Structure of PDB 6jsj Chain A Binding Site BS01

Receptor Information
>6jsj Chain A (length=625) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLNLTKQMIEIRTILNKVDSSSAHLTLPSIVVIGSQSSGKSSVLESIVGR
EFLPKMVTRRPIELTLVNTPNSNNVTADFPSMRLYNIKDFKEVKRMLMEL
NMEEPIQLTIKSSRVPDLSLVDLPGYIQVETKIRDLCEKYLTAPNIILAI
SAADVDLANSSALKASKAADPKGLRTIGVITKLDLVDPEKARSILNNKKY
PLSMGYVGVITKTENTNGLKQIVSHQFEKAYFKENKKYFTNCQVSTKKLR
EKLIKILEISMSNALEPTSTLIQQELDDTSYLFKVEFNDRHLTPKSYLLN
NIDVLKLGIKEFQEKFHRNELKSILRAELDQKVLDVLATRYWKDDNLQDL
SSSKLESDTDMLYWHKKLELASSGLTKMGIGRLSTMLTTNAILKELDNIL
ESTQLKNHELIKDLVSNTAINVLNSKYYSTADQVENCIKPFKYEIDLEER
DWSLARQHSINLIKEELRQCNSRYQAIKNAVGSKKLANVMGYLENESNKL
LLERGSEAIFLDKRCKVLSFRLKMLKNKCHSTIEKDRCPEVFLSAVSDKL
TSTAVLFLNVELLSDFFYNFPIELDRRLTLLGDEQVEMFAKEDPKISRHI
ELQKRKELLELALEKIDSILVFKKS
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 chain6jsj Chain A Residue 701 [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]
PDB6jsj Structural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase Mgm1.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		S37 S38 G39 K40 S41 S42 K55 T202 K203 D205 L206 I231 T232 K233
Binding residue
(residue number reindexed from 1)		S37 S38 G39 K40 S41 S42 K55 T181 K182 D184 L185 I210 T211 K212
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.5: dynamin GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding

View graph for
Molecular Function
External links
PDB RCSB:6jsj, PDBe:6jsj, PDBj:6jsj
PDBsum6jsj
PubMed32041880
UniProtP32266|MGM1_YEAST Dynamin-like GTPase MGM1, mitochondrial (Gene Name=MGM1)

[Back to BioLiP]