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

Chain	GOid	namespace	contents
E	0000166	molecular_function	nucleotide binding
E	0003676	molecular_function	nucleic acid binding
E	0003677	molecular_function	DNA binding
E	0003824	molecular_function	catalytic activity
E	0003887	molecular_function	DNA-directed DNA polymerase activity
E	0004518	molecular_function	nuclease activity
E	0004527	molecular_function	exonuclease activity
E	0006260	biological_process	DNA replication
E	0006261	biological_process	DNA-templated DNA replication
E	0008408	molecular_function	3'-5' exonuclease activity
E	0016740	molecular_function	transferase activity
E	0016779	molecular_function	nucleotidyltransferase activity
E	0016787	molecular_function	hydrolase activity
E	0034061	molecular_function	DNA polymerase activity
E	0039686	biological_process	bidirectional double-stranded viral DNA replication
E	0039693	biological_process	viral DNA genome replication
E	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG E 914

Chain	Residue
E	ASP114
E	ILE115
E	GLU116
E	HOH1091

---

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
E	TYR619-VAL627

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	237
Details	Region: {"description":"3'-5'exonuclease","evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"9215631","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	16
Details	Region: {"description":"Beta hairpin","evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"17098747","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	523
Details	Region: {"description":"Polymerase","evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"9215631","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	3
Details	Region: {"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"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	6
Details	Region: {"description":"Interaction with the polymerase clamp","evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23214497","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	Binding 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"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	Binding 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"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	3
Details	Binding 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"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	1
Details	Binding 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"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	1
Details	Binding 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"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	1
Details	Site: {"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"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	1
Details	Site: {"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"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	1
Details	Site: {"description":"Essential for viral replication","evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"24116139","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---