Structure of PDB 5ldm Chain A Binding Site BS01

Receptor Information

>5ldm Chain A (length=174) Species: 469008 (Escherichia coli BL21(DE3))

EPQRLFFAIDLPAEIREQIIHWRAKHFPPEAGRPVAADNLHLTLAFLGEV
SAEKEKALSLLAGRIRQPGFTLTLDDAGQWLRSRVVWLGMRQPPRGLIQL
ANMLRSQAARSGCFQSNRPFHPHITLLRDASEAVTIPPPGFNWSYAVTEF
TLYASSFARGRTRYTPLKRWALTQ

Ligand information

• Ligand ID: 2AM
• InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(22-23(18,19)20)6(17)4(1-16)21-10/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: QDFHPFSBQFLLSW-KQYNXXCUSA-N
• SMILES:
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O[P](O)(O)=O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)OP(=O)(O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)OP(=O)(O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O[P](O)(O)=O
  ACDLabs 10.04: O=P(O)(O)OC3C(O)C(OC3n2cnc1c(ncnc12)N)CO
• Formula: C10 H14 N5 O7 P
• Name: ADENOSINE-2'-MONOPHOSPHATE
• ChEMBL: CHEMBL57445
• ZINC: ZINC000003861741
• PDB chain: 5ldm Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ldm Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase.
• Resolution: 2.46 Å
• Binding residue (original residue number in PDB): F8 H43 T45 F48 H125 T127 R130
• Binding residue (residue number reindexed from 1): F6 H41 T43 F46 H123 T125 R128
• Annotation score: 1
• Binding affinity: MOAD: Ka=7210M^-1
  PDBbind-CN: -logKd/Ki=3.86,Kd=139uM

Enzymatic activity

• Enzyme Commision number: 3.1.4.58: RNA 2',3'-cyclic 3'-phosphodiesterase.

Gene Ontology

Molecular Function

• GO:0004113 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity
• GO:0005524 ATP binding
• GO:0008081 phosphoric diester hydrolase activity
• GO:0008664 RNA 2',3'-cyclic 3'-phosphodiesterase activity
• GO:0016787 hydrolase activity
• GO:0016874 ligase activity

External links

• PDB: RCSB:5ldm, PDBe:5ldm, PDBj:5ldm
• PDBsum: 5ldm
• PubMed: 28141848
• UniProt: A0A140NFI1