SMTL ID : 5fyi.1 (1 other biounit)

Crystal structure of human JMJD2A in complex with pyruvate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: PYR.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, PYR.2, H2O.4

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 11 residues within 4Å: Chain A: F.207, H.210, E.212, S.218, N.220, W.230, H.298, S.310 Ligands: NI.1, PYR.3, EDO.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.207, A:W.230 Hydrogen bonds: A:S.218, A:N.220, A:S.310 Salt bridges: A:H.298 PYR.3: 7 residues within 4Å: Chain A: Y.154, Y.199, N.220, K.228, S.310 Ligands: PYR.2, EDO.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.199 Hydrogen bonds: A:N.220, A:S.310 Salt bridges: A:K.228

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

DMS.4: 4 residues within 4Å: Chain A: F.249, P.250, G.251, S.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.251, A:S.252

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

EDO.5: 5 residues within 4Å: Chain A: H.210, T.211, L.260, R.261, Y.297 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.211, A:T.211, A:Y.297, A:Y.297 Water bridges: A:R.261, A:K.263 EDO.6: 5 residues within 4Å: Chain A: G.102, F.104, W.144, S.268, L.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.268 Water bridges: A:G.102, A:W.144 EDO.7: 2 residues within 4Å: Chain A: E.185, S.186 No protein-ligand interaction detected (PLIP) EDO.8: 7 residues within 4Å: Chain A: F.104, T.105, F.249, S.252, F.259, M.264, T.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.105, A:S.252 EDO.9: 5 residues within 4Å: Chain A: Y.133, F.136, T.283, E.285, H.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.133, A:T.283 EDO.10: 3 residues within 4Å: Chain A: D.180, E.183, K.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.183, A:K.184 Water bridges: A:D.180 EDO.11: 4 residues within 4Å: Chain A: S.33, A.34, E.236, H.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.33 EDO.12: 7 residues within 4Å: Chain A: Y.154, Y.199, F.207, H.210, K.263 Ligands: PYR.2, PYR.3 No protein-ligand interaction detected (PLIP) EDO.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.13: 5 residues within 4Å: Chain A: C.256, H.262, C.328, S.329, C.330 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.256, A:H.262, A:C.328, A:C.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nowak, R. et al., Crystal Structure of Human Jmjd2A in Complex with Pyruvate. To be Published

Release Date

2016-03-16

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 4A

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