Structure of PDB 9f17 Chain B Binding Site BS03

Receptor Information

>9f17 Chain B (length=413) Species: 85962 (Helicobacter pylori 26695) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SHMADVVVGIQWGDEGKGKIVDRIAKDYDFVVRYQGGHNAGHTIVHKGVK
HSLHLMPSGVLYPKCKNIISSAVVVSVKDLCEEISAFEDLENRLFVSDRA
HVILPYHAKKDAFKEKSQNIGTTKKGIGPCYEDKMARSGIRMGDLLDDKI
LEEKLNAHFKAIEPFKKAYDLGENYEKDLMGYFKTYAPKICPFIKDTTSM
LIEANQKGEKILLEGAQGTLLDIDLGTYPFVTSSNTTSASACVSTGLNPK
AINEVIGITKAYSTRVGNGPFPSEDTTPMGDHLRTKGAEFGTTTKRPRRC
GWLDLVALKYACALNGCTQLALMKLDVLDGIDAIKVCVAYERKGERLEIF
PSDLKDCVPIYQTFKGWEKSVGVRKLDDLEPNVREYIRFIEKEVGVKIRL
ISTSPEREDTIFL

Ligand information

Ligand ID

GDP

InChI

InChI=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

InChIKey

QGWNDRXFNXRZMB-UUOKFMHZSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385	NC1=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 3.385	NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01	O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6	c1nc2c(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

Formula

C10 H15 N5 O11 P2

Name

GUANOSINE-5'-DIPHOSPHATE

PDB chain

9f17 Chain B Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	9f17 Location Is Everything: Influence of His-Tag Fusion Site on Properties of Adenylosuccinate Synthetase from Helicobacter pylori.
Resolution	1.7 Å
Binding residue (original residue number in PDB)	D12 G14 K15 G16 G39 H40 T41 K322 D324 S400 S402 P403
Binding residue (residue number reindexed from 1)	D14 G16 K17 G18 G41 H42 T43 K324 D326 S402 S404 P405
Annotation score	4

External links

PDB	RCSB:9f17, PDBe:9f17, PDBj:9f17
PDBsum	9f17
PubMed	39062851
UniProt	P56137\|PURA_HELPY Adenylosuccinate synthetase (Gene Name=purA)

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