Structure of PDB 1obt Chain A Binding Site BS01

Receptor Information

>1obt Chain A (length=258) Species: 3988 (Ricinus communis)

YPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQ
RFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAIT
HLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYS
TGGTQLPTLARSFIICIQMISEAAHFQYIEGEMRTRIRYNRRSAPDPSVI
TLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALM
VYRCAPPP

Ligand information

• Ligand ID: AMP
• InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: UDMBCSSLTHHNCD-KQYNXXCUSA-N
• SMILES:
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
  ACDLabs 12.01: O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
• Formula: C10 H14 N5 O7 P
• Name: ADENOSINE MONOPHOSPHATE
• ChEMBL: CHEMBL752
• DrugBank: DB00131
• ZINC: ZINC000003860156
• PDB chain: 1obt Chain A Residue 701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1obt Structure and activity of an active site substitution of ricin A chain.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): Y80 G121 N122 Y123 I172
• Binding residue (residue number reindexed from 1): Y75 G116 N117 Y118 I167
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): V81 E177 H180
• Catalytic site (residue number reindexed from 1): V76 E172 H175
• 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:1obt, PDBe:1obt, PDBj:1obt
• PDBsum: 1obt
• PubMed: 8780513
• UniProt: P02879|RICI_RICCO Ricin