Structure of PDB 3u61 Chain D Binding Site BS02

Receptor Information
>3u61 Chain D (length=320) Species: 10665 (Tequatrovirus T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMITVNEKEHILEQKYRPSTIDECILPAFDKETFKSITSKGKIPHIILHS
PSPGTGKTTVAKALCHDVNADMMFVNGSDCKIDFVRGPLTNFASAASFDG
RQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQ
SRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKK
NFPDFRKTIGELDSYSSKGVLDAGILSLVTNDRGAIDDVLESLKNKDVKQ
LRALAPKYAADYSWFVGKLAEEIYSRVTPQSIIRMYEIVGENNQYHGIAA
NTELHLAYLFIQLACEMQWK
Ligand information
Ligand ID08T
InChIInChI=1S/C10H15N5O10P2.Be.3FH/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20;;;;/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20);;3*1H/q;+4;;;/p-4/t4-,6-,7-,10-;;;;/m1..../s1
InChIKeyWOGYHYSOODLXII-KWIZKVQNSA-J
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2[Be](OP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)(F)(F)F
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[Be](F)(F)F)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[Be](F)(F)F)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.2[Be](OP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)(F)(F)F
FormulaC10 H14 Be F3 N5 O10 P2
Name[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium
ChEMBL
DrugBank
ZINC
PDB chain3u61 Chain D Residue 700 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3u61 How a DNA polymerase clamp loader opens a sliding clamp.
Resolution3.2 Å
Binding residue
(original residue number in PDB)
E12 R16 P17 I24 P52 G53 T54 G55 K56 T57 T58 E108 N139 F204 R205
Binding residue
(residue number reindexed from 1)
E13 R17 P18 I25 P53 G54 T55 G56 K57 T58 T59 E109 N140 F205 R206
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.4.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003689 DNA clamp loader activity
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006281 DNA repair
GO:0039686 bidirectional double-stranded viral DNA replication
GO:0039693 viral DNA genome replication
Cellular Component
GO:0005663 DNA replication factor C complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:3u61, PDBe:3u61, PDBj:3u61
PDBsum3u61
PubMed22194570
UniProtP04526|LOADL_BPT4 Sliding-clamp-loader large subunit (Gene Name=44)

[Back to BioLiP]