Structure of PDB 4cd4 Chain A Binding Site BS01

Receptor Information

>4cd4 Chain A (length=367) Species: 498211 (Cellvibrio japonicus Ueda107)

LPALIDTQATAETRALYRNLAKLRYKHLLFGHEDSLAYGVHWEGDMDRSD
VRDVTGANPAVYGWELGGLELGHTANLDAVNFEKMQHWIKAGYSRGGVIT
ISWHVFNPVSGGNSWDKTPAVHELIPGGARHATLKAYLDTFVAFNEGLAD
VDAQGNKHYPPIIFRPWHEHNGDWFWWGKGHASEQDYIALWRFTVHYLRD
EKKLRNLIYAYSPDRSRIDMANFEAGYLYGYPGDAYVDIIGLDNYWDVGH
EANTASADEQKAALTASLKQLVQIARSKGKIAALTETGNNRLTIDNFWTE
RLLGPISADADASEIAYVMVWRNANLAREKSEQFFAPFPGQATADDFKRF
YQSEVVLFEDELPPLYR

Ligand information

• Ligand ID: BMA
• InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5+,6-/m1/s1
• InChIKey: WQZGKKKJIJFFOK-RWOPYEJCSA-N
• SMILES:
  CACTVS 3.341: OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)O)O)O)O
  CACTVS 3.341: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@@H]([C@@H](O1)O)O)O)O)O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: beta-D-mannopyranose;
  beta-D-mannose;
  D-mannose;
  mannose
• ZINC: ZINC000003830679
• PDB chain: 4cd4 Chain A Residue 1422

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4cd4 Combined Inhibitor Free-Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate.
• Resolution: 1.2 Å
• Binding residue (original residue number in PDB): D130 W373 R374 Q385
• Binding residue (residue number reindexed from 1): D78 W321 R322 Q333
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=6.58,Ki=263nM

Enzymatic activity

• Enzyme Commision number: 3.2.1.78: mannan endo-1,4-beta-mannosidase.

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0016985 mannan endo-1,4-beta-mannosidase activity

Biological Process

• GO:0006080 substituted mannan metabolic process

External links

• PDB: RCSB:4cd4, PDBe:4cd4, PDBj:4cd4
• PDBsum: 4cd4
• PubMed: 24339341
• UniProt: B3PGI1