Structure of PDB 4c2u Chain A Binding Site BS02

Receptor Information

>4c2u Chain A (length=658) Species: 1299 (Deinococcus radiodurans)

SAGPDLLQALNPTQAQAADHFTGPALVIAGAGSGKTRTLIYRIAHLIGHY
GVHPGEILAVTFTNKAAAEMRERAGHLVPGAGDLWMSTFHSAGVRILRTY
GEHIGLRRGFVIYDDDDQLDIIKEVMGSIPGETQPRVIRGIIDRAKSNLW
TPDDLDRSREPFISGLPRDAAAEAYRRYEVRKKGQNAIDFGDLITETVRL
FKEVPGVLDKVQNKAKFIHVDEYQDTNRAQYELTRLLASRDRNLLVVGDP
DQSIYKFRGADIQNILDFQKDYPDAKVYMLEHNYRSSARVLEAANKLIEN
NTERLDKTLKPVKEAGQPVTFHRATDHRAEGDYVADWLTRLHGEGRAWSE
MAILYRTNAQSRVIEESLRRVQIPARIVGGVGFYDRREIRDILAYARLAL
NPADDVALRRIIGRPRRGIGDTALQKLMEWARTHHTSVLTACANAAEQNI
LDRGAHKATEFAGLMEAMSEAADNYEPAAFLRFVMETSGYLDLLRQEGQE
GQVRLENLEELVSAAEEWSQDEANVGGSIADFLDDAALLSSVDDMRTKAE
NKGAPEDAVTLMTLHNAKGLEFPVVFIVGVEQGLLPSKGAIAEGPSGIEE
ERRLFYVGITRAMERLLMTAAQNRMQFGKTNAAEDSAFLEDIEGLFDTVD
PYGQPIEY

Ligand information

• Ligand ID: ANP
• InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
• InChIKey: PVKSNHVPLWYQGJ-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
  ACDLabs 12.01: O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
• Formula: C10 H17 N6 O12 P3
• Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
• ChEMBL: CHEMBL1230989
• ZINC: ZINC000008660410
• PDB chain: 4c2u Chain A Residue 1665

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4c2u Structural and Mechanistic Insight Into DNA Unwinding by Deinococcus Radiodurans Uvrd.
• Resolution: 2.55 Å
• Binding residue (original residue number in PDB): Q17 G35 S36 G37 K38 T39 R40 Q258 Y290 R291 E577 R617
• Binding residue (residue number reindexed from 1): Q14 G32 S33 G34 K35 T36 R37 Q252 Y284 R285 E571 R611
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): K38 T39 D227 E228 Q258 R617
• Catalytic site (residue number reindexed from 1): K35 T36 D221 E222 Q252 R611
• Enzyme Commision number: 5.6.2.4: DNA 3'-5' helicase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003678 DNA helicase activity
• GO:0005524 ATP binding
• GO:0016787 hydrolase activity

External links

• PDB: RCSB:4c2u, PDBe:4c2u, PDBj:4c2u
• PDBsum: 4c2u
• PubMed: 24143224
• UniProt: Q9RTI9