Structure of PDB 4ncl Chain A Binding Site BS01

Receptor Information
>4ncl Chain A (length=428) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LRSPICCILGHVDTGKTKLLDKIRQTNVGGITQQIGATYFPVEAIKQKTA
VVNKDGKFEFKVPGLLIIDTPGHESFSNLRSRGSSLCNIAILVVDIMHGL
EPQTIESLRLLRERKTPFVVALNKIDRLYGWKKIENNGFRESFALQNKAV
QNEFRNRLDQVKLQFAEQGFNSELFYENKNFARYVSLVPTSAHTGEGIPD
MLKLIVQLCQERMAELQATVLEVKAGVTIDVILSNGILREGDRIVLCGLE
GPIKTNIRALLTPAPKGQYIHHKEVKAAQGVKISAPGLEGAIAGSRLLVV
GPDDDEEELEEEVESDLQSLFSRVEKTGKGVSVQASTLGSLEALLDFLKD
CKIPVANVGIGPVYKRDVMQCGIMLEKAPDYAVMLCFDVKVDKEAQQYAD
ENGIKIFTADIIYHLFDQFTKHMQEQLE
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 chain4ncl Chain A Residue 1001 [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]
PDB4ncl eIF5B employs a novel domain release mechanism to catalyze ribosomal subunit joining.
Resolution2.115 Å
Binding residue
(original residue number in PDB)		V532 D533 T534 G535 K536 T537 K538 K649 D651 S716 A717 H718
Binding residue
(residue number reindexed from 1)		V12 D13 T14 G15 K16 T17 K18 K124 D126 S191 A192 H193
Annotation score4
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:4ncl, PDBe:4ncl, PDBj:4ncl
PDBsum4ncl
PubMed24686316
UniProtG0S8G9|IF2P_CHATD Eukaryotic translation initiation factor 5B (Gene Name=CTHT_0029840)

[Back to BioLiP]