Structure of PDB 5a6m Chain A Binding Site BS04

Receptor Information

>5a6m Chain A (length=389) Species: 203119 (Acetivibrio thermocellus ATCC 27405)

MASATINLSAEKQVIRGFGGMNHPVWISDLTPQQRDTAFGNGEGQLGFTI
LRIHVDENRNNWSKEVATARRAIELGAIVSASPWNPPSNMVETFTRNGVP
NQKRLRYDKYGDYVQHLNDFVAYMKSNGVDLYAISVQNEPDYAHEWTWWT
PQEMLRFMRDYAGQINCRVMAPESFQYLKNMSDPILNDPQALANLDILGA
HFYGTTVNNMPYPLFEQKGAGKELWMTAVYVPNSDSNSADRWPEALEVAH
NMHNALVEGNFQAYVWWYIRRSYGPMKEDGTISKRGYMMAHYSKFVRPGY
VRVDATKNPTYNVYLSACKNKKDNSVVAVVINKSTEAKTINISVPGTSIR
KWERYVTTGSKNLRKESDINASGTTFQVTLEPQSVTTFV

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: 5a6m Chain C Residue 2

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5a6m Conservation in the Mechanism of Glucuronoxylan Hydrolysis Revealed by the Structure of Glucuronoxylan Xylano-Hydrolase (Ctxyn30A) from Clostridium Thermocellum
• Resolution: 1.17 Å
• Binding residue (original residue number in PDB): E136 Y139 F172 Y200 Y227
• Binding residue (residue number reindexed from 1): E139 Y142 F175 Y203 Y230
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.2.1.8: endo-1,4-beta-xylanase.

Gene Ontology

Molecular Function

• GO:0004348 glucosylceramidase activity

Biological Process

• GO:0006665 sphingolipid metabolic process

External links

• PDB: RCSB:5a6m, PDBe:5a6m, PDBj:5a6m
• PDBsum: 5a6m
• PubMed: 27841749
• UniProt: A3DJS9