SMTL ID : 4hon.2 (1 other biounit)

Crystal structure of human JMJD2D/KDM4D in complex with an H3K9me3 peptide and 2-oxoglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

AKG.1: 13 residues within 4Å: Chain A: Y.125, Y.170, F.178, H.181, E.183, S.189, N.191, K.199, W.201, H.269, A.281 Chain B: K.4 Ligands: NI.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.178, A:W.201 Hydrogen bonds: A:Y.125, A:S.189, A:N.191 Salt bridges: A:K.199, A:H.269

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

NI.2: 4 residues within 4Å: Chain A: H.181, E.183, H.269 Ligands: AKG.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.181, A:E.183, A:H.269, H2O.1

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.227, H.233, C.299, C.301 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.227, A:H.233, A:C.299, A:C.301

3 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.4: 7 residues within 4Å: Chain A: R.49, T.51, Y.52, D.53, N.54, I.55, L.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.49, A:N.54, A:N.54 SCN.5: 3 residues within 4Å: Chain A: K.47, E.50, T.138 No protein-ligand interaction detected (PLIP) SCN.6: 3 residues within 4Å: Chain A: K.113, K.116, N.117 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.113

4 x NO3: NITRATE ION(Non-functional Binders)

NO3.7: 5 residues within 4Å: Chain A: E.213, G.228, A.229, F.230, L.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.230, A:L.231 NO3.8: 3 residues within 4Å: Chain A: D.323, L.324, R.327 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.327, A:R.327 NO3.9: 4 residues within 4Å: Chain A: P.206, E.207, Y.266, Y.292 3 PLIP interactions: 3 interactions with chain A Water bridges: A:P.206, A:G.209, A:Y.292 NO3.10: 5 residues within 4Å: Chain A: P.102, K.113, N.117, W.174, K.175 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.113, A:N.117, A:W.174, A:K.175 Water bridges: A:N.117, A:N.121

1 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.11: 3 residues within 4Å: Chain A: I.58, I.129, S.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.132, A:S.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krishnan, S. et al., Structural and Functional Analysis of JMJD2D Reveals Molecular Basis for Site-Specific Demethylation among JMJD2 Demethylases. Structure (2013)

Release Date

2012-11-21

Peptides

Lysine-specific demethylase 4D: A
Histone H3 Peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
G

Lysine-specific demethylase 4D

Histone H3 Peptide

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