SMTL ID : 4d6s.1

crystal structure of human JMJD2D in complex with N-OXALYLGLYCINE and bound 5,6-Dimethylbenzimidazole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 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

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

NI.2: 4 residues within 4Å: Chain A: H.193, E.195, H.281 Ligands: OGA.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.193, A:E.195, A:H.281, H2O.11

1 x DMD: 5,6-DIMETHYLBENZIMIDAZOLE(Non-covalent)

DMD.3: 5 residues within 4Å: Chain A: D.198, Q.222, Y.278, Y.304, M.307 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.222, A:Y.304 Water bridges: A:Q.222, A:E.225, A:S.309 pi-Stacking: A:Y.278, A:Y.278

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

OGA.4: 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

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

EDO.5: 1 residues within 4Å: Chain A: N.107 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.103, A:H.104 EDO.6: 6 residues within 4Å: Chain A: Y.180, Y.182, E.195, A.293, N.295 Ligands: OGA.4 No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain A: K.151, Q.152, W.153, N.154, H.157, L.158 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.154 Water bridges: A:N.30, A:T.150, A:W.153, A:W.153, A:H.157 EDO.8: 6 residues within 4Å: Chain A: A.37, E.40, Y.200, T.298, P.299, R.300 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.200, A:T.298, A:R.300 Water bridges: A:D.33, A:A.37 EDO.9: 3 residues within 4Å: Chain A: S.81, T.88, F.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.88 EDO.10: 2 residues within 4Å: Chain A: M.20, I.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.21 Water bridges: A:I.19, A:I.19 EDO.11: 6 residues within 4Å: Chain A: T.160, Q.162, D.163, G.175, V.176 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.163 EDO.12: 6 residues within 4Å: Chain A: G.85, W.127, K.128, S.251, T.253, V.254 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.127, A:S.251, A:S.251 Water bridges: A:T.253 EDO.13: 2 residues within 4Å: Chain A: D.163 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.163 EDO.14: 6 residues within 4Å: Chain A: F.119, E.120, E.123, R.264, I.265, T.266 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.119, A:T.266 Water bridges: A:R.264, A:T.266, A:T.266

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.15: 5 residues within 4Å: Chain A: P.114, K.125, N.129, W.186, K.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.187 Water bridges: A:N.133

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

SO4.16: 3 residues within 4Å: Chain A: K.125, K.128, N.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.129 Salt bridges: A:K.125

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 5,6- Dimethylbenzimidazole. To be Published

Release Date

2014-12-24

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 4D

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