Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4KI6

Ternary complex of rb69 mutant l415f with ribonucleotides at -1 and -2 position

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	18
Details	BINDING SITE FOR RESIDUE TTP A 1001

Chain	Residue
A	ASP411
A	TYR567
A	ASP623
A	CA1002
A	CA1003
A	HOH1101
A	HOH1148
P	DC115
T	DA3
T	G4
A	LEU412
A	THR413
A	SER414
A	PHE415
A	TYR416
A	ARG482
A	LYS560
A	ASN564

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA A 1002

Chain	Residue
A	ASP411
A	LEU412
A	ASP623
A	TTP1001

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA A 1003

Chain	Residue
A	ASP411
A	ASP623
A	TTP1001
A	HOH1168

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA A 1004

Chain	Residue
A	GLU116
A	HOH1126
A	HOH1240

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA A 1005

Chain	Residue
A	GLU660
A	ASP684
A	HOH1251

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA A 1006

Chain	Residue
A	GLU172
A	GLU177
A	GLN389
A	HOH1202

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA A 1007

Chain	Residue
A	ASP192
A	GLU196
A	ASP856
A	ASP860

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA A 1008

Chain	Residue
A	ASN505
A	ASN507
A	LYS531

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NA A 1009

Chain	Residue
A	SER220
A	ASP275

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 A 1010

Chain	Residue
A	SER127
A	GLN128
A	LYS231
A	ASN232

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	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	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_FI4
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
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_FI6
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_FI7
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_FI8
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_FI9
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_FI10
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_FI11
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_FI12
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_FI13
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

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)