process	SOS response
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016787	molecular_function	hydrolase activity
A	0039686	biological_process	bidirectional double-stranded viral DNA replication
A	0039693	biological_process	viral DNA genome replication
A	0045004	biological_process	DNA replication proofreading
A	0046872	molecular_function	metal ion binding
B	0000166	molecular_function	nucleotide binding
B	0003676	molecular_function	nucleic acid binding
B	0003677	molecular_function	DNA binding
B	0003824	molecular_function	catalytic activity
B	0003887	molecular_function	DNA-directed DNA polymerase activity
B	0004518	molecular_function	nuclease activity
B	0004527	molecular_function	exonuclease activity
B	0006260	biological_process	DNA replication
B	0006287	biological_process	base-excision repair, gap-filling
B	0006297	biological_process	nucleotide-excision repair, DNA gap filling
B	0008152	biological_process	metabolic process
B	0008296	molecular_function	3'-5'-DNA exonuclease activity
B	0008408	molecular_function	3'-5' exonuclease activity
B	0009432	biological_process	SOS response
B	0016740	molecular_function	transferase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0016787	molecular_function	hydrolase activity
B	0039686	biological_process	bidirectional double-stranded viral DNA replication
B	0039693	biological_process	viral DNA genome replication
B	0045004	biological_process	DNA replication proofreading
B	0046872	molecular_function	metal ion binding
C	0000166	molecular_function	nucleotide binding
C	0003676	molecular_function	nucleic acid binding
C	0003677	molecular_function	DNA binding
C	0003824	molecular_function	catalytic activity
C	0003887	molecular_function	DNA-directed DNA polymerase activity
C	0004518	molecular_function	nuclease activity
C	0004527	molecular_function	exonuclease activity
C	0006260	biological_process	DNA replication
C	0006287	biological_process	base-excision repair, gap-filling
C	0006297	biological_process	nucleotide-excision repair, DNA gap filling
C	0008152	biological_process	metabolic process
C	0008296	molecular_function	3'-5'-DNA exonuclease activity
C	0008408	molecular_function	3'-5' exonuclease activity
C	0009432	biological_process	SOS response
C	0016740	molecular_function	transferase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0016787	molecular_function	hydrolase activity
C	0039686	biological_process	bidirectional double-stranded viral DNA replication
C	0039693	biological_process	viral DNA genome replication
C	0045004	biological_process	DNA replication proofreading
C	0046872	molecular_function	metal ion binding
D	0000166	molecular_function	nucleotide binding
D	0003676	molecular_function	nucleic acid binding
D	0003677	molecular_function	DNA binding
D	0003824	molecular_function	catalytic activity
D	0003887	molecular_function	DNA-directed DNA polymerase activity
D	0004518	molecular_function	nuclease activity
D	0004527	molecular_function	exonuclease activity
D	0006260	biological_process	DNA replication
D	0006287	biological_process	base-excision repair, gap-filling
D	0006297	biological_process	nucleotide-excision repair, DNA gap filling
D	0008152	biological_process	metabolic process
D	0008296	molecular_function	3'-5'-DNA exonuclease activity
D	0008408	molecular_function	3'-5' exonuclease activity
D	0009432	biological_process	SOS response
D	0016740	molecular_function	transferase activity
D	0016779	molecular_function	nucleotidyltransferase activity
D	0016787	molecular_function	hydrolase activity
D	0039686	biological_process	bidirectional double-stranded viral DNA replication
D	0039693	biological_process	viral DNA genome replication
D	0045004	biological_process	DNA replication proofreading
D	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA A 1001

Chain	Residue
A	ASP623
A	SER624

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA A 1002

Chain	Residue
A	ASP684
A	HOH1112

site_id	AC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CA B 1003

Chain	Residue
B	ASP684

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA B 1004

Chain	Residue
B	ASP623
B	SER624

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA C 1005

Chain	Residue
C	HOH1093
G	DGP908
C	ASP411
C	ASP623

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA C 1006

Chain	Residue
C	ASP684
C	GLU716

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA D 1007

Chain	Residue
D	ASP411
D	THR413
D	ASP684
D	HOH1091

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA D 1008

Chain	Residue
D	ASP411
D	ASP623
D	SER624

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE DGP F 908

Chain	Residue
B	LEU415
B	TYR416
B	TYR567
B	ASP623
F	HOH387
F	DG913
J	DOC953

site_id	BC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE DGP G 907

Chain	Residue
G	DGP908
K	DOC953

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE DGP G 908

Chain	Residue
C	LEU415
C	TYR416
C	TYR567
C	ASP623
C	CA1005
G	DGP907
G	DG913
K	DOC953

