SMTL ID : 4qu1.1

Crystal structure of human JMJD5 jmj-c domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

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

NI.1: 5 residues within 4Å: Chain A: H.141, D.143, H.220, W.234 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.141, A:D.143, A:H.220, H2O.1

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

AKG.2: 13 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: NI.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.130, A:W.130, A:V.222 Hydrogen bonds: A:Y.92, A:S.138, A:S.138, A:N.147, A:W.234 Water bridges: A:S.138 Salt bridges: A:K.156, A:H.220

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.9, P.10, S.11, L.12, V.31, D.113, Y.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.9, A:P.10, A:D.113, A:D.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H.L. et al., The Histone Arginine Demethylase JMJD5. To be Published

Release Date

2015-07-15

Peptides

Lysine-specific demethylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 8

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