Structure of PDB 7wdt Chain A Binding Site BS01

Receptor Information

>7wdt Chain A (length=819) Species: 398514 (Bifidobacterium bifidum JCM 1254)

TVSNLATMATVTASGREVSSGFGPELAADNQDLPDNPTDKSVHNASGASR
WSADRGSGPWWLAYEFPGEATISSVNIAWGNTYATNYSIQTSDDGSNWTD
VKTGLKATAQAQWVKTTFDTPIKTRHIRMIATTKSQSWSLSVWEMRTMGT
ISAVATDPLSRLTPRPLYAQSADGEAFELKKNTCVSVSDGSLLPAVDVMR
DELGTSYGLKLAEGTNCPITFTLDENLDVTGHVGSAQSITADEAYTIVSD
ADSVTVKARSATAGIWAAQTLLQLIGPWTNSTVKLADVAFIPAVNIADAP
RYQWRGVLVDPARSFYPLDEMKQMIDVMSAYKMNTLHLHLSEDEGFRVEI
TNDGRADGDTTDYTQLAIKSGAISYQSAWTSNWSPAQDGRTGYWTQSEFI
ELVAYAADHGIAIVPEIDGPGHSFSLLHGLAELNTGNSNPKPAAGEDTPA
FIQSAQGRSSLATDADITYTVLGHIMDQLDGMIDKGIKASTMPASELKRM
YFHLGGDELFLSGGAGNKTERLQEYLGRSGALVKERDKTTIVWNDGLDAV
DQIPEGSVVQHWTGNAANNASIQKLLNQRNGKIIMSPAGNTYFPQRPGTE
TTGVTWACGACTTSNFYQWNPTSSAGTTEDKVLGVEDALWSEHLRSLNDA
EFLMYTRMMATAEVGWTQQNRKDYDNWNKRVGDIAIDLMNRGANFHKATE
VTSWKGSYAAVDAAEQKVTDGKVLVGRYAEPGLTGTDGLSFTATYTAEGG
AVNLPVTPDMKQTYSQQQLKNGRLVVNGAHMNSIVDVYVTLPSDVLAADS
VGRLDVSVSSSTYHHHHHH

Ligand information

• Ligand ID: NGS
• InChI: InChI=1S/C8H15NO9S/c1-3(10)9-5-7(12)6(11)4(18-8(5)13)2-17-19(14,15)16/h4-8,11-13H,2H2,1H3,(H,9,10)(H,14,15,16)/t4-,5-,6-,7-,8-/m1/s1
• InChIKey: WJFVEEAIYIOATH-FMDGEEDCSA-N
• SMILES:
  ACDLabs 10.04: O=S(=O)(O)OCC1OC(O)C(NC(=O)C)C(O)C1O
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(C(C(OC1O)COS(=O)(=O)O)O)O
  CACTVS 3.341: CC(=O)N[CH]1[CH](O)O[CH](CO[S](O)(=O)=O)[CH](O)[CH]1O
  CACTVS 3.341: CC(=O)N[C@H]1[C@H](O)O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O)COS(=O)(=O)O)O)O
• Formula: C8 H15 N O9 S
• Name: 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose;
  2-(acetylamino)-2-deoxy-6-O-sulfo-beta-D-glucopyranose;
  N-ACETYL-D-GLUCOSAMINE-6-SULFATE;
  N-acetyl-6-O-sulfo-beta-D-glucosamine;
  2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucose;
  2-acetamido-2-deoxy-6-O-sulfo-D-glucose;
  2-acetamido-2-deoxy-6-O-sulfo-glucose
• ZINC: ZINC000004096329
• PDB chain: 7wdt Chain A Residue 901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7wdt A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
• Resolution: 1.65 Å
• Binding residue (original residue number in PDB): R358 D552 E553 W588 W607 Y637 P639 Q640 W651 W685 E687
• Binding residue (residue number reindexed from 1): R313 D507 E508 W543 W562 Y592 P594 Q595 W606 W640 E642
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.2.1.52: beta-N-acetylhexosaminidase.

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0004563 beta-N-acetylhexosaminidase activity

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:7wdt, PDBe:7wdt, PDBj:7wdt
• PDBsum: 7wdt
• PubMed: 36864192
• UniProt: D4QAP5