Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2P5G

Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template

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	0006261	biological_process	DNA-templated DNA replication
A	0008408	molecular_function	3'-5' exonuclease activity
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016787	molecular_function	hydrolase activity
A	0034061	molecular_function	DNA polymerase activity
A	0039686	biological_process	bidirectional double-stranded viral DNA replication
A	0039693	biological_process	viral DNA genome replication
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	0006261	biological_process	DNA-templated DNA replication
B	0008408	molecular_function	3'-5' exonuclease activity
B	0016740	molecular_function	transferase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0016787	molecular_function	hydrolase activity
B	0034061	molecular_function	DNA polymerase activity
B	0039686	biological_process	bidirectional double-stranded viral DNA replication
B	0039693	biological_process	viral DNA genome replication
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	0006261	biological_process	DNA-templated DNA replication
C	0008408	molecular_function	3'-5' exonuclease activity
C	0016740	molecular_function	transferase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0016787	molecular_function	hydrolase activity
C	0034061	molecular_function	DNA polymerase activity
C	0039686	biological_process	bidirectional double-stranded viral DNA replication
C	0039693	biological_process	viral DNA genome replication
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	0006261	biological_process	DNA-templated DNA replication
D	0008408	molecular_function	3'-5' exonuclease activity
D	0016740	molecular_function	transferase activity
D	0016779	molecular_function	nucleotidyltransferase activity
D	0016787	molecular_function	hydrolase activity
D	0034061	molecular_function	DNA polymerase activity
D	0039686	biological_process	bidirectional double-stranded viral DNA replication
D	0039693	biological_process	viral DNA genome replication
D	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE 3DR I 6

Chain	Residue
C	SER360
C	PRO361
C	ILE362
C	GLY568
C	ASN572
C	HOH996
I	DG5
I	DC7

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

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

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