SMTL ID : 3dxt.2 (1 other biounit)

Crystal structure of the catalytic core domain of JMJD2D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 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 ZN.9: 4 residues within 4Å: Chain B: C.238, H.244, C.310, C.312 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.238, B:H.244, B:C.310, B:C.312

6 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 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Water bridges: B:E.165, B:E.165, A:R.60, A:R.60 Hydrogen bonds: A:E.61, A:T.62 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 SO4.10: 6 residues within 4Å: Chain B: P.113, K.124, N.128, N.132, W.185, K.186 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.128, B:W.185 Water bridges: B:N.132 Salt bridges: B:K.186 SO4.11: 4 residues within 4Å: Chain B: R.60, E.61, T.62, N.65 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.61, B:T.62 Water bridges: B:R.60, B:R.60, B:R.60, B:T.62, B:D.146 Salt bridges: B:R.60 SO4.12: 4 residues within 4Å: Chain B: R.123, K.124, K.127, N.128 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.128 Salt bridges: B:R.123, B:K.124, B:K.127

8 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 GOL.13: 5 residues within 4Å: Chain B: S.80, G.81, T.87, L.230, F.231 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.80 Water bridges: B:R.82, B:V.85, B:T.87, B:L.230 GOL.14: 6 residues within 4Å: Chain B: F.31, K.150, Q.151, W.152, N.153, H.156 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.31, B:W.152, B:N.153 Water bridges: B:D.32, B:K.150, B:H.156 GOL.15: 5 residues within 4Å: Chain B: Y.181, F.189, N.202, K.210 Ligands: GOL.16 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.181, B:N.202, B:K.210 Water bridges: B:K.210, B:N.284 GOL.16: 8 residues within 4Å: Chain B: Y.179, Y.181, E.194, S.200, A.292, I.293, N.294 Ligands: GOL.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.181, B:S.200, B:S.200 Water bridges: B: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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

JmjC domain-containing histone demethylation protein 3D

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