SMTL ID : 4hon.1 (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: 14 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, PDO.15 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: 5 residues within 4Å: Chain A: C.227, H.233, C.299, S.300, 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: 3 residues within 4Å: Chain A: K.139, Q.140 Ligands: SCN.6 No protein-ligand interaction detected (PLIP) SCN.5: 4 residues within 4Å: Chain A: E.16, K.22, Y.23, Y.26 No protein-ligand interaction detected (PLIP) SCN.6: 4 residues within 4Å: Chain A: W.46, K.47, T.138 Ligands: SCN.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.47

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

NO3.7: 6 residues within 4Å: Chain A: E.213, G.228, A.229, F.230, L.231, Y.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.213, A:L.231, A:R.232 NO3.8: 4 residues within 4Å: Chain A: K.294, R.321, L.324, W.325 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.294, A:R.321 Water bridges: A:W.325 NO3.9: 4 residues within 4Å: Chain A: K.294, M.310, W.325, Q.329 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.329 Water bridges: A:K.294, A:M.310, A:W.325 NO3.10: 2 residues within 4Å: Chain A: D.291, M.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.291 NO3.11: 6 residues within 4Å: Chain A: E.303, A.304, R.305, V.306 Chain B: A.2, R.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.3, B:R.3, A:R.305 Water bridges: A:V.306 NO3.12: 5 residues within 4Å: Chain A: P.102, K.113, N.117, W.174, K.175 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.117, A:K.175, A:K.175 Water bridges: A:N.117, A:N.121 NO3.13: 3 residues within 4Å: Chain A: H.194, A.257, G.258 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.257 Water bridges: A:Y.192, A:H.194, A:H.194 NO3.14: 5 residues within 4Å: Chain A: I.55, S.56, V.87, G.88, R.91 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.56, A:G.88, A:H.92

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

PDO.15: 8 residues within 4Å: Chain A: F.178, A.179, H.181, K.234 Chain B: K.4, S.5, T.6 Ligands: AKG.1 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.178 Hydrogen bonds: A:A.179, A:K.234, B:T.6 Water bridges: A:Y.170, B:S.5 PDO.16: 4 residues within 4Å: Chain A: T.76, Y.78, F.220, P.221 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.76 Hydrogen bonds: A:T.76, A:P.221 PDO.17: 3 residues within 4Å: Chain A: G.131, S.132, L.169 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.169 Hydrogen bonds: A:S.132 PDO.18: 2 residues within 4Å: Chain A: M.8, I.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.9

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
A

B
F

Lysine-specific demethylase 4D

Histone H3 Peptide

Related Entries With Identical Sequence