Structure of PDB 7kd0 Chain A Binding Site BS01

Receptor Information

>7kd0 Chain A (length=259) Species: 3988 (Ricinus communis)

QYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPIN
QRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAI
THLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYY
STGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSV
ITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIAL
MVYRCAPPP

Ligand information

• Ligand ID: GAL
• 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-FPRJBGLDSA-N
• SMILES:
  CACTVS 3.370: OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@H]1O
  OpenEye OEToolkits 1.7.2: C(C1C(C(C(C(O1)O)O)O)O)O
  CACTVS 3.370: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  ACDLabs 12.01: OC1C(O)C(OC(O)C1O)CO
  OpenEye OEToolkits 1.7.2: C([C@@H]1[C@@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O
• Formula: C6 H12 O6
• Name: beta-D-galactopyranose;
  beta-D-galactose;
  D-galactose;
  galactose
• ChEMBL: CHEMBL300520
• ZINC: ZINC000002597049
• PDB chain: 7kd0 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7kd0 Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies that Bridge Ricin's A-B Subunit Interface.
• Resolution: 2.768 Å
• Binding residue (original residue number in PDB): D124 E127 R134
• Binding residue (residue number reindexed from 1): D120 E123 R130
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.2.2.22: rRNA N-glycosylase.

Gene Ontology

Molecular Function

• GO:0030598 rRNA N-glycosylase activity

Biological Process

• GO:0017148 negative regulation of translation

External links

• PDB: RCSB:7kd0, PDBe:7kd0, PDBj:7kd0
• PDBsum: 7kd0
• PubMed: 34089718
• UniProt: P02879|RICI_RICCO Ricin