SMTL ID : 3dxt.1 (1 other biounit)

Crystal structure of the catalytic core domain of JMJD2D

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.238, H.244, C.310, C.312 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.238, A:H.244, A:C.310, A:C.312

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: P.113, K.124, N.128, N.132, W.185, K.186 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.128, A:W.185 Water bridges: A:N.132 Salt bridges: A:K.186 SO4.3: 4 residues within 4Å: Chain A: R.60, E.61, T.62, N.65 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.61, A:T.62 Water bridges: A:R.60, A:R.60 Salt bridges: A:R.60 SO4.4: 4 residues within 4Å: Chain A: R.123, K.124, K.127, N.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.128 Salt bridges: A:R.123, A:K.124, A:K.127

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: S.80, G.81, T.87, L.230, F.231 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.80 Water bridges: A:R.82, A:V.85, A:L.230 GOL.6: 6 residues within 4Å: Chain A: F.31, K.150, Q.151, W.152, N.153, H.156 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.31, A:W.152, A:N.153 Water bridges: A:D.32, A:K.150, A:H.156 GOL.7: 5 residues within 4Å: Chain A: Y.181, F.189, N.202, K.210 Ligands: GOL.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.181, A:N.202, A:K.210 Water bridges: A:K.210, A:N.284 GOL.8: 8 residues within 4Å: Chain A: Y.179, Y.181, E.194, S.200, A.292, I.293, N.294 Ligands: GOL.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.181, A:Y.181, A:S.200, A:S.200 Water bridges: A:N.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Z. et al., Crystal structure of the catalytic core domain of jmjd2d. To be Published

Release Date

2009-10-06

Peptides

JmjC domain-containing histone demethylation protein 3D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

JmjC domain-containing histone demethylation protein 3D

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