SMTL ID : 9gle.1 (1 other biounit)

Jumonji domain-containing protein 2A with crystallization epitope mutations A91T:T93S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION

NI.1: 4 residues within 4Å: Chain A: H.189, E.191, T.271, H.277 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.189, A:E.191, A:H.277, H2O.3, H2O.4, H2O.8

3 x SO4: SULFATE ION

SO4.2: 4 residues within 4Å: Chain A: F.228, P.229, G.230, S.231 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.230, A:S.231, A:S.231 Water bridges: A:S.231, A:S.231 SO4.3: 2 residues within 4Å: Chain A: K.90, K.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.91 Salt bridges: A:K.90 SO4.4: 1 residues within 4Å: Chain A: K.106 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.106

1 x ZN: ZINC ION

ZN.5: 7 residues within 4Å: Chain A: C.235, F.238, H.241, C.307, S.308, C.309, R.310 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.235, A:H.241, A:C.307, A:C.309

5 x EDO: 1,2-ETHANEDIOL

EDO.6: 8 residues within 4Å: Chain A: E.221, K.225, E.236, A.237, F.238, L.239, R.240, Y.276 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.235, A:F.238, A:L.239 EDO.7: 8 residues within 4Å: Chain A: Y.60, D.61, I.63, D.64, V.95, R.99, F.203, F.284 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.99 EDO.8: 3 residues within 4Å: Chain A: R.99, K.100, N.103 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.99 EDO.9: 6 residues within 4Å: Chain A: Y.133, Y.178, F.186, H.189, K.207, K.242 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.242 Water bridges: A:Y.133, A:N.199, A:N.199, A:K.207 EDO.10: 6 residues within 4Å: Chain A: I.316, S.317, M.318, D.319, W.333, K.334 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.317, A:M.318, A:D.319, A:K.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fairhead, M. et al., A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants. To be published

Release Date

2024-09-18

Peptides

Lysine-specific demethylase 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4A

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