SMTL ID : 4hoo.1 (1 other biounit)

Crystal structure of human JMJD2D/KDM4D apoenzyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 3 residues within 4Å: Chain A: H.181, E.183, H.269 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.181, A:E.183, A:H.269, H2O.1, H2O.1

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.227, H.233, C.299, C.301 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.233, A:C.299, A:C.301

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: N.4, N.6, F.250, N.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.6, A:N.251 ACT.4: 1 residues within 4Å: Chain A: E.16 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krishnan, S. et al., Structural and Functional Analysis of JMJD2D Reveals Molecular Basis for Site-Specific Demethylation among JMJD2 Demethylases. Structure (2013)

Release Date

2012-11-21

Peptides

Lysine-specific demethylase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4D

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