Structure of PDB 2ywf Chain A Binding Site BS01

Receptor Information
>2ywf Chain A (length=532) Species: 224324 (Aquifex aeolicus VF5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEQKNVRNFCIIAHVDHGKSTLADRLLEYTGAIGITVKMQAVRMFYKAKD
GNTYKLHLIDTPGHVDFSYEVSRALAACEGALLLIDASQGIEAQTVANFW
KAVEQDLVIIPVINKIDLPSADVDRVKKQIEEVLGLDPEEAILASAKEGI
GIEEILEAIVNRIPPPKGDPQKPLKALIFDSYYDPYRGAVAFVRIFDGEV
KPGDKIMLMSTGKEYEVTEVGAQTPKMTKFDKLSAGDVGYIAASIKDVRD
IRIGDTITHAKNPTKEPVPGFQPAKPMVYAGIYPAEDTTYEELRDALEKY
AINDAAIVYEPESSPALGMGFRVGFLGLLHMEIVQERLEREYGVKIITTA
PNVIYRVKKKFTDEVIEVRNPMDFPDNAGLIEYVEEPFVLVTIITPKEYV
GPIIQLCQEKRGIQKNMTYLDPNTVYLEYEMPLSEIIVDFHDKIKSISRG
FASYDYEFIGYRPSDLIKLTVLINKKPVDALSFIVHADRAQKFARRVAEK
LRETIPRQLFEVHIQVAKGGKVIASERIKPLR
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain2ywf Chain A Residue 801 [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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PDB2ywf Crystal structures of GTP-binding protein LepA from Aquifex aeolicus
Resolution2.24 Å
Binding residue
(original residue number in PDB)		V15 D16 G18 K19 S20 T21 N133 K134 D136 L137 S164 K166
Binding residue
(residue number reindexed from 1)		V15 D16 G18 K19 S20 T21 N114 K115 D117 L118 S145 K147
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) D16
Catalytic site (residue number reindexed from 1) D16
Enzyme Commision number 3.6.5.n1: elongation factor 4.
Gene Ontology
Molecular Function
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0043022 ribosome binding
Biological Process
GO:0006412 translation
GO:0006414 translational elongation
GO:0045727 positive regulation of translation
Cellular Component
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2ywf, PDBe:2ywf, PDBj:2ywf
PDBsum2ywf
PubMed
UniProtO67618|LEPA_AQUAE Elongation factor 4 (Gene Name=lepA)

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