Structure of PDB 5jbh Chain 7 Binding Site BS04

Receptor Information
>5jbh Chain 7 (length=409) Species: 272844 (Pyrococcus abyssi GE5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QPEVNIGVVGHVDHGKTTLVQAITGIWTSKHSEELKRGMTIKLGYAETNI
GVCESCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPGHEVLMATMLS
GAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSK
EEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPY
RDLSQKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVL
PGLRVEKQGKVSYEPIFTKISSIRFGDEEFKEAKPGGLVAIGTYLDPSLT
KADNLLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPIRAKET
LMLSVGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQIAGRWR
MIGWGLVEI
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 chain5jbh Chain 7 Residue 502 [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]
PDB5jbh Cryo-EM study of start codon selection during archaeal translation initiation.
Resolution5.34 Å
Binding residue
(original residue number in PDB)		V18 D19 G21 K22 T23 T24 K36 M45 G96 N149 K150 D152 L186
Binding residue
(residue number reindexed from 1)		V12 D13 G15 K16 T17 T18 K30 M39 G90 N143 K144 D146 L180
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K22 T23 T46 H97
Catalytic site (residue number reindexed from 1) K16 T17 T40 H91
Enzyme Commision number 3.6.5.3: protein-synthesizing GTPase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003743 translation initiation factor activity
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0001731 formation of translation preinitiation complex
GO:0006412 translation
GO:0006413 translational initiation
GO:0006414 translational elongation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5jbh, PDBe:5jbh, PDBj:5jbh
PDBsum5jbh
PubMed27819266
UniProtQ980A5|IF2G_SACS2 Translation initiation factor 2 subunit gamma (Gene Name=eif2g)

[Back to BioLiP]