6VYP Nuclear Protein Dna date Feb 27, 2020
title Crystal Structure Of The Lsd1corest Histone Demethylase Bou Nucleosome Substrate
authors S.Kim, J.Zhu, P.Eek, N.Yennawar, T.Song
compound source
Molecule: Histone H3
Chain: A, E, a, e
Engineered: Yes
Mutation: Yes
 Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Xelaev_18002543mg
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: B, F, b, f
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a Type 1
Chain: C, G, c, g
Engineered: Yes
Mutation: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b 1.1
Chain: D, H, d, h
Synonym: H2b1.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (191-Mer)
Chain: I, I
Engineered: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (191-Mer)
Chain: J, j
Engineered: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Lysine-Specific Histone Demethylase 1a
Chain: M, m, K, k
Synonym: Braf35-Hdac Complex Protein Bhc110,Flavin-Containi Oxidase Domain-Containing Protein 2;
Ec: 1.-.-.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdm1a, Aof2, Kdm1, Kiaa0601, Lsd1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rest Corepressor 1
Chain: N, n, L, l
Synonym: Protein Corest
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rcor1, Kiaa0071, Rcor
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.229 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
103.771 335.770 174.633 90.00 91.07 90.00
method X-Ray Diffractionresolution 4.99 Å
ligand FAD enzyme Oxidoreductase E.C.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, f, B, b


K, k, M, m


a, E, A, e


d, h, H, D


g, C, c, G


Primary referenceCrystal Structure of the LSD1/CoREST Histone Demethylase Bound to Its Nucleosome Substrate., Kim SA, Zhu J, Yennawar N, Eek P, Tan S, Mol Cell. 2020 May 4. pii: S1097-2765(20)30261-6. doi:, 10.1016/j.molcel.2020.04.019. PMID:32396821
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2352 Kb) [Save to disk]
  • Biological Unit Coordinates (6vyp.pdb1.gz) 1171 Kb
  • Biological Unit Coordinates (6vyp.pdb2.gz) 1162 Kb
  • LPC: Ligand-Protein Contacts for 6VYP
  • CSU: Contacts of Structural Units for 6VYP
  • Structure Factors (1477 Kb)
  • Retrieve 6VYP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6VYP from S2C, [Save to disk]
    • View 6VYP 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 6VYP
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6vyp_A] [6vyp_G] [6vyp_d] [6vyp_b] [6vyp_j] [6vyp_D] [6vyp_I] [6vyp_g] [6vyp_a] [6vyp_F] [6vyp_E] [6vyp_l] [6vyp_i] [6vyp_f] [6vyp_N] [6vyp_e] [6vyp_h] [6vyp_H] [6vyp_C] [6vyp_L] [6vyp_m] [6vyp_J] [6vyp_K] [6vyp_M] [6vyp_k] [6vyp_n] [6vyp_B] [6vyp_c]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6VYP
  • Community annotation for 6VYP at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science