Structure of PDB 5oeb Chain B Binding Site BS01

Receptor Information
>5oeb Chain B (length=405) Species: 749413 (Deep-sea thermophilic phage D6E) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PFSKKQLKVLTWWRKASPVSDKDGIICDGSIRAGKTIVMSFSYVMWAMDT
FNEQNFGMAGKTIGALRRNVITPLKRMLKSRGYRVKDHRADNYLTITFKG
KTNYFYLFGGKDESSQDLIQGITLAGMFFDEVALMPESFVNQATARCSVD
GAKLWFNCNPAGPYHWFKVEYLDKLDEKNLLHLHFTMDDNLSLSKQVKER
YQRMYKGVFYQRYILGLWVLAEGIIYDMFDQDEHVVPTVPRPYEKYYVSC
DYGTQNPTTFGLWGLYNGVWYKVKEYHYDGRKENKQKTDQEYYEDLMKFI
EDIEKHKFKGVIVDPSAASFIALLRQKGIKVIKAKNDVLDGIRNVATALN
KKMILYNDCCKETFREYSSYVWDEKAAERGEDKPVKQNDHQLDADRYFVN
TILFG
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/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)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain5oeb Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5oeb Structure of the large terminase from a hyperthermophilic virus reveals a unique mechanism for oligomerization and ATP hydrolysis.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		F14 Q18 I43 R44 A45 G46 K47 T48 N202
Binding residue
(residue number reindexed from 1)		F2 Q6 I31 R32 A33 G34 K35 T36 N190
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:5oeb, PDBe:5oeb, PDBj:5oeb
PDBsum5oeb
PubMed29069443
UniProtE5DV50

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