SMTL ID : 8wug.1

The Crystal Structure of JMJD2D from Biortus.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.238, H.244, C.310, C.312 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.238, A:H.244, A:C.310, A:C.312

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: H.192, E.194, H.280 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.194

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 10 residues within 4Å: Chain A: F.28, N.29, D.30, F.31, K.150, Q.151, W.152, N.153, H.156, L.157 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.28, A:F.31, A:W.152, A:N.153, A:N.153

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

SO4.4: 5 residues within 4Å: Chain A: P.113, K.124, N.128, W.185, K.186 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.124 Water bridges: A:N.132, A:N.132 Salt bridges: A:K.186 SO4.5: 4 residues within 4Å: Chain A: G.99, R.102, H.103, N.106 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.102, A:N.106 Water bridges: A:R.102 Salt bridges: A:R.102, A:H.103 SO4.6: 4 residues within 4Å: Chain A: R.60, E.61, T.62, N.65 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.61, A:T.62, A:N.65 Water bridges: A:T.62, A:T.62 Salt bridges: A:R.60

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

EDO.7: 3 residues within 4Å: Chain A: Y.277, Y.303, M.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.306 Water bridges: A:S.308, A:S.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., The Crystal Structure of JMJD2D from Biortus. To Be Published

Release Date

2023-11-22

Peptides

Lysine-specific demethylase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4D

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