Structure of PDB 4f97 Chain A Binding Site BS01

Receptor Information
>4f97 Chain A (length=472) Species: 264445 (Streptomyces hygroscopicus subsp. limoneus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSEIFLASKRAAITYDTDPATGEPRAWLAPGGTGNVVAEQAGVLNISWIA
SADSEDDRRASALNPDGVTMELHSGREILVRLIRHDPAVFRNVQNFMTAN
LMWAANNYGWDRWTQPSFGSDAREGWADFGRFTRDFADAILKSSAQSADP
VYLVHDYQLVGVPALLREQRPDAPILLFVHIPWPSADYWRILPKEIRTGI
LHGMLPATTIGFFADRWCRNFLESVADLLPDARIDREAMTVEWRGHRTRL
RTMPLGYSPLTPQLPEGIEEWADGHRLVVHSGRTDPIKNAERAVRAFVLA
ARGGGLEKTRMLVRMNPNRLYVPANADYVHRVETAVAEANAELGSDTVRI
DNDNDVNHTIACFRRADLLIFNSTVDGQNLSTFEAPLVNERDADVILSET
CGAAEVLGEYCRSVNPFDLVEQAEAISAALAAGPRQRAEAAARRRDAARP
WTLEAWVQAQLDGLAADHAART
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 chain4f97 Chain A Residue 501 [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]
PDB4f97 Mechanistic Insights into Validoxylamine A 7'-Phosphate Synthesis by VldE Using the Structure of the Entire Product Complex.
Resolution2.108 Å
Binding residue
(original residue number in PDB)		R290 K295 N323 N361 D362 V363 T366 N386 L387 S388 E391
Binding residue
(residue number reindexed from 1)		R283 K288 N316 N354 D355 V356 T359 N379 L380 S381 E384
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) H182 D383
Catalytic site (residue number reindexed from 1) H180 D376
Enzyme Commision number 2.5.1.135: validamine 7-phosphate valienyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016740 transferase activity
GO:0016758 hexosyltransferase activity
Biological Process
GO:0005992 trehalose biosynthetic process
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4f97, PDBe:4f97, PDBj:4f97
PDBsum4f97
PubMed23028689
UniProtQ15JG1|VLDE_STRHL Validamine 7-phosphate valienyltransferase (Gene Name=vldE)

[Back to BioLiP]