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

Crystal structure of human KDM4C catalytic domain bound to tris

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.227, H.233, C.299, C.301 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.227, A:H.233, A:C.299, A:C.301

1 x FE: FE (III) ION(Non-covalent)

FE.2: 4 residues within 4Å: Chain A: H.181, E.183, H.269 Ligands: TRS.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.181, A:E.183, A:H.269

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 10 residues within 4Å: Chain A: F.178, H.181, E.183, S.189, N.191, K.234, T.263, H.269, S.281 Ligands: FE.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.189, A:N.191, A:K.234, A:S.281, A:S.281

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 6 residues within 4Å: Chain A: D.54, I.55, L.58, N.130, S.132, I.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.54 PGE.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 1 residues within 4Å: Chain A: G.218 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.214

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain A: R.315, K.316 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: P.102, R.103 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: N.117, W.174 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: V.149, T.286, V.287 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wigle, T.J. et al., A High-Throughput Mass Spectrometry Assay Coupled with Redox Activity Testing Reduces Artifacts and False Positives in Lysine Demethylase Screening. J Biomol Screen (2015)

Release Date

2015-03-25

Peptides

Lysine-specific demethylase 4C: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4C

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