Structure of PDB 8r4b Chain A Binding Site BS01

Receptor Information
>8r4b Chain A (length=808) Species: 1097 (Chlorobaculum tepidum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLDVIRQIEQELGMQLEPVDKLKWYSKGYKLDKDQRVTAIGLYDCGSDTL
DRIIQPLESLKSLSELSLSSNQITDISPLASLNSLSMLWLDRNQITDIAP
LASLNSLSMLWLFGNKISDIAPLESLKSLTELQLSSNQITDIAPLASLKS
LTELSLSGNNISDIAPLESLKSLTELSLSSNQITDIAPLASLKSLTELSL
SSNQISDIAPLESLKSLTELQLSRNQISDIAPLESLKSLTELQLSSNQIT
DIAPLASLKSLTELQLSRNQISDIAPLESLNSLSKLWLNGNQITDIAPLA
SLNSLTELELSSNQITDIAPLASLKSLSTLWLSSNQISDIAPLASLESLS
ELSLSSNQISDISPLASLNSLTGFDVRRNPIKRLPETITGFDMEILWNDF
SSSGFITFFDNPLESPPPEIVKQGKEAVRQYFQSIEELVHLQEIKVHLIG
DGKTSLLKQLIGLNVVTKQAPNIKGLENDDELKECLFHFWDFGGQEIMHA
SHRSSVYMLLLDSRTDSNKHYWLRHIEKYGGKSPVIVVMNKIDENPSYNI
EQKKINERFPAIENRFHRISCESIAKSLKSAVLHPDSIYGTPLAPSWIKV
KEKLVEATTAQRYLNRTEVEKICNDSGITDPGERKTLLGYLNNLGIVLYF
EALDLSEIYVLDPHWVTIGVYRIINSSKTKNGHLNTSALGYILNTYTLLE
QRYLLDIMKQFELCYDEGKGLFIIPSFIMKYDYLPSTIIPRLMIAMQHQI
LDRMQWRYGMVLKSQDHEGALAKVVAETKDSTITIAIIIWYEIKKINANF
TNLDVKEF
Ligand information
Ligand IDGSP
InChIInChI=1S/C10H16N5O13P3S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(26-9)1-25-29(19,20)27-30(21,22)28-31(23,24)32/h2-3,5-6,9,16-17H,1H2,(H,19,20)(H,21,22)(H2,23,24,32)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXOFLBQFBSOEHOG-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
ACDLabs 10.04S=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O13 P3 S
Name5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
ChEMBLCHEMBL1204628
DrugBankDB01864
ZINCZINC000008217391
PDB chain8r4b Chain A Residue 1201 [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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PDB8r4b Structural insights in the GTP-driven monomerization and activation of a bacterial LRRK2 homologue using allosteric nanobodies
Resolution3.88 Å
Binding residue
(original residue number in PDB)		G459 D460 G464 K465 F516 G517 C600
Binding residue
(residue number reindexed from 1)		G450 D451 G452 K453 F492 G493 C571
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0005525 GTP binding
GO:0042802 identical protein binding

View graph for
Molecular Function
External links
PDB RCSB:8r4b, PDBe:8r4b, PDBj:8r4b
PDBsum8r4b
PubMed38666771
UniProtQ8KC98

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