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE DGP H 908

Chain	Residue
D	LEU415
D	TYR416
D	TYR567
D	ASP623
H	DG913
L	DOC953

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DGP K 955

Chain	Residue
B	ARG59
B	ASP95
G	DG927
G	DG928
K	DG940

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE DGP L 955

Chain	Residue
A	SER36
A	ARG59
A	ASP95
H	DG927
H	DG928
L	DG940

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE 3DR E 912

Chain	Residue
A	SER360
A	PRO361
A	ILE362
E	DC911
E	DG913

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE 3DR F 912

Chain	Residue
B	SER360
B	PRO361
B	ILE362
F	DC911
F	DG913

site_id	BC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE 3DR G 912

Chain	Residue
C	SER360
C	PRO361
C	ILE362
C	GLY568
C	ASN572
G	DC911
G	DG913

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE 3DR H 912

Chain	Residue
D	SER360
D	PRO361
D	ILE362
D	ASN572
H	DC911
H	DG913

site_id	CC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE DOC I 953

Chain	Residue
A	ASP621
A	THR622
A	ASP623
A	TYR708
E	DG913
E	DG914
I	DC952

site_id	CC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE DOC J 953

Chain	Residue
B	ASP623
B	TYR708
B	MET728
F	DGP908
F	DG913
F	DG914
J	DC952

site_id	CC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE DOC K 953

Chain	Residue
K	DC952
C	ASP621
C	ASP623
C	TYR708
C	MET728
G	DGP907
G	DGP908
G	DG913
G	DG914

site_id	CC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE DOC L 953

Chain	Residue
D	ASP623
D	TYR708
D	MET728
D	HOH1107
H	DGP908
H	DG913
H	DG914
L	HOH23
L	DC952

Functional Information from PROSITE/UniProt

site_id	PS00116
Number of Residues	9
Details	DNA_POLYMERASE_B DNA polymerase family B signature. YGDTDSIYV

Chain	Residue	Details
A	TYR619-VAL627

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_04100

Chain	Residue	Details
A	ASP114
A	GLU116
B	ASP114
B	GLU116
C	ASP114
C	GLU116
D	ASP114
D	GLU116

site_id	SWS_FT_FI2
Number of Residues	8
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_04100, ECO:0000305\|PubMed:23214497

Chain	Residue	Details
A	ALA222
A	ALA327
B	ALA222
B	ALA327
C	ALA222
C	ALA327
D	ALA222
D	ALA327

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_04100, ECO:0000269\|PubMed:15057283, ECO:0000269\|PubMed:17718515, ECO:0000269\|PubMed:21566148, ECO:0000269\|PubMed:21923197, ECO:0000269\|PubMed:22026756, ECO:0000305\|PubMed:11389835, ECO:0000305\|PubMed:15057282, ECO:0000305\|PubMed:18503083, ECO:0000305\|PubMed:20166748, ECO:0000305\|PubMed:21158418, ECO:0000305\|PubMed:22571765, ECO:0000305\|PubMed:23214497, ECO:0000305\|PubMed:23921641, ECO:0000305\|PubMed:24116139, ECO:0007744\|PDB:2OZM, ECO:0007744\|PDB:2OZS, ECO:0007744\|PDB:3KD5, ECO:0007744\|PDB:3SI6, ECO:0007744\|PDB:3SNN, ECO:0007744\|PDB:3SPY

Chain	Residue	Details
A	ASP411
B	ASP411
C	ASP411
D	ASP411

site_id	SWS_FT_FI4
Number of Residues	4
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_04100, ECO:0000269\|PubMed:17718515, ECO:0000269\|PubMed:21566148, ECO:0000269\|PubMed:21923197, ECO:0000305\|PubMed:18503083, ECO:0000305\|PubMed:23214497, ECO:0000305\|PubMed:23921641, ECO:0007744\|PDB:2OZM, ECO:0007744\|PDB:2OZS, ECO:0007744\|PDB:3KD5, ECO:0007744\|PDB:3SI6, ECO:0007744\|PDB:3SNN, ECO:0007744\|PDB:3SPY

Chain	Residue	Details
A	LEU412
B	LEU412
C	LEU412
D	LEU412

site_id	SWS_FT_FI5
Number of Residues	8
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_04100, ECO:0007744\|PDB:1IG9, ECO:0007744\|PDB:3CFP, ECO:0007744\|PDB:3CFR, ECO:0007744\|PDB:3CQ8, ECO:0007744\|PDB:3LZJ, ECO:0007744\|PDB:3NGI, ECO:0007744\|PDB:3NHG, ECO:0007744\|PDB:3QEP, ECO:0007744\|PDB:3QET, ECO:0007744\|PDB:3QNO, ECO:0007744\|PDB:3RWU, ECO:0007744\|PDB:3SQ2, ECO:0007744\|PDB:3SQ4, ECO:0007744\|PDB:3SUN, ECO:0007744\|PDB:3SUO, ECO:0007744\|PDB:4DTJ, ECO:0007744\|PDB:4DTX, ECO:0007744\|PDB:4FJ9, ECO:0007744\|PDB:4FJJ, ECO:0007744\|PDB:4FJN, ECO:0007744\|PDB:4FK2, ECO:0007744\|PDB:4J2A, ECO:0007744\|PDB:4J2B, ECO:0007744\|PDB:4J2D, ECO:0007744\|PDB:4J2E, ECO:0007744\|PDB:4KHS, ECO:0007744\|PDB:4KHU, ECO:0007744\|PDB:4KHW, ECO:0007744\|PDB:4KHY, ECO:0007744\|PDB:4KI4, ECO:0007744\|PDB:4KI6, ECO:0007744\|PDB:4M3R, ECO:0007744\|PDB:4M3T, ECO:0007744\|PDB:4M3U, ECO:0007744\|PDB:4M3W, ECO:0007744\|PDB:4M3X, ECO:0007744\|PDB:4M3Y, ECO:0007744\|PDB:4M3Z, ECO:0007744\|PDB:4M41, ECO:0007744\|PDB:4M42, ECO:0007744\|PDB:4M45

