Structure of PDB 3geh Chain A Binding Site BS01

Receptor Information
>3geh Chain A (length=442) Species: 103690 (Nostoc sp. PCC 7120 = FACHB-418) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMAITGTIAAIATAIVPQQGSVGIVRVSGSQAIAIAQTLFDAPGKQVW
ESHRILYGYIRHPQTRQIVDEALLLLMKAPRSYTREDVVEFHCHGGIIAV
QQVLQLCLESGARLAQPGEFTLRAFLNGRLDLTQAESIADLVGARSPQAA
QTALAGLQGKLAHPIRQLRANCLDILAEIEARIDFEEDLPPLDDEAIISD
IENIAAEISQLLATKDKGELLRTGLKVAIVGRPNVGKSSLLNAWSQSDRA
IVTDLPGTTRDVVESQLVVGGIPVQVLDQAANTADLVLLTIDAATGWTTG
DQEIYEQVKHRPLILVMNKIDLVEKQLITSLEYPENITQIVHTAAAQKQG
IDSLETAILEIVQTGKVQAADMDLAINQRQAAALTQAKMSLEQVQATITQ
QLPLDFWTIDLRGAIQALGEITGEEVTESVLDRIFSRFCIGK
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 chain3geh Chain A Residue 460 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3geh Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy
Resolution3.2 Å
Binding residue
(original residue number in PDB)		N231 G233 K234 S235 S236 N335 K336 D338 A361 A362
Binding residue
(residue number reindexed from 1)		N234 G236 K237 S238 S239 N318 K319 D321 A344 A345
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.-.-
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0002098 tRNA wobble uridine modification
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3geh, PDBe:3geh, PDBj:3geh
PDBsum3geh
PubMed19806182
UniProtQ8YN91|MNME_NOSS1 tRNA modification GTPase MnmE (Gene Name=mnmE)

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