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3KD1

Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.

Functional Information from GO Data
ChainGOidnamespacecontents
E0000166molecular_functionnucleotide binding
E0003676molecular_functionnucleic acid binding
E0003677molecular_functionDNA binding
E0003824molecular_functioncatalytic activity
E0003887molecular_functionDNA-directed DNA polymerase activity
E0004518molecular_functionnuclease activity
E0004527molecular_functionexonuclease activity
E0006260biological_processDNA replication
E0006261biological_processDNA-templated DNA replication
E0008408molecular_function3'-5' exonuclease activity
E0016740molecular_functiontransferase activity
E0016779molecular_functionnucleotidyltransferase activity
E0016787molecular_functionhydrolase activity
E0034061molecular_functionDNA polymerase activity
E0039686biological_processbidirectional double-stranded viral DNA replication
E0039693biological_processviral DNA genome replication
E0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG E 914
ChainResidue
EASP114
EILE115
EGLU116
EHOH1091

Functional Information from PROSITE/UniProt
site_idPS00116
Number of Residues9
DetailsDNA_POLYMERASE_B DNA polymerase family B signature. YGDTDSIYV
ChainResidueDetails
ETYR619-VAL627

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues237
DetailsRegion: {"description":"3'-5'exonuclease","evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"9215631","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues16
DetailsRegion: {"description":"Beta hairpin","evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"17098747","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues523
DetailsRegion: {"description":"Polymerase","evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"9215631","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues3
DetailsRegion: {"description":"Binding of DNA in B-conformation","evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"11389835","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24116139","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues6
DetailsRegion: {"description":"Interaction with the polymerase clamp","evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23214497","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"15057283","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17718515","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21566148","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21923197","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22026756","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11389835","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"15057282","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"18503083","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"20166748","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"21158418","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"22571765","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"23214497","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"23921641","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"24116139","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2OZM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OZS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KD5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SI6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SNN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SPY","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"17718515","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21566148","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21923197","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18503083","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"23214497","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"23921641","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2OZM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OZS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KD5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SI6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SNN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SPY","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues3
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PDB","id":"1IG9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3CFP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3CFR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3CQ8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3LZJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3NGI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3NHG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QEP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QET","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QNO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RWU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SQ2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SQ4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SUN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SUO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4DTJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4DTX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FJ9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FJJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FJN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FK2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4J2A","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4J2B","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4J2D","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4J2E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KHS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KHU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KHW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KHY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KI4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KI6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3R","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3T","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3U","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3W","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3X","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3Y","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3Z","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M41","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M42","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M45","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI11
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PDB","id":"1IG9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3CFP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3CFR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3CQ8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3LZJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3NGI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3NHG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QEP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QET","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QNO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RWU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SQ2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SQ4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SUN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SUO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4DTJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4DTX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FJJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FJN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FK2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4J2A","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4J2B","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4J2D","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4J2E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KHS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KHU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KHW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KHY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KI4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KI6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3R","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3T","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3U","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3W","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3X","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3Y","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M3Z","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M41","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M42","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4M45","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI12
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"15057283","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17718515","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20166748","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20166752","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21566148","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21923197","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22026756","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11389835","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"15057282","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"18503083","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"21158418","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"22571765","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"23214497","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"23921641","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"24116139","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2OZM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OZS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KD5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SI6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SNN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3SPY","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI13
Number of Residues1
DetailsSite: {"description":"Optimization of metal coordination by the polymerase active site","evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"15057283","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"20166752","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"22571765","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"24116139","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI14
Number of Residues1
DetailsSite: {"description":"Optimization of metal coordination by the polymerase active site","evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"15057283","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22571765","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI15
Number of Residues1
DetailsSite: {"description":"Essential for viral replication","evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"24116139","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

243083

PDB entries from 2025-10-15

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