4QKD Oxidoreductase date Jun 06, 2014
title Crystal Structure Of Human Alkbh7 In Complex With Alpha-Keto And Mn(II)
authors G.Wang, Z.Chen
compound source
Molecule: Alpha-Ketoglutarate-Dependent Dioxygenase Alkb Ho Mitochondrial;
Chain: A, B, C
Fragment: Unp Residues 17-215
Synonym: Alkylated Dna Repair Protein Alkb Homolog 7, Sperm Cell Proliferation-Related Protein, Spermatogenesis-Associa Protein 11;
Ec: 1.14.11.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Abh7, Alkbh7, Spata11, Unq6002pro34564
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.146 R_Free 0.163
length a length b length c angle alpha angle beta angle gamma
66.426 82.048 66.414 90.00 120.03 90.00
method X-Ray Diffractionresolution 1.35 Å
ligand AKG, LED, MN enzyme Oxidoreductase E.C.1.14.11 BRENDA
A, C, B

Primary referenceThe atomic resolution structure of human AlkB homolog 7 (ALKBH7), a key protein for programmed necrosis and fat metabolism., Wang G, He Q, Feng C, Liu Y, Deng Z, Qi X, Wu W, Mei P, Chen Z, J Biol Chem. 2014 Oct 3;289(40):27924-36. doi: 10.1074/jbc.M114.590505. Epub 2014, Aug 13. PMID:25122757
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (220 Kb) [Save to disk]
  • Biological Unit Coordinates (4qkd.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (4qkd.pdb2.gz) 74 Kb
  • Biological Unit Coordinates (4qkd.pdb3.gz) 71 Kb
  • Biological Unit Coordinates (4qkd.pdb4.gz) 213 Kb
  • LPC: Ligand-Protein Contacts for 4QKD
  • CSU: Contacts of Structural Units for 4QKD
  • Structure Factors (1365 Kb)
  • Retrieve 4QKD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4QKD from S2C, [Save to disk]
  • Re-refined 4qkd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4QKD 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 4QKD
  • 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
  • 3D motif for 4QKD, from MSDmotif at EBI
  • Fold representative 4qkd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4qkd_A] [4qkd_B] [4qkd] [4qkd_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4QKD
  • Community annotation for 4QKD at PDBWiki (http://pdbwiki.org)

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