Structure of PDB 5ub8 Chain A Binding Site BS01

Receptor Information
>5ub8 Chain A (length=174) Species: 237561 (Candida albicans SC5314) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YSYDYEYLYKIVLIGDSGVGKSNLLSRFTRDEFNLEGVEFATRTLEIDGK
RVKAQIWDTAGQERYRAITSAYYRGAVGALIVYDIAKTESYESVSRWLKE
LKEHADANIIIELVGNKSDLDHLRAVPTEEAKNFAMENNLLFTEASALSS
DNVDLSFHQLLKNIYEMISKHQLE
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 chain5ub8 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ub8 Crystal structure of YPT31, a Rab family GTPase from Candida albicans, in complex with GDP and Zn(II)
Resolution2.35 Å
Binding residue
(original residue number in PDB)		G25 V26 G27 K28 S29 N30 F40 N41 E43 N128 K129 D131 L132 S158 A159 L160
Binding residue
(residue number reindexed from 1)		G18 V19 G20 K21 S22 N23 F33 N34 E36 N116 K117 D119 L120 S146 A147 L148
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0046872 metal ion binding
Biological Process
GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006887 exocytosis
GO:0042273 ribosomal large subunit biogenesis
Cellular Component
GO:0005794 Golgi apparatus
GO:0031521 spitzenkorper
GO:0055037 recycling endosome
GO:1903561 extracellular vesicle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ub8, PDBe:5ub8, PDBj:5ub8
PDBsum5ub8
PubMed
UniProtA0A1D8PTI2

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