Structure of PDB 5m03 Chain A Binding Site BS04

Receptor Information

>5m03 Chain A (length=349) Species: 657309 (Bacteroides xylanisolvens XB1A)

NLGTELDYDTFCFYYDWYGSEAIDGQYRHWAHAIAPDPNGGSGQNPGTIP
GTQESIASNFYPQLGRYSSSDPNILTKHMDMFVMARTGVLALTWWNEQDE
TEAKRIGLILDAADKKKIKVCFHLEPYPSRNVQNLRENIVKLITRYGNHP
AFYRKDGKPLFFIYDSYLIEPSEWEKLLSPGGSITIRNTAYDALMIGLWT
SSPTVQRPFILNAHFDGFYTYFAATGFTYGSTPTNWVSMQKWAKENGKIF
IPSVGPGYIDTRIRPWNGSVIRTRTDGQYYDAMYRKAIEAGVSAISITSF
NEWHEGSQIEPAVPYTSSEFTYLDYENREPDYYLTRTAYWVGKFRESKQ

Ligand information

• Ligand ID: MNM
• InChI: InChI=1S/C6H13NO4/c8-2-3-1-7-6(11)5(10)4(3)9/h3-11H,1-2H2/t3-,4-,5+,6+/m1/s1
• InChIKey: BHOYFRIRWXBNHP-ZXXMMSQZSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1C(C(C(C(N1)O)O)O)CO
  CACTVS 3.341: OC[CH]1CN[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: OC[C@H]1CN[C@@H](O)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H]([C@@H]([C@@H](N1)O)O)O)CO
  ACDLabs 10.04: OC1C(CNC(O)C1O)CO
• Formula: C6 H13 N O4
• Name: (2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-HYDROXYMETHYL-PIPERIDINE
• PDB chain: 5m03 Chain A Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5m03 Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-alpha-1,2-Mannanase.
• Resolution: 1.05 Å
• Binding residue (original residue number in PDB): Y46 W126 H154 E156 Y195 Y252 E333 E336
• Binding residue (residue number reindexed from 1): Y15 W95 H123 E125 Y164 Y221 E302 E305
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0004559 alpha-mannosidase activity
• GO:0016787 hydrolase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:5m03, PDBe:5m03, PDBj:5m03
• PDBsum: 5m03
• PubMed: 27992199
• UniProt: D6D1V7