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› 5lwb

X-ray diffraction
2.39Å resolution

Crystal structure of human JARID1B in complex with S40650a

Released:
DOI: 10.2210/pdb5lwb/pdb
Model geometry
Fit model/data
PDB entry 5lwb coloured by chain, front view.
PDB entry 5lwb coloured by chain, side view.
PDB entry 5lwb coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Srikannathasan V, Le Bihan YV, Szykowska A, Johansson C, Gileadi C, Arrowsmith CH, Edwards AM, Bountra C, von Delft F, Oppermann U, Huber K

Function and Biology Details

Reaction catalysed: 
N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + 3 2-oxoglutarate +3 O2 = L-lysyl(4)-[histone H3] + 3 formaldehyde + 3 succinate + 3 CO2.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193714 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 5B Chain: A
Molecule details ›
Chain: A
Length: 481 amino acids
Theoretical weight: 55.46 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9UGL1 (Residues: 26-101, 374-772; Coverage: 31%)
  • Best match: Q9UGL1-2 (Residues: 410-808)
Gene names: JARID1B, KDM5B, PLU1, RBBP2H1
Sequence domains:
Structure domains: Cupin

Ligands and Environments

5 bound ligands:
Ligand ZN 1 x ZN
Ligand MN 3 x MN
Ligand EDO 4 x EDO
Ligand DMS 5 x DMS
Ligand 79H 1 x 79H
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P6522
Unit cell:
a: 142.36Å b: 142.36Å c: 151.54Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.184 0.182 0.218
Expression system: Spodoptera frugiperda

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