SMTL ID : 4c8d.1

Crystal structure of JmjC domain of human histone 3 Lysine-specific demethylase 3B (KDM3B)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.182, D.184, H.311 Ligands: OGA.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.182, A:D.184, A:H.311, H2O.2

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

OGA.2: 11 residues within 4Å: Chain A: Y.163, T.179, H.182, D.184, N.190, W.236, I.305, H.311, V.313, K.321 Ligands: MN.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.179, A:N.190 Water bridges: A:Y.163, A:Y.163, A:N.315 Salt bridges: A:H.311, A:K.321

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: W.24, K.25, R.28, E.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.28, A:R.28

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 3 residues within 4Å: Chain A: W.6, G.10, Q.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.35 ACT.5: 6 residues within 4Å: Chain A: R.71, R.94, V.104, G.167, I.169, E.201 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.104, A:I.169 Hydrogen bonds: A:G.167, A:G.167 Water bridges: A:R.94 Salt bridges: A:R.94

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: L.133, P.134, E.135 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vollmar, M. et al., Crystal Structure of Jmjc Domain of Human Histone 3 Lysine-Specific Demethylase 3B (Kdm3B). To be Published

Release Date

2013-10-16

Peptides

LYSINE-SPECIFIC DEMETHYLASE 3B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 3B