Structure of PDB 3rdk Chain B Binding Site BS02

Receptor Information

>3rdk Chain B (length=334) Species: 324057 (Paenibacillus sp. JDR-2)

MAPLKDVYKNDFLIGNAISAEDLEGTRLELLKMHHDVVTAGNAMKPDALQ
PTKGNFTFTAADAMIDKVLAEGMKMHGHVLVWHQQSPAWLNTKKDDNNNT
VPLGRDEALDNLRTHIQTVMKHFGNKVISWDVVNEAMNDNPSNPADYKAS
LRQTPWYQAIGSDYVEQAFLAAREVLDENPSWNIKLYYNDYNEDNQNKAT
AIYNMVKDINDRYAAAHNGKLLIDGVGMQGHYNINTNPDNVKLSLEKFIS
LGVEVSVSELDVTAGNNYTLPENLAVGQAYLYAQLFKLYKEHADHIARVT
FWGMDDNTSWRAENNPLLFDKNLQAKPAYYGVID

Ligand information

• Ligand ID: XYS
• 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-LECHCGJUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1C(C(C(C(O1)O)O)O)O
  CACTVS 3.341: O[CH]1CO[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: C1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O
  CACTVS 3.341: O[C@@H]1CO[C@H](O)[C@H](O)[C@H]1O
  ACDLabs 10.04: OC1C(O)COC(O)C1O
• Formula: C5 H10 O5
• Name: alpha-D-xylopyranose;
  alpha-D-xylose;
  D-xylose;
  xylose;
  XYLOPYRANOSE
• DrugBank: DB03389
• ZINC: ZINC000001529214
• PDB chain: 3rdk Chain D Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3rdk Novel structural features of xylanase A1 from Paenibacillus sp. JDR-2.
• Resolution: 1.49 Å
• Binding residue (original residue number in PDB): K48 H81 W85 N137 E138 Q232 E262 W305 W313
• Binding residue (residue number reindexed from 1): K45 H78 W82 N134 E135 Q229 E259 W302 W310
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): E138 N192 H234 E262 D264
• Catalytic site (residue number reindexed from 1): E135 N189 H231 E259 D261
• Enzyme Commision number: 3.2.1.8: endo-1,4-beta-xylanase.

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:3rdk, PDBe:3rdk, PDBj:3rdk
• PDBsum: 3rdk
• PubMed: 23000703
• UniProt: C6CRV0|XYNA1_PAESJ Endo-1,4-beta-xylanase A (Gene Name=xynA1)