Structure of PDB 5vyu Chain B Binding Site BS02

Receptor Information
>5vyu Chain B (length=244) Species: 224914 (Brucella melitensis bv. 1 str. 16M) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AIAPNTRVLVAGYGLPAEFCVTTLIGMGVEIDKIAVATHREDNRNCGLHS
MLRLRNIQFTTAAANSEEFYEFGANFAPDMIISMHYRSLIPGRFLKLAKK
GSVNLHPSLLPAYRGTNSVAWVIINGESETGFSYHRMDENADTGAILLQE
RISVEETDTAFSLFHRQIARAMLRLEEVILKLDQGDPGFAQLGEASYYAR
ELPFGGVIDPRWSEVQIDRFIRAMFFPPFPPAVLKIDGKVYYVP
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 chain5vyu 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

[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]
PDB5vyu Biochemical Characterization of WbkC, an N-Formyltransferase from Brucella melitensis.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R88 T117 N118 L203 F227 F230
Binding residue
(residue number reindexed from 1)		R87 T116 N117 L202 F226 F229
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) N105 H107 S134 D143
Catalytic site (residue number reindexed from 1) N104 H106 S133 D142
Enzyme Commision number 2.1.2.14: GDP-perosamine N-formyltransferase.
Gene Ontology
Molecular Function
GO:0004479 methionyl-tRNA formyltransferase activity
GO:0008446 GDP-mannose 4,6-dehydratase activity
GO:0016740 transferase activity
Biological Process
GO:0006413 translational initiation
GO:0009058 biosynthetic process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0071951 conversion of methionyl-tRNA to N-formyl-methionyl-tRNA
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5vyu, PDBe:5vyu, PDBj:5vyu
PDBsum5vyu
PubMed28636341
UniProtF8WJP6|WBKC_BRUME GDP-perosamine N-formyltransferase (Gene Name=wbkC)

[Back to BioLiP]