SMTL ID : 4d6q.1

crystal structure of human JMJD2D in complex with 2,4-PDCA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.239, H.245, C.311, C.313 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.239, A:H.245, A:C.311, A:C.313 ZN.10: 4 residues within 4Å: Chain B: C.239, H.245, C.311, C.313 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.239, B:H.245, B:C.311, B:C.313

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

NI.2: 5 residues within 4Å: Chain A: H.193, E.195, H.281 Ligands: PD2.3, EDO.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.193, A:E.195, A:H.281, H2O.12 NI.11: 5 residues within 4Å: Chain B: H.193, E.195, H.281 Ligands: PD2.12, EDO.17 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.193, B:E.195, B:H.281, H2O.27

2 x PD2: PYRIDINE-2,4-DICARBOXYLIC ACID(Non-covalent)

PD2.3: 12 residues within 4Å: Chain A: Y.137, Y.182, F.190, H.193, E.195, N.203, K.211, W.213, K.246, H.281 Ligands: NI.2, EDO.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.213 Hydrogen bonds: A:Y.137, A:Y.182, A:N.203 Salt bridges: A:H.193, A:K.211, A:K.246 pi-Stacking: A:F.190 PD2.12: 12 residues within 4Å: Chain B: Y.137, Y.182, F.190, H.193, E.195, N.203, K.211, W.213, K.246, H.281 Ligands: NI.11, EDO.17 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.213 Hydrogen bonds: B:N.203 Salt bridges: B:H.193, B:K.211, B:K.246 pi-Stacking: B:F.190

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

EDO.4: 6 residues within 4Å: Chain A: K.151, Q.152, W.153, N.154, H.157, L.158 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.154, A:N.154 Water bridges: A:N.30, A:W.153, A:W.153 EDO.5: 4 residues within 4Å: Chain A: P.252, T.253, K.256, R.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.252, A:R.264, A:R.264 EDO.6: 6 residues within 4Å: Chain A: F.119, E.123, T.212, R.264, I.265, T.266 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.266 Water bridges: A:T.266, A:T.266, A:T.266 EDO.7: 3 residues within 4Å: Chain A: K.125, K.128, N.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.125, A:N.129 EDO.8: 9 residues within 4Å: Chain A: Y.180, Y.182, E.195, S.201, A.293, I.294, N.295 Ligands: NI.2, PD2.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.182, A:E.195, A:N.295 Water bridges: A:S.201, A:N.295 EDO.13: 6 residues within 4Å: Chain B: K.151, Q.152, W.153, N.154, H.157, L.158 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.154, B:N.154 Water bridges: B:N.30, B:W.153, B:W.153, B:H.157 EDO.14: 4 residues within 4Å: Chain B: P.252, T.253, K.256, R.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.252, B:R.264, B:R.264 EDO.15: 6 residues within 4Å: Chain B: F.119, E.123, T.212, R.264, I.265, T.266 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.266 Water bridges: B:T.266, B:T.266, B:T.266 EDO.16: 3 residues within 4Å: Chain B: K.125, K.128, N.129 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.125, B:N.129 EDO.17: 9 residues within 4Å: Chain B: Y.180, Y.182, E.195, S.201, A.293, I.294, N.295 Ligands: NI.11, PD2.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.182, B:Y.182, B:E.195, B:N.295 Water bridges: B:S.201, B:N.295

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

SO4.9: 4 residues within 4Å: Chain A: R.61, E.62, T.63, N.66 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.62, A:T.63, A:N.66 Water bridges: A:R.61, A:R.61, A:T.63, A:T.63 Salt bridges: A:R.61 SO4.18: 4 residues within 4Å: Chain B: R.61, E.62, T.63, N.66 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.62, B:T.63, B:N.66, A:E.166 Water bridges: B:R.61, B:R.61, B:R.61 Salt bridges: B:R.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krojer, T. et al., Crystal Structure of Human Jmjd2D in Complex with 2,4-Pdca. To be Published

Release Date

2014-12-24

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

LYSINE-SPECIFIC DEMETHYLASE 4D

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