Structure of PDB 4ywh Chain B Binding Site BS01

Receptor Information

>4ywh Chain B (length=307) Species: 339671 (Actinobacillus succinogenes 130Z)

DLTIGMSIDDLRLERWQKDRDIFVKKAESLGAKVLVQSANGDDSAQISQI
ENMLNKNVDVLVIIPHNGDVLSNVISEAKKEGVKVLAYDRLINNADLDFY
VSFDNEKVGELQADAIIKEKPEGNYFLMGGSPVDNNAKLFRKGQMKVLQP
LIDSGKIKVVGDQWVDSWLAEKALQIMENALTANKNNIDAVVASNDATAG
GAIQALSAQGLSGKVAISGQDADLAAIKRIVEGTQTMTVYKPITNLADKA
AELSVALGKEEKLEPNAKLNNGLKEVDAYLLDPIVVTKDNIDSTVIKDGF
HSKEAVY

Ligand information

• Ligand ID: XYP
• InChI: InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5-/m1/s1
• InChIKey: SRBFZHDQGSBBOR-KKQCNMDGSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1C(C(C(C(O1)O)O)O)O
  CACTVS 3.341: O[C@@H]1CO[C@@H](O)[C@H](O)[C@H]1O
  OpenEye OEToolkits 1.5.0: C1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O
  CACTVS 3.341: O[CH]1CO[CH](O)[CH](O)[CH]1O
  ACDLabs 10.04: OC1C(O)COC(O)C1O
• Formula: C5 H10 O5
• Name: beta-D-xylopyranose;
  beta-D-xylose;
  D-xylose;
  xylose
• ZINC: ZINC000001529215
• PDB chain: 4ywh Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ywh CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM ACTINOBACILLUS SUCCINOGENES 130Z (Asuc_0499, TARGET EFI-511068) WITH BOUND D-XYLOSE
• Resolution: 2.35 Å
• Binding residue (original residue number in PDB): L37 R39 D113 R114 D158 N160 W192 N219 D245 K265
• Binding residue (residue number reindexed from 1): L13 R15 D89 R90 D134 N136 W168 N195 D221 K241
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.6.3.17: Transferred entry: 7.5.2.8.

Gene Ontology

Molecular Function

• GO:0016787 hydrolase activity
• GO:0030246 carbohydrate binding
• GO:0048029 monosaccharide binding

Biological Process

• GO:0015753 D-xylose transmembrane transport

Cellular Component

• GO:0030288 outer membrane-bounded periplasmic space
• GO:0042597 periplasmic space

External links

• PDB: RCSB:4ywh, PDBe:4ywh, PDBj:4ywh
• PDBsum: 4ywh
• UniProt: A6VLM7