Structure of PDB 3sz4 Chain A Binding Site BS02

Receptor Information

>3sz4 Chain A (length=195) Species: 557598 (Laribacter hongkongensis HLHK9)

TEEWFAARLGKVTASRVADVMTKAASRQNYMAELICQRLTGTQEISNAAM
QRGTELEPHARARYIIETGEIVTEVGLIDHPTIAGFGASPDGLVGDTGLI
EIKCPNTWTHIETIKTGKPKPEYIKQMQTQMACTGRQWCDFVSYDDRLPD
DMQYFCTRIERDDALIAEIETEVSAFLAELEAEIEYLKRKAAKLA

Ligand information

• Ligand ID: D5M
• InChI: InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
• InChIKey: KHWCHTKSEGGWEX-RRKCRQDMSA-N
• SMILES:
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
  ACDLabs 10.04: O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
• Formula: C10 H14 N5 O6 P
• Name: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL1206239
• ZINC: ZINC000001713574
• PDB chain: 3sz4 Chain A Residue 218

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3sz4 Structural and functional insight into the mechanism of an alkaline exonuclease from Laribacter hongkongensis.
• Resolution: 2.59 Å
• Binding residue (original residue number in PDB): F9 R12 T17 A18 S19 S100
• Binding residue (residue number reindexed from 1): F5 R8 T13 A14 S15 S89
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): I76 E85 P92 E112 I113 K114
• Catalytic site (residue number reindexed from 1): I65 E74 P81 E101 I102 K103

Gene Ontology

Molecular Function

• GO:0004527 exonuclease activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:3sz4, PDBe:3sz4, PDBj:3sz4
• PDBsum: 3sz4
• PubMed: 21893587
• UniProt: C1D7P6