Structure of PDB 5x4k Chain A Binding Site BS05

Receptor Information

>5x4k Chain A (length=471) Species: 186497 (Pyrococcus furiosus DSM 3638)

SHMDKEGFLNKVREAVDVVKLHIELGHTIRIISHRDADGITSAAILAKAL
GREGASFHISIVKQVSEDLLRELKDEDYKIFIFSALGSGSLSLIKEYLKE
KTVIILDHHPPENVKLEEKHILVNPVQFGANSVRDLSGSGVTYFFARELN
EKNRDLAYIAIVGAVGDMQENDGVFHGMNLDIIEDGKSLGILEVKKELRL
FGRETRPLYQMLAYATNPEIPEVTGDERKAIEWLKNKGFNPEKKYWELSE
EEKKKLHDFLIIHMIKHGAGKEDIDRLIGDVVISPLYPEGDPRHEAREFA
TLLNATGRLNLGNLGVAVCLGDEEAFRKALKMVEDYKREQIEARKWLLQN
WNSEVWEGDHVYVLYVGKSIRDTLVGIAASMAINAGLADPEKPVIVFADT
DEDPNLLKGSARTTERALAKGYNLGEALRKAAELVNGEGGGHAIAAGIRI
PRARLAEFRKLIDKILGEQVS

Ligand information

• Ligand ID: C5P
• InChI: InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: IERHLVCPSMICTF-XVFCMESISA-N
• SMILES:
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
  ACDLabs 10.04: O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
• Formula: C9 H14 N3 O8 P
• Name: CYTIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL307679
• DrugBank: DB03403
• ZINC: ZINC000003861744
• PDB chain: 5x4k Chain A Residue 506

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5x4k The crystal structure of Pyrococcus furiosus RecJ implicates it as an ancestor of eukaryotic Cdc45.
• Resolution: 1.749 Å
• Binding residue (original residue number in PDB): T214 Q338 I375 S378
• Binding residue (residue number reindexed from 1): T216 Q340 I377 S380
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0004527 exonuclease activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:5x4k, PDBe:5x4k, PDBj:5x4k
• PDBsum: 5x4k
• PubMed: 30053256
• UniProt: Q8TZE0