Structure of PDB 4re3 Chain A Binding Site BS01

Receptor Information

>4re3 Chain A (length=483) Species: 39946 (Oryza sativa Indica Group)

AAPFTYWLNPEIYDAGGLSRRAFPEGFVFGTAASAYQVEGMAKQGGRGPS
IWDAFIEKPGTIPNNATADVTVDEYHRYKEDVNIMKNMGFDAYRFSISWS
RIFPNGTGMVNQEGVDYYNRLIDYMVKKGIKPYANLYHYDLPLALHEQYL
GWLSPNIVEAFADYADFCFQTFGDRVKDWFTFNEPRCVAALGYDNGFHAP
GRCSGCDAGGNSTTEPYLAAHHLILSHAAAVKRYREKYQLYQKGRIGILL
DFVWYEPFSDSNADRAAAQRARDFHLGWFLDPIIHGRYPYSMLEIVKDRM
PTFSDEESRMVKDSIDYVGINHYTSFYMKDPGPWNLTPTSYQDDWHVGFA
YERNGVPIGAQANSYWLYIVPWGINKAVTYVKETYGNPTMILSENGMDQP
GNVSITQGVHDTVRIRYYRNYITELKKAIDDGAKVIGYFAWSLLDNFEWR
LGYTSRFGIVYVDYKTLKRYPKDSAFWFKNMLS

Ligand information

• Ligand ID: GIM
• InChI: InChI=1S/C8H12N2O4/c11-3-4-5(12)6(13)7(14)8-9-1-2-10(4)8/h1-2,4-7,11-14H,3H2/p+1/t4-,5-,6+,7-/m1/s1
• InChIKey: RZRDQZQPTISYKY-MVIOUDGNSA-O
• SMILES:
  OpenEye OEToolkits 1.5.0: c1c[n+]2c([nH]1)C(C(C(C2CO)O)O)O
  ACDLabs 10.04: OCC2[n+]1ccnc1C(O)C(O)C2O
  CACTVS 3.341: OC[CH]1[CH](O)[CH](O)[CH](O)c2[nH]cc[n+]12
  OpenEye OEToolkits 1.5.0: c1c[n+]2c([nH]1)[C@@H]([C@H]([C@@H]([C@H]2CO)O)O)O
  CACTVS 3.341: OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)c2[nH]cc[n+]12
• Formula: C8 H13 N2 O4
• Name: GLUCOIMIDAZOLE;
  (5S,6S,7R,8R)-5-(HYDROXYMETHYL)-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL
• ZINC: ZINC000103543099
• PDB chain: 4re3 Chain A Residue 507

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4re3 A Single Glycosidase Harnesses Different Pyranoside Ring Transition State Conformations for Hydrolysis of Mannosides and Glucosides
• Resolution: 2.55 Å
• Binding residue (original residue number in PDB): Q32 H133 E179 Y318 W361 E389 W436 E443 F452
• Binding residue (residue number reindexed from 1): Q37 H138 E184 Y323 W366 E394 W441 E448 F457
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.57,Ki=2.7nM

Enzymatic activity

• Catalytic site (original residue number in PDB): R89 H133 E179 C182 N316 Y318 E389
• Catalytic site (residue number reindexed from 1): R94 H138 E184 C187 N321 Y323 E394
• Enzyme Commision number: 3.2.1.25: beta-mannosidase.

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0004565 beta-galactosidase activity
• GO:0008422 beta-glucosidase activity
• GO:0033907 beta-D-fucosidase activity

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:4re3, PDBe:4re3, PDBj:4re3
• PDBsum: 4re3
• UniProt: A2YPH1