5JH5 Metal Binding Protein Transcription date Apr 20, 2016
title Structural Basis For The Hierarchical Assembly Of The Core O
authors S.J.Wong, A.B.Taylor, P.J.Hart, C.A.Kim
compound source
Molecule: Lysine-Specific Demethylase 2b
Chain: A
Fragment: Residues 1059-1336
Synonym: Cxxc-Type Zinc Finger Protein 2,F-Box And Leucine- Repeat Protein 10,F-Box Protein Fbl10,F-Boxlrr-Repeat Prot Jmjc Domain-Containing Histone Demethylation Protein 1b,Jum Domain-Containing Emsy-Interactor Methyltransferase Motif P Protein Jemma,Protein-Containing Cxxc Domain 2,[Histone-H3] Demethylase 1b;
Ec: 1.14.11.27
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdm2b, Cxxc2, Fbl10, Fbxl10, Jhdm1b, Pccx2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: S-Phase Kinase-Associated Protein 1
Chain: B
Fragment: Residues 2-163
Synonym: Cyclin-Acdk2-Associated Protein P19,P19a,Organ Of Protein 2,Ocp-2,Organ Of Corti Protein II,Ocp-II,Rna Polyme Elongation Factor-Like Protein,Siii,Transcription Elongatio Polypeptide 1-Like,P19skp1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Skp1, Emc19, Ocp2, Skp1a, Tceb1l
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Polycomb Group Ring Finger Protein 1
Chain: C
Fragment: Residues 150-255
Synonym: Nervous System Polycomb-1,Nspc1,Ring Finger Protei
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pcgf1, Nspc1, Rnf68
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Bcl-6 Corepressor-Like Protein 1
Chain: D
Fragment: Residues 1594-1711
Synonym: Bcor-Like Protein 1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bcorl1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.206 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.049 73.796 123.014 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.55 Å
ligand MSE enzyme Oxidoreductase E.C.1.14.11.27 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
B
  • cellular iron ion homeostasi...

  • Primary referenceKDM2B Recruitment of the Polycomb Group Complex, PRC1.1, Requires Cooperation between PCGF1 and BCORL1., Wong SJ, Gearhart MD, Taylor AB, Nanyes DR, Ha DJ, Robinson AK, Artigas JA, Lee OJ, Demeler B, Hart PJ, Bardwell VJ, Kim CA, Structure. 2016 Aug 23. pii: S0969-2126(16)30222-2. doi:, 10.1016/j.str.2016.07.011. PMID:27568929
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (5jh5.pdb1.gz) 103 Kb
  • LPC: Ligand-Protein Contacts for 5JH5
  • CSU: Contacts of Structural Units for 5JH5
  • Structure Factors (301 Kb)
  • Retrieve 5JH5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JH5 from S2C, [Save to disk]
  • Re-refined 5jh5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5JH5 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 5JH5
  • 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 5jh5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jh5_A] [5jh5] [5jh5_B] [5jh5_D] [5jh5_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5JH5: [FBOX] [LRR] [Skp1 ] by SMART
  • Other resources with information on 5JH5
  • Community annotation for 5JH5 at PDBWiki (http://pdbwiki.org)

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