Structure of PDB 4yp9 Chain B Binding Site BS01

Receptor Information
>4yp9 Chain B (length=342) Species: 669 (Vibrio harveyi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVLNGYWGYQEFLDEFPEQRNLTNALSEAVRAQPVPLSKPTQRPIKISVV
YPGQQVSDYWVRNIASFEKRLYKLNINYQLNQVFTRPNADIKQQSLSLME
ALKSKSDYLIFTLDTTRHRKFVEHVLDSTNTKLILQNITTPVREWDKHQP
FLYVGFDHAEGSRELATEFGKFFPKHTYYSVLYFSEGYISDVRGDTFIHQ
VNRDNNFELQSAYYTKATKQSGYDAAKASLAKHPDVDFIYACSTDVALGA
VDALAELGREDIMINGWGGGSAELDAIQKGDLDITVMRMNDDTGIAMAEA
IKWDLEDKPVPTVYSGDFEIVTKADSPERIEALKKRAFRYSD
Ligand information
Ligand IDA1B
InChIInChI=1S/C5H10BO6/c1-5-4(3(7)2-10-5)11-6(8,9)12-5/h3-4,7-9H,2H2,1H3/q-1/t3-,4+,5+/m0/s1
InChIKeyGNABZUZRGYHKDZ-VPENINKCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2[B-]1(O[C@@H]2[C@H](CO[C@@]2(O1)C)O)(O)O
CACTVS 3.385C[C@]12OC[C@H](O)[C@H]1O[B-](O)(O)O2
ACDLabs 12.01C21O[B-](OC1(OCC2O)C)(O)O
CACTVS 3.385C[C]12OC[CH](O)[CH]1O[B-](O)(O)O2
OpenEye OEToolkits 1.9.2[B-]1(OC2C(COC2(O1)C)O)(O)O
FormulaC5 H10 B O6
Name1-deoxy-alpha-L-xylulofuranose-1,2-borate
ChEMBL
DrugBank
ZINCZINC000584905494
PDB chain4yp9 Chain B Residue 402 [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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PDB4yp9 Discovery of Glycomimetic Agonists from a Protocell Metabolism, Proto-natural Product Libraries
Resolution2.7 Å
Binding residue
(original residue number in PDB)		S79 Y81 W82 N159 R215 S265 T266 W289 R310
Binding residue
(residue number reindexed from 1)		S57 Y59 W60 N137 R193 S243 T244 W267 R288
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0030246 carbohydrate binding
Cellular Component
GO:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space

View graph for
Molecular Function
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Cellular Component
External links
PDB RCSB:4yp9, PDBe:4yp9, PDBj:4yp9
PDBsum4yp9
PubMed
UniProtP54300|LUXP_VIBHA Autoinducer 2-binding periplasmic protein LuxP (Gene Name=luxP)

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