Structure of PDB 4ncf Chain B Binding Site BS01

Receptor Information
>4ncf Chain B (length=429) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KDLRSPICCILGHVDTGKTKLLDKIRQTGITQQIGATYFPIDAIKAKTKV
MAEYEKQTFDVPGLLVIDTPNLRSRGSSLCNIAILVIDIMHGLEQQTIES
IKLLRDRKAPFVVALNKIDRLYDWKAIPNNSFRDSFAKQSRAVQEEFQSR
YSKIQLELAEQGLNSELYFQNKNMSKYVSIVPTSAVTGEGVPDLLWLLLE
LTQKRMSKQLMYLSHVEATILEVKVVEGFGTTIDVILSNGYLREGDRIVL
CGMNGPIVTNIRALLTPQPLRELRLKSEYVHHKEVKAALGVKIAANDLEK
AVSGSRLLVVGPEDDEDELMDDVMDDLTGLLDSKGVVVQASTLGSLEALL
DFLKDMKIPVMSIGLGPVYKRDVMKASTMLEKAPEYAVMLCFDVKVDKEA
EQYAEQEGIKIFNADVIYHLFDSFTAYQE
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 chain4ncf 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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PDB4ncf eIF5B employs a novel domain release mechanism to catalyze ribosomal subunit joining.
Resolution3.015 Å
Binding residue
(original residue number in PDB)		V414 D415 G417 K418 T419 K420 N530 K531 D533 R534 S598 A599 V600
Binding residue
(residue number reindexed from 1)		V14 D15 G17 K18 T19 K20 N116 K117 D119 R120 S184 A185 V186
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:4ncf, PDBe:4ncf, PDBj:4ncf
PDBsum4ncf
PubMed24686316
UniProtP39730|IF2P_YEAST Eukaryotic translation initiation factor 5B (Gene Name=FUN12)

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