SMTL ID : 4d6r.1

crystal structure of human JMJD2D in complex with N-OXALYLGLYCINE and bound o-toluenesulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 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.11: 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: 4 residues within 4Å: Chain A: H.193, E.195, H.281 Ligands: OGA.7 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.12: 4 residues within 4Å: Chain B: H.193, E.195, H.281 Ligands: OGA.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.29

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

EDO.3: 7 residues within 4Å: Chain A: F.32, K.151, Q.152, W.153, N.154, H.157, L.158 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.153, A:N.154, A:N.154 Water bridges: A:N.30, A:F.32 EDO.4: 3 residues within 4Å: Chain A: K.256, G.259 Ligands: IEJ.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.256, A:G.259 EDO.5: 4 residues within 4Å: Chain A: P.114, N.129, W.186, K.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.129, A:K.187 EDO.6: 6 residues within 4Å: Chain A: Y.180, Y.182, E.195, A.293, N.295 Ligands: OGA.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.295 Water bridges: A:Y.182 EDO.13: 7 residues within 4Å: Chain B: F.32, K.151, Q.152, W.153, N.154, H.157, L.158 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.153, B:N.154, B:N.154 Water bridges: B:N.30, B:F.32, B:H.157 EDO.14: 3 residues within 4Å: Chain B: K.256, G.259 Ligands: IEJ.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.256, B:G.259 EDO.15: 4 residues within 4Å: Chain B: P.114, N.129, W.186, K.187 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.129, B:K.187 EDO.16: 6 residues within 4Å: Chain B: Y.180, Y.182, E.195, A.293, N.295 Ligands: OGA.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.182, B:N.295

2 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.7: 12 residues within 4Å: Chain A: Y.137, F.190, H.193, E.195, S.201, N.203, K.211, W.213, H.281, A.293 Ligands: NI.2, EDO.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.137, A:S.201, A:N.203 Salt bridges: A:K.211, A:H.281 OGA.17: 12 residues within 4Å: Chain B: Y.137, F.190, H.193, E.195, S.201, N.203, K.211, W.213, H.281, A.293 Ligands: NI.12, EDO.16 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.195, B:S.201, B:N.203 Salt bridges: B:K.211, B:H.281

6 x IEJ: O-TOLUENESULFONAMIDE(Non-covalent)

IEJ.8: 2 residues within 4Å: Chain A: M.20, I.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.21 Water bridges: A:H.23 IEJ.9: 5 residues within 4Å: Chain A: K.256, I.260, P.261, F.262 Ligands: EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.256, A:K.256, A:F.262 Hydrogen bonds: A:F.262 Water bridges: A:I.260 IEJ.10: 7 residues within 4Å: Chain A: K.26, F.29, N.30, P.55, E.57, W.58, Q.152 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.26, A:K.26 Water bridges: A:Q.152 IEJ.18: 2 residues within 4Å: Chain B: M.20, I.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.21 Water bridges: B:H.23 IEJ.19: 5 residues within 4Å: Chain B: K.256, I.260, P.261, F.262 Ligands: EDO.14 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.256, B:K.256, B:F.262 Hydrogen bonds: B:F.262 Water bridges: B:I.260 IEJ.20: 7 residues within 4Å: Chain B: K.26, F.29, N.30, P.55, E.57, W.58, Q.152 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.26, B:K.26 Water bridges: B:Q.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krojer, T. et al., Crystal Structure of Human Jmjd2D in Complex with N-Oxalylglycine and Bound O-Toluenesulfonamide. 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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