Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2DTU

Crystal structure of the beta hairpin loop deletion variant of RB69 gp43 in complex with DNA containing an abasic site analog

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	0003887	molecular_function	DNA-directed DNA polymerase 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	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	0003887	molecular_function	DNA-directed DNA polymerase 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	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	0003887	molecular_function	DNA-directed DNA polymerase 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	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	0003887	molecular_function	DNA-directed DNA polymerase 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	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 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	ILE334
B	ALA222
B	ILE334
C	ALA222
C	ILE334
D	ALA222
D	ILE334

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	SER418
B	SER418
C	SER418
D	SER418

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	ILE419
B	ILE419
C	ILE419
D	ILE419

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	ARG421
A	MET489
B	ARG421
B	MET489
C	ARG421
C	MET489
D	ARG421
D	MET489

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	TYR567
B	TYR567
C	TYR567
D	TYR567

Chain	Residue	Details
A	ASP630
B	ASP630
C	ASP630
D	ASP630

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	SER628
B	SER628
C	SER628
D	SER628

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	TRP713
B	TRP713
C	TRP713
D	TRP713

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	ALA721
B	ALA721
C	ALA721
D	ALA721

		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