Structure of PDB 1d2e Chain B Binding Site BS01

Receptor Information
>1d2e Chain B (length=397) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPHVNVGTIGHVDHGKTTLTAAITKILAEGGGAKFKKYEEIDNAPEERAR
GITINAAHVEYSTAARHYAHTDCPGHADYVKNMITGTAPLDGCILVVAAN
DGPMPQTREHLLLARQIGVEHVVVYVNKADAVQDSEMVELVELEIRELLT
EFGYKGEETPIIVGSALCALEQRDPELGLKSVQKLLDAVDTYIPVPTRDL
EKPFLLPVESVYSIPGRGTVVTGTLERGILKKGDECEFLGHSKNIRTVVT
GIEMFHKSLDRAEAGDNLGALVRGLKREDLRRGLVMAKPGSIQPHQKVEA
QVYILTKEEGGRHKPFVSHFMPVMFSLTWDMACRIILPPGKELAMPGEDL
KLTLILRQPMILEKGQRFTLRDGNRTIGTGLVTDTPAMTEEDKNIKW
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain1d2e Chain B Residue 1302 [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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PDB1d2e High resolution crystal structure of bovine mitochondrial EF-Tu in complex with GDP.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		D67 G69 K70 T71 T72 Y92 N181 K182 D184 S219 L221
Binding residue
(residue number reindexed from 1)		D13 G15 K16 T17 T18 Y38 N127 K128 D130 S165 L167
Annotation score4
Binding affinityMOAD: Kd=1uM
Enzymatic activity
Catalytic site (original residue number in PDB) D67 K70 T71 T107 H130
Catalytic site (residue number reindexed from 1) D13 K16 T17 T53 H76
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005525 GTP binding
Biological Process
GO:0006414 translational elongation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1d2e, PDBe:1d2e, PDBj:1d2e
PDBsum1d2e
PubMed10715211
UniProtP49410|EFTU_BOVIN Elongation factor Tu, mitochondrial (Gene Name=TUFM)

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