3KD5

Closed ternary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair and phosphonoformic acid.

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	0003887	molecular_function	DNA-directed DNA polymerase activity
E	0004527	molecular_function	exonuclease activity
E	0006260	biological_process	DNA replication
E	0006261	biological_process	DNA-templated DNA replication
E	0006287	biological_process	base-excision repair, gap-filling
E	0006297	biological_process	nucleotide-excision repair, DNA gap filling
E	0008296	molecular_function	3'-5'-DNA exonuclease activity
E	0008408	molecular_function	3'-5' exonuclease activity
E	0009432	biological_process	SOS response
E	0039686	biological_process	bidirectional double-stranded viral DNA replication
E	0039693	biological_process	viral DNA genome replication
E	0045004	biological_process	DNA replication proofreading
E	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	13
Details	BINDING SITE FOR RESIDUE PPF E 914

Chain	Residue
E	ASP411
E	HOH935
E	HOH972
E	HOH1020
E	HOH1117
E	LEU412
E	THR413
E	SER414
E	LEU415
E	ARG482
E	LYS560
E	ASP623
E	MG916

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG E 915

Chain	Residue
E	ASP411
E	ASP623
E	MG916
E	HOH1077
P	DA113
P	HOH206

---

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG E 916

Chain	Residue
E	ASP411
E	LEU412
E	ASP623
E	PPF914
E	MG915

---

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG E 917

Chain	Residue
E	ASP114
E	GLU116
E	ASN324
E	ASP327
E	HOH1065

---

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	2
Details	BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100

Chain	Residue	Details
E	ASP114
E	GLU116

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000305|PubMed:23214497

Chain	Residue	Details
E	ALA222
E	ASP327

---

site_id	SWS_FT_FI3
Number of Residues	1
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
E	ASP411

---

site_id	SWS_FT_FI4
Number of Residues	1
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
E	LEU412

---

site_id	SWS_FT_FI5
Number of Residues	2
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
E	ARG482
E	SER414

---

site_id	SWS_FT_FI6
Number of Residues	1
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
E	LYS560

---

site_id	SWS_FT_FI7
Number of Residues	1
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

Chain	Residue	Details
E	ASP623

---

site_id	SWS_FT_FI8
Number of Residues	1
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
E	ASP621

---

site_id	SWS_FT_FI9
Number of Residues	1
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
E	LYS706

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	SITE: Essential for viral replication => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:24116139

Chain	Residue	Details
E	ASP714

---