Structure of PDB 2gmk Chain A Binding Site BS01

Receptor Information

>2gmk Chain A (length=104) Species: 8404 (Lithobates pipiens)

QDWLTFQKKHITNTRDVDCDNIMSTNLFHCKDKNTFIYSRPEPVKAICKG
IIASKNVLTTSEFYLSDCNVTSRPCKYKLKKSTNKFCVNCANQAPVHFVG
VGSC

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: 2gmk Chain A Residue 940

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2gmk Structural basis for catalysis by onconase.
• Resolution: 1.65 Å
• Binding residue (original residue number in PDB): K9 K31
• Binding residue (residue number reindexed from 1): K9 K31
• Annotation score: 4
• Binding affinity: MOAD: Ki=590uM
  PDBbind-CN: -logKd/Ki=3.23,Ki=590uM

Enzymatic activity

• Enzyme Commision number: 3.1.27.-

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0004519 endonuclease activity
• GO:0004540 RNA nuclease activity

Biological Process

• GO:0050830 defense response to Gram-positive bacterium

External links

• PDB: RCSB:2gmk, PDBe:2gmk, PDBj:2gmk
• PDBsum: 2gmk
• PubMed: 18001769
• UniProt: P22069|RNP30_LITPI Protein P-30