Chain	Residue	Details
A	SER414
A	ARG482
B	SER414
B	ARG482
C	SER414
C	ARG482
D	SER414
D	ARG482

site_id	SWS_FT_FI6
Number of Residues	4
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_04100, ECO:0007744\|PDB:1IG9, ECO:0007744\|PDB:3CFP, ECO:0007744\|PDB:3CFR, ECO:0007744\|PDB:3CQ8, ECO:0007744\|PDB:3LZJ, ECO:0007744\|PDB:3NGI, ECO:0007744\|PDB:3NHG, ECO:0007744\|PDB:3QEP, ECO:0007744\|PDB:3QET, ECO:0007744\|PDB:3QNO, ECO:0007744\|PDB:3RWU, ECO:0007744\|PDB:3SQ2, ECO:0007744\|PDB:3SQ4, ECO:0007744\|PDB:3SUN, ECO:0007744\|PDB:3SUO, ECO:0007744\|PDB:4DTJ, ECO:0007744\|PDB:4DTX, ECO:0007744\|PDB:4FJJ, ECO:0007744\|PDB:4FJN, ECO:0007744\|PDB:4FK2, ECO:0007744\|PDB:4J2A, ECO:0007744\|PDB:4J2B, ECO:0007744\|PDB:4J2D, ECO:0007744\|PDB:4J2E, ECO:0007744\|PDB:4KHS, ECO:0007744\|PDB:4KHU, ECO:0007744\|PDB:4KHW, ECO:0007744\|PDB:4KHY, ECO:0007744\|PDB:4KI4, ECO:0007744\|PDB:4KI6, ECO:0007744\|PDB:4M3R, ECO:0007744\|PDB:4M3T, ECO:0007744\|PDB:4M3U, ECO:0007744\|PDB:4M3W, ECO:0007744\|PDB:4M3X, ECO:0007744\|PDB:4M3Y, ECO:0007744\|PDB:4M3Z, ECO:0007744\|PDB:4M41, ECO:0007744\|PDB:4M42, ECO:0007744\|PDB:4M45

Chain	Residue	Details
A	LYS560
B	LYS560
C	LYS560
D	LYS560

Chain	Residue	Details
A	ASP623
B	ASP623
C	ASP623
D	ASP623

site_id	SWS_FT_FI8
Number of Residues	4
Details	SITE: Optimization of metal coordination by the polymerase active site => ECO:0000255\|HAMAP-Rule:MF_04100, ECO:0000305\|PubMed:15057283, ECO:0000305\|PubMed:20166752, ECO:0000305\|PubMed:22571765, ECO:0000305\|PubMed:24116139

Chain	Residue	Details
A	ASP621
B	ASP621
C	ASP621
D	ASP621

site_id	SWS_FT_FI9
Number of Residues	4
Details	SITE: Optimization of metal coordination by the polymerase active site => ECO:0000255\|HAMAP-Rule:MF_04100, ECO:0000269\|PubMed:15057283, ECO:0000269\|PubMed:22571765

Chain	Residue	Details
A	LYS706
B	LYS706
C	LYS706
D	LYS706

site_id	SWS_FT_FI10
Number of Residues	4
Details	SITE: Essential for viral replication => ECO:0000255\|HAMAP-Rule:MF_04100, ECO:0000269\|PubMed:24116139

Chain	Residue	Details
A	ASP714
B	ASP714
C	ASP714
D	ASP714

site_id	SWS_FT_FI7
Number of Residues	4
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_04100, ECO:0000269\|PubMed:15057283, ECO:0000269\|PubMed:17718515, ECO:0000269\|PubMed:20166748, ECO:0000269\|PubMed:20166752, ECO:0000269\|PubMed:21566148, ECO:0000269\|PubMed:21923197, ECO:0000269\|PubMed:22026756, ECO:0000305\|PubMed:11389835, ECO:0000305\|PubMed:15057282, ECO:0000305\|PubMed:18503083, ECO:0000305\|PubMed:21158418, ECO:0000305\|PubMed:22571765, ECO:0000305\|PubMed:23214497, ECO:0000305\|PubMed:23921641, ECO:0000305\|PubMed:24116139, ECO:0007744\|PDB:2OZM, ECO:0007744\|PDB:2OZS, ECO:0007744\|PDB:3KD5, ECO:0007744\|PDB:3SI6, ECO:0007744\|PDB:3SNN, ECO:0007744\|PDB:3SPY

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)