Structure of PDB 4lps Chain B Binding Site BS04

Receptor Information
>4lps Chain B (length=215) Species: 85962 (Helicobacter pylori 26695) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKNDIKAAEMKERYLKEGLYVLNFMSSPGSGKTTMLENLADFKDFKFCVV
EGDLQTNRDADRLRKKGVSAHQITTGEACHLEASMIEGAFDLLKDEGALE
KSDFLIIENVGNLVCPSSYNLGAAMNIVLLSVPEGDDKVLKYPTMFMCAD
AVIISKADMVEVFNFRVSQVKEDMQKLKPEAPIFLMSSKDPKSLEDFKNF
LLEKKRENYQSTHSF
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 chain4lps Chain B Residue 302 [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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PDB4lps Relationship between Ni(II) and Zn(II) Coordination and Nucleotide Binding by the Helicobacter pylori [NiFe]-Hydrogenase and Urease Maturation Factor HypB.
Resolution2.0 Å
Binding residue
(original residue number in PDB)
G56 G58 K59 T60 T61 K183 D185 S214 S215
Binding residue
(residue number reindexed from 1)
G29 G31 K32 T33 T34 K156 D158 S187 S188
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0008270 zinc ion binding
GO:0016151 nickel cation binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0051604 protein maturation

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Molecular Function

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Biological Process
External links
PDB RCSB:4lps, PDBe:4lps, PDBj:4lps
PDBsum4lps
PubMed24338018
UniProtO25560|HYPB_HELPY Hydrogenase/urease maturation factor HypB (Gene Name=hypB)

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