SMTL ID : 5oy3.1

The structural basis of the histone demethylase KDM6B histone 3 lysine 27 specificity

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

hetero-1-1-mer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: H.250, E.252, S.258, H.330 Ligands: AKG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.250, A:E.252, A:H.330, H2O.6

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.435, E.437, C.438, V.440, C.462, C.465 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.435, A:C.438, A:C.462, A:C.465

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

AKG.3: 15 residues within 4Å: Chain A: F.188, Y.239, K.241, T.247, H.250, E.252, S.258, N.260, W.270, I.324, H.330, V.332, N.340, A.342 Ligands: FE.1 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.332 Hydrogen bonds: A:T.247, A:T.247, A:S.258, A:N.260 Water bridges: A:T.247, B:K.11 Salt bridges: A:K.241, A:H.330

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: L.62, F.213, S.218, G.220, N.221, P.347, L.348 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.213, A:L.348 Water bridges: A:G.220 EDO.5: 4 residues within 4Å: Chain A: I.48, V.60, L.61, F.64 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: K.27, E.275, H.276, W.278, E.279 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.27, A:E.275 EDO.7: 9 residues within 4Å: Chain A: L.41, N.42, L.301, D.302, L.304, Y.305, I.309, V.311, R.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.309 EDO.8: 3 residues within 4Å: Chain A: R.416, A.417, G.418 No protein-ligand interaction detected (PLIP) EDO.9: 6 residues within 4Å: Chain A: W.379, N.380, R.383, Y.482, L.487, A.490 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.380 Water bridges: A:N.380 EDO.10: 6 residues within 4Å: Chain A: Q.144, A.145, F.148, P.265, W.337, C.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.144 Water bridges: A:T.91, A:Q.144 EDO.11: 4 residues within 4Å: Chain A: E.279, S.282, A.283, D.286 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.282, A:D.286

1 x TBU: TERTIARY-BUTYL ALCOHOL(Non-functional Binders)

TBU.12: 5 residues within 4Å: Chain A: T.102, V.103, E.104, H.134 Chain B: R.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.104 Water bridges: A:D.193, A:D.193, A:D.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, S.E. et al., Structural Basis of Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity. Biochemistry (2018)

Release Date

2017-09-20

Peptides

Lysine-specific demethylase 6B: A
Histone 3 peptide H3(17-33)A21M: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine-specific demethylase 6B

Histone 3 peptide H3(17-33)A21M

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