SMTL ID : 5pmm.1

PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 180)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.260, H.266, C.332, C.334 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.260, A:H.266, A:C.332, A:C.334

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

NI.2: 4 residues within 4Å: Chain A: H.214, E.216, H.302 Ligands: OGA.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.214, A:E.216, A:H.302, H2O.4

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: N.87, I.88, S.89, E.90, I.91 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.87

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

OGA.4: 12 residues within 4Å: Chain A: Y.158, F.211, H.214, E.216, S.222, N.224, K.232, W.234, H.302, A.314 Ligands: NI.2, EDO.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.158, A:S.222, A:N.224 Salt bridges: A:K.232, A:H.302

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

EDO.5: 6 residues within 4Å: Chain A: K.172, Q.173, W.174, N.175, H.178, L.179 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.175, A:N.175 Water bridges: A:N.51, A:W.174, A:W.174 EDO.6: 4 residues within 4Å: Chain A: P.273, T.274, K.277, R.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.285, A:R.285 EDO.7: 7 residues within 4Å: Chain A: E.246, A.262, F.263, L.264, R.265, Y.301, S.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.264, A:Y.301 EDO.8: 5 residues within 4Å: Chain A: D.86, N.87, I.88, S.89, E.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.89 Water bridges: A:D.86, A:R.124 EDO.9: 6 residues within 4Å: Chain A: F.140, E.144, T.233, R.285, I.286, T.287 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.286, A:T.287 Water bridges: A:T.287 EDO.10: 6 residues within 4Å: Chain A: W.79, K.80, A.81, R.82, Y.85, Y.225 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.81, A:R.82, A:R.82, A:Y.85, A:Y.225 Water bridges: A:W.79, A:Y.225 EDO.11: 3 residues within 4Å: Chain A: S.102, T.109, F.253 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.109 EDO.12: 6 residues within 4Å: Chain A: Y.203, E.216, A.314, I.315, N.316 Ligands: OGA.4 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.216, A:N.316, A:N.316, A:N.316

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

SO4.13: 3 residues within 4Å: Chain A: R.124, H.125, N.128 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.128 Water bridges: A:R.124, A:H.125, A:H.125 Salt bridges: A:R.124 SO4.14: 4 residues within 4Å: Chain A: R.82, E.83, T.84, N.87 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.83, A:T.84, A:T.84 Water bridges: A:T.84 Salt bridges: A:R.82 SO4.15: 3 residues within 4Å: Chain A: K.146, K.149, N.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.150 Water bridges: A:K.149 Salt bridges: A:K.146, A:K.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pearce, N.M. et al., A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun (2017)

Release Date

2017-03-15

Peptides

Lysine-specific demethylase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4D

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