Structure of PDB 7yyp Chain A Binding Site BS01

Receptor Information
>7yyp Chain A (length=597) Species: 272844 (Pyrococcus abyssi GE5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKRIRQPIIAVLGHVDHGKTTLLDRIRKTNVAAKEAGGITQHIGATEVPI
EVVKKIAGPLIKLWKAEIKLPGLLFIDTPGHEAFTSLRARGGSLADLAVL
VVDINEGFQPQTIESIEILRKYRTPFVVAANKIDRIKGWVIEEDEPFLMN
IKKQDQRAVQELETKLWELIGKFYEFGFQANRFDRVQNFTRELAIVPISA
KYGIGIAELLVLIAGLSQRYLEEKLKIEVEGPARGTILEVREEPGLGHTI
DVIIYDGTLHKDDTIVVGGKDKAIVTKIRALLKPKPLDEIRDPRFRFDYV
DEVTAAAGVKIAAPGLEEALAGSPVIAAPTPEDVEKAKQEILEQIERVVI
STDKVGVIVKADTLGSLEALSKELQEKEIPIRKADVGNVSKTDVMEALSV
KEEEPKYGVILGFNVKVNEDAEEVAKAKDVKIFVGNVIYKLIEDYEEWVK
EEEEKKKRELLSKVTFPGVIRLYPDERYVFRRSNPAIVGIEVIEGRIKPG
VTLIKQNGQKVGVIRSIKSRDEFLQEAKKGQAVAIAIEGAIVGRHIHPGE
TLYVDLSRDDAITLLKHLRDTLEDTDIKALKMIAKVKAKEDPFWRAI
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain7yyp Chain A Residue 601 [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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PDB7yyp Role of aIF5B in archaeal translation initiation.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		D17 G19 K20 T21 T22 N132 K133 D135 R136 S200 K202
Binding residue
(residue number reindexed from 1)		D16 G18 K19 T20 T21 N131 K132 D134 R135 S199 K201
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003743 translation initiation factor activity
GO:0003924 GTPase activity
GO:0005525 GTP binding
Biological Process
GO:0006413 translational initiation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7yyp, PDBe:7yyp, PDBj:7yyp
PDBsum7yyp
PubMed35694843
UniProtQ9UZK7|IF2P_PYRAB Probable translation initiation factor IF-2 (Gene Name=infB)

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