Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4KHN

Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	13
Details	BINDING SITE FOR RESIDUE XG4 A 1001

Chain	Residue
A	SER36
A	LYS374
A	LYS378
A	VAL379
A	ILE380
A	PHE38
A	LYS48
A	TYR49
A	ARG59
A	GLY84
A	MET85
A	ASP95
A	PHE370

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

Chain	Residue
A	ASP623
A	HOH1126
A	HOH1317
C	XG4101

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 1003

Chain	Residue
A	THR413
A	SER414
A	ARG482
A	LYS486
A	LYS560
A	HOH1126

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 1004

Chain	Residue
A	TRP216
A	ASN217
A	SER289
A	LEU290

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 1005

Chain	Residue
A	GLY637
A	GLU638
A	SER639

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 1006

Chain	Residue
A	TYR49
A	ARG59
A	HOH1151

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 A 1007

Chain	Residue
A	HIS105
A	VAL110

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 1008

Chain	Residue
A	ILE557
A	LEU561
A	ASN564
C	XG4101

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 1009

Chain	Residue
A	PHE650
A	LYS653
A	PHE654
A	ARG658

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA A 1010

Chain	Residue
A	TYR619
A	ASP621
A	LYS706
D	DA114
D	DC115

site_id	BC2
Number of Residues	14
Details	BINDING SITE FOR RESIDUE XG4 C 101

Chain	Residue
A	LEU415
A	TYR416
A	LYS560
A	ASN564
A	THR622
A	ASP623
A	CA1002
A	GOL1008
A	HOH1114
A	HOH1317
C	DC4
C	DG5
C	HOH201
D	DC115

site_id	BC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE XG4 B 1001

Chain	Residue
B	SER36
B	PHE38
B	TYR49
B	GLY84
B	MET85
B	ASP95
B	PHE370
B	LYS374
B	ASN377
B	LYS378
B	VAL379
B	ILE380
B	HOH1101

site_id	BC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE XG4 B 1002

Chain	Residue
B	LEU415
B	TYR416
B	LYS560
B	ASN564
B	THR622
B	ASP623
B	SO41003
B	CA1004
E	DC4
E	DG5
F	DC115

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 1003

Chain	Residue
B	THR413
B	SER414
B	ARG482
B	LYS560
B	XG41002

site_id	BC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA B 1004

Chain	Residue
B	ASP623
B	XG41002

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	474
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	32
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	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_FI4
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04100","evidenceCode":"ECO:0000255"}]}

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":"23214497","evidenceCode":"ECO:0000305"}]}

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"},{"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	2
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	6
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	2
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	2
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	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: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	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_FI13
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

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