Structure of PDB 4zu9 Chain A Binding Site BS01

Receptor Information
>4zu9 Chain A (length=582) Species: 224324 (Aquifex aeolicus VF5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKYILFATAGHVDHGKTTLIKTLTGIDTDRLPEEKKRGLSIDIGFAYIDF
PDINTRLEIIDVPGHERFIKNAIAGICSASGLILVVDPNEGIMPQTIEHL
RVAKSFGIKHGIAVLTKMDKVDEELAHIAEEELIAFLEKEEMNMEIVKVS
AVTGQGIEDLKNSIKKLLESINNLNKHKPLRIFVDSAFVVKGYGTVLRGS
CFEGEVKEGDKVVVEPIGVISRVRKMQNHGVFVKKAVAGERIALNLPEVD
AKKVKRGFLILKPESYEKSNVLIVKTEIDLKPGKIYQVFFGMRETVGKIS
VIDKGIYLVRLKENAIVRRGDKLVVLDSSGNFLGGAEVLHPKVRVTKKAF
IKKNIKDLLENFECYLLKERGPIGLKLEFFKRITGVSPKVANLKPESIEI
RGVYYLKGFIENLKLKIKKFLDTELQNAFGVDKEKVKSMFSLNEELLKYI
LDELKTYKIVNELIIDERKSDLEKNEDFQKLMSILKGGIKEEREIILEGI
PKEILTLSIKRKYAHRIGEYLIISDELLKKYINELKELGKTFNVQQAKNK
LGLTRKYLIPLLEYLDYLGLTVREGNERRWKR
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 chain4zu9 Chain A Residue 2001 [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]
PDB4zu9 Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB
Resolution3.191 Å
Binding residue
(original residue number in PDB)		V12 D13 G15 K16 T17 T18 S40 G64 K117 D119 A151 V152
Binding residue
(residue number reindexed from 1)		V12 D13 G15 K16 T17 T18 S40 G64 K117 D119 A151 V152
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) D13 K16 T17 S40 H65
Catalytic site (residue number reindexed from 1) D13 K16 T17 S40 H65
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0046872 metal ion binding
Biological Process
GO:0001514 selenocysteine incorporation
GO:0006414 translational elongation
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4zu9, PDBe:4zu9, PDBj:4zu9
PDBsum4zu9
PubMed26304550
UniProtO67141

[Back to BioLiP]