SMTL ID : 5fbj.1

Complex structure of JMJD5 and substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

monomer

Ligands

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.1: 14 residues within 4Å: Chain A: Y.92, W.130, S.138, H.141, D.143, N.147, L.149, K.156, H.220, V.222, S.232, W.234 Ligands: NMM.2, ZN.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.130, A:W.130, A:V.222 Hydrogen bonds: A:S.138, A:S.138, A:N.147, A:S.232 Water bridges: A:S.138 Salt bridges: A:K.156, A:H.220

1 x NMM: (2S)-2-amino-5-[(N-methylcarbamimidoyl)amino]pentanoic acid(Non-covalent)

NMM.2: 11 residues within 4Å: Chain A: E.58, Y.63, Y.92, Q.95, W.130, S.138, H.141, D.143, W.234 Ligands: AKG.1, ZN.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.63 Hydrogen bonds: A:S.138, A:S.138 Salt bridges: A:E.58, A:H.141

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.141, D.143, H.220 Ligands: AKG.1, NMM.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.141, A:D.143, A:H.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H.L. et al., to be published. To Be Published

Release Date

2016-12-14

Peptides

Lysine-specific demethylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 8

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