SMTL ID : 5fyi.2 (1 other biounit)

Crystal structure of human JMJD2A in complex with pyruvate

Coordinates

PDB Format Compare

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.3 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.3, H2O.4

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 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

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.3: 12 residues within 4Å: Chain A: F.207, H.210, E.212, S.218, N.220, W.230, T.292, H.298, S.310 Ligands: NI.1, PYR.4, EDO.13 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.4: 8 residues within 4Å: Chain A: Y.154, Y.199, F.207, N.220, K.228, S.310 Ligands: PYR.3, EDO.13 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.5: 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

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

EDO.6: 9 residues within 4Å: Chain A: Y.143, W.144, F.207, A.208, W.209, L.266, I.267, A.299, G.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.143, A:W.209, A:I.267, A:G.300 EDO.7: 3 residues within 4Å: Chain A: G.102, S.268, L.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.268 EDO.8: 5 residues within 4Å: Chain A: E.242, E.257, A.258, F.259, L.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.256, A:F.259, A:L.260 EDO.9: 6 residues within 4Å: Chain A: T.98, G.99, L.103, F.104, T.105, F.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.103 EDO.10: 2 residues within 4Å: Chain A: R.120, N.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.124 EDO.11: 7 residues within 4Å: Chain A: K.127, Y.128, N.150, P.152, M.202, W.203, K.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.203 EDO.12: 4 residues within 4Å: Chain A: Y.40, K.68, E.285, E.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.40, A:K.68 Water bridges: A:T.38 EDO.13: 7 residues within 4Å: Chain A: Y.154, S.206, F.207, H.210, K.263 Ligands: PYR.3, PYR.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.106

1 x 1KA: (2-hydroxyethoxy)acetaldehyde(Non-covalent)

1KA.14: 5 residues within 4Å: Chain A: S.33, A.34, E.236, H.237, P.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.236 Water bridges: A:F.279

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
B

LYSINE-SPECIFIC DEMETHYLASE 4A

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