6P93 Lyase Dna date Jun 09, 2019
title Human Ape1 K98a Ap-Endonuclease Product Complex
authors A.W.Whitaker, W.J.Stark, B.D.Freudenthal
compound source
Molecule: Dna-(Apurinic Or Apyrimidinic Site) Lyase
Chain: A, B
Synonym: Apex Nuclease,Apen,Apurinic-Apyrimidinic Endonucle 1,Ref-1,Redox Factor-1;
Ec: 3.1.-.-,4.2.99.18
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apex1, Ape, Ape1, Apex, Apx, Hap1, Ref1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(P(3dr)Pcpgpapcpgpgpaptpcpc)-
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpc)-3')
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Gpgpaptpcpcpgptpcpgpgpgpcpgpcpaptpcpap 3');
Chain: V
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor 0.172 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.351 60.493 72.620 83.72 79.66 88.46
method X-Ray Diffractionresolution 2.10 Å
ligand 3DR, CL, EDO, MG, PEG enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (6p93.pdb1.gz) 112 Kb
  • LPC: Ligand-Protein Contacts for 6P93
  • CSU: Contacts of Structural Units for 6P93
  • Structure Factors (394 Kb)
  • Retrieve 6P93 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6P93 from S2C, [Save to disk]
  • View 6P93 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6P93
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6p93 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6p93_V] [6p93_B] [6p93_A] [6p93_P] [6p93_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6P93
  • Community annotation for 6P93 at PDBWiki (http://pdbwiki.org)

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