6KSF Gene Regulation date Aug 23, 2019
title Crystal Structure Of Alkbh1 Bound To 21-Mer Dna Bulge
authors H.Li, M.Zhang
compound source
Molecule: Alpha-Ketoglutarate-Dependent Dioxygenase Alkb Ho
Chain: A
Fragment: Brd4-Bromo2
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Alkbh1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet

Molecule: Dna (5'- D(Dgpdcpdtpdgpdapdgpdtpdgpdcpdcpdcpdgpdcpdgp Pdtpdgpdgpdapdtpdcpdc)-3');
Chain: B
Fragment: Histone H2a.Z Peptide
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'- D(Dgpdgpdapdtpdcpdcpdapdgpdcpdapdcpdgpdcpdcp Pdcpdapdgpdc)-3');
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 41 21 2
R_factor 0.228 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.482 67.482 263.641 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand CL, SIN, XL3 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMammalian ALKBH1 serves as an N(6)-mA demethylase of unpairing DNA., Zhang M, Yang S, Nelakanti R, Zhao W, Liu G, Li Z, Liu X, Wu T, Xiao A, Li H, Cell Res. 2020 Mar;30(3):197-210. doi: 10.1038/s41422-019-0237-5. Epub 2020 Feb, 12. PMID:32051560
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (6ksf.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 6KSF
  • CSU: Contacts of Structural Units for 6KSF
  • Structure Factors (493 Kb)
  • Retrieve 6KSF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6KSF from S2C, [Save to disk]
  • View 6KSF 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 6KSF
  • 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 6ksf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ksf_B] [6ksf_A] [6ksf_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6KSF
  • Community annotation for 6KSF at PDBWiki (http://pdbwiki.org)

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