Structure of PDB 4gji Chain B Binding Site BS04

Receptor Information

>4gji Chain B (length=421) Species: 316 (Stutzerimonas stutzeri)

FRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVA
VPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLNIP
WDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTNAAT
RAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAM
AEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLV
DLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLF
LVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQA
LLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPV
ATYRASGYRARVAAERPASVA

Ligand information

• Ligand ID: RM4
• InChI: InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5+,6-/m0/s1
• InChIKey: SHZGCJCMOBCMKK-YJRYQGEOSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O)O)O)O
  CACTVS 3.341: C[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)C
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)O)O)O)O
  CACTVS 3.341: C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
• Formula: C6 H12 O5
• Name: beta-L-rhamnopyranose;
  beta-L-rhamnose;
  6-deoxy-beta-L-mannopyranose;
  L-rhamnose;
  rhamnose
• ZINC: ZINC000003861281
• PDB chain: 4gji Chain B Residue 504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4gji Structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): R5 D83 R414 E418
• Binding residue (residue number reindexed from 1): R2 D80 R411 E415
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 5.3.1.14: L-rhamnose isomerase.

Gene Ontology

Molecular Function

• GO:0016853 isomerase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:4gji, PDBe:4gji, PDBj:4gji
• PDBsum: 4gji
• PubMed: 23772372
• UniProt: Q75WH8