2P5O

Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog

Replaces:  1RV2

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 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	6
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_FI2
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	8
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_FI4
Number of Residues	4
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_FI5
Number of Residues	4
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_FI6
Number of Residues	8
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_FI7
Number of Residues	4
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_FI8
Number of Residues	4
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_FI9
Number of Residues	4
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_FI10
Number of Residues	2
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_FI11
Number of Residues	2
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

---