Structure of PDB 4tmz Chain A Binding Site BS01

Receptor Information
>4tmz Chain A (length=331) Species: 209285 (Thermochaetoides thermophila) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMNKDNLRSPICCILGHVDTGKTKLLDKIRQTNVQEGEAGGITQQIGATY
FPVEAIKQKTAVVNKDGKFEFKVPGLLIIDTPGHESFSNLRSRGSSLCNI
AILVVDIMHGLEPQTIESLRLLRERKTPFVVALNKIDRLYGWKKIENNGF
RESFALQNKAVQNEFRNRLDQVKLQFAEQGFNSELFYENKNFARYVSLVP
TSAHTGEGIPDMLKLIVQLCQERMASSLMYLSELQATVLEVKAIEGFGVT
IDVILSNGILREGDRIVLCGLEGPIKTNIRALLTPAPMRELRIKGQYIHH
KEVKAAQGVKISAPGLEGAIAGSRLLVVGPD
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 chain4tmz Chain A 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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PDB4tmz A monovalent cation acts as structural and catalytic cofactor in translational GTPases.
Resolution2.28 Å
Binding residue
(original residue number in PDB)		V532 D533 G535 K536 T537 K538 Q549 I556 T557 G597 N648 K649 D651 S716 A717 H718
Binding residue
(residue number reindexed from 1)		V18 D19 G21 K22 T23 K24 Q35 I42 T43 G83 N134 K135 D137 S202 A203 H204
Annotation score3
Binding affinityMOAD: Kd=0.92uM
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:4tmz, PDBe:4tmz, PDBj:4tmz
PDBsum4tmz
PubMed25225612
UniProtG0S8G9|IF2P_CHATD Eukaryotic translation initiation factor 5B (Gene Name=CTHT_0029840)

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