Structure of PDB 4tmv Chain B Binding Site BS01

Receptor Information
>4tmv Chain B (length=345) Species: 209285 (Thermochaetoides thermophila) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GHMNKDNLRSPICCILGHVDTGKTKLLDKIRQTNVQEGEAGGITQQIGAT
YFPVEAIKQKTAVVNKDGKFEFKVPGLLIIDTPGHESFSNLRSRGSSLCN
IAILVVDIMHGLEPQTIESLRLLRERKTPFVVALNKIDRLYGWKKIENNG
FRESFALQNKAVQNEFRNRLDQVKLQFAEQGFNSELFYENKNFARYVSLV
PTSAHTGEGIPDMLKLIVQLCQERMASSLMYLSELQATVLEVKAIEGFGV
TIDVILSNGILREGDRIVLCGLEGPIKTNIRALLTPAPMRELRIKGQYIH
HKEVKAAQGVKISAPGLEGAIAGSRLLVVGPDDDEEELEEEVESD
Ligand information
Ligand IDGSP
InChIInChI=1S/C10H16N5O13P3S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(26-9)1-25-29(19,20)27-30(21,22)28-31(23,24)32/h2-3,5-6,9,16-17H,1H2,(H,19,20)(H,21,22)(H2,23,24,32)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXOFLBQFBSOEHOG-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(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)O[P](O)(O)=S)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
ACDLabs 10.04S=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O13 P3 S
Name5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
ChEMBLCHEMBL1204628
DrugBankDB01864
ZINCZINC000008217391
PDB chain4tmv Chain B Residue 901 [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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PDB4tmv A monovalent cation acts as structural and catalytic cofactor in translational GTPases.
Resolution1.53 Å
Binding residue
(original residue number in PDB)		V532 D533 T534 G535 K536 T537 K538 Q549 I556 T557 G597 N648 K649 D651 S716 A717 H718
Binding residue
(residue number reindexed from 1)		V19 D20 T21 G22 K23 T24 K25 Q36 I43 T44 G84 N135 K136 D138 S203 A204 H205
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.5.3: protein-synthesizing GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding

View graph for
Molecular Function
External links
PDB RCSB:4tmv, PDBe:4tmv, PDBj:4tmv
PDBsum4tmv
PubMed25225612
UniProtG0S8G9|IF2P_CHATD Eukaryotic translation initiation factor 5B (Gene Name=CTHT_0029840)

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