Structure of PDB 5ymx Chain A Binding Site BS01

Receptor Information
>5ymx Chain A (length=202) Species: 246197 (Myxococcus xanthus DK 1622) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFINYSSREINCKIVYYGPGLCGKTTNLQYIYNKTAAETKGKLISLSTET
DRTLFFDFLPLSLGEIRGFKTRFHLYTVPGQVFYDASRKLILKGVDGVVF
VADSQIERMEANMESLENLRINLAEQGYDLNKIPYVIQYNKRDLPNAVTV
EEMRKALNHRNIPEYQAVAPTGVGVFDTLKAVAKLVLTELKKGGGSHHHH
HH
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 chain5ymx Chain A Residue 301 [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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PDB5ymx Allosteric regulation of a prokaryotic small Ras-like GTPase contributes to cell polarity oscillations in bacterial motility.
Resolution1.35 Å
Binding residue
(original residue number in PDB)		L22 C23 G24 K25 T26 T27 G81 N141 K142 D144 L145 V169 P171
Binding residue
(residue number reindexed from 1)		L21 C22 G23 K24 T25 T26 G80 N140 K141 D143 L144 V168 P170
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=6.92,Kd=0.12uM
Enzymatic activity
Enzyme Commision number 3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
Biological Process
GO:0032880 regulation of protein localization
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ymx, PDBe:5ymx, PDBj:5ymx
PDBsum5ymx
PubMed31560685
UniProtQ1DB04|MGLA_MYXXD Mutual gliding-motility protein MglA (Gene Name=mglA)

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