Structure of PDB 1f31 Chain A Binding Site BS02

Receptor Information

>1f31 Chain A (length=1280) Species: 1491 (Clostridium botulinum)

PVTINNFNYNDPIDNNNIIMMEPPFARGTGRYYKAFKITDRIWIIPERYT
FGYKPEDFNKSSGIFNRDVCEYYDPDYLNTNDKKNIFLQTMIKLFNRIKS
KPLGEKLLEMIINGIPYLGDRRVPLEEFNTNIASVTVNKLISNPGEVERK
KGIFANLIIFGPGPVLNENETIDIGIQNHFASREGFGGIMQMKFCPEYVS
VFNNVQEASIFNRRGYFSDPALILMHELIHVLHGLYGIKVDDLPIVPNEK
KFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYDKVLQNFRGIVDRLN
KVLVCISDPNININIYKNKFKDKYKFVEDSEGKYSIDVESFDKLYKSLMF
GFTETNIAENYKIKTRASYFSDSLPPVKIKNLLDNEIYTIEEGFNISDKD
MEKEYRGQNKAINKQAYEEISKEHLAVYKIQMCKSGICIDVDNEDLFFIA
DKNSFSDDLSKNERIEYNTQSNYIENDFPINELILDTDLISKIELPSENT
ESLTDFNVDVPVYEKQPAIKKIFTDENTIFQYLYSQTFPLDIRDISLTSS
FDDALLFSNKVYSFFSMDYIKTANKVVEAGLFAGWVKQIVNDFVIEANKS
NTMDKIADISLIVPYIGLALNVGNETAKGNFENAFEIAGASILLEFIPEL
LIPVVGAFLLESYIDNKNKIIKTIDNALTKRNEKWSDMYGLIVAQWLSTV
NTQFYTIKEGMYKALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINS
KLNEGINQAIDNINNFINGCSVSYLMKKMIPLAVEKLLDFDNTLKKNLLN
YIDENKIGSAEYEKSKVNKYLKTIMPFDLSIYTNDTILIEMFNKYNSEIL
NNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRV
TQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSG
WKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNL
NNAKIYINGKLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSI
FNTELSQSNIEERYKIQSYSEYLKDFWGNPLMYNKEYYMFNAGNKNSYIK
LKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSNSQSINDDIV
RKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIK
EYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCISK
WYLKEVKRKPYNLKLGCNWQFIPKDEGWTE

Ligand information

• Ligand ID: SIA
• InChI: InChI=1S/C11H19NO9/c1-4(14)12-7-5(15)2-11(20,10(18)19)21-9(7)8(17)6(16)3-13/h5-9,13,15-17,20H,2-3H2,1H3,(H,12,14)(H,18,19)/t5-,6+,7+,8+,9+,11+/m0/s1
• InChIKey: SQVRNKJHWKZAKO-YRMXFSIDSA-N
• SMILES:
  CACTVS 3.341: CC(=O)N[CH]1[CH](O)C[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)O)O
  OpenEye OEToolkits 1.5.0: CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](CO)O)O)(C(=O)O)O)O
  ACDLabs 10.04: O=C(O)C1(O)OC(C(O)C(O)CO)C(NC(=O)C)C(O)C1
  CACTVS 3.341: CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
• Formula: C11 H19 N O9
• Name: N-acetyl-alpha-neuraminic acid;
  N-acetylneuraminic acid;
  sialic acid;
  alpha-sialic acid;
  O-SIALIC ACID
• ChEMBL: CHEMBL1234621
• DrugBank: DB03721
• ZINC: ZINC000004081651
• PDB chain: 1f31 Chain B Residue 3

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1f31 Structural analysis of the catalytic and binding sites of Clostridium botulinum neurotoxin B.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): E1189 I1239 H1240 S1259 W1261 Y1262
• Binding residue (residue number reindexed from 1): E1179 I1229 H1230 S1249 W1251 Y1252
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): H229 E230 H233 E267 R369
• Catalytic site (residue number reindexed from 1): H226 E227 H230 E264 R366
• Enzyme Commision number: 3.4.24.69: bontoxilysin.

Gene Ontology

Molecular Function

• GO:0004222 metalloendopeptidase activity
• GO:0005515 protein binding
• GO:0008237 metallopeptidase activity
• GO:0008270 zinc ion binding
• GO:0008289 lipid binding
• GO:0008320 protein transmembrane transporter activity
• GO:0046872 metal ion binding
• GO:0090729 toxin activity

Biological Process

• GO:0006508 proteolysis
• GO:0035821 modulation of process of another organism
• GO:0071806 protein transmembrane transport

Cellular Component

• GO:0005576 extracellular region
• GO:0016020 membrane
• GO:0020002 host cell plasma membrane
• GO:0030430 host cell cytoplasm
• GO:0044161 host cell cytoplasmic vesicle
• GO:0044164 host cell cytosol
• GO:0044221 host cell synapse
• GO:0044231 host cell presynaptic membrane

External links

• PDB: RCSB:1f31, PDBe:1f31, PDBj:1f31
• PDBsum: 1f31
• PubMed: 10932256
• UniProt: P10844|BXB_CLOBO Botulinum neurotoxin type B (Gene Name=botB)