SMTL ID : 6f6d.1

The catalytic domain of KDM6B in complex with H3(17-33)K18IA21M peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 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.251, E.253, S.259, H.331 Ligands: AKG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.251, A:E.253, A:H.331, H2O.12

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.436, E.438, C.439, V.441, C.463, C.466 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.436, A:C.439, A:C.463, A:C.466

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

AKG.3: 15 residues within 4Å: Chain A: F.189, Y.240, K.242, T.248, H.251, E.253, S.259, N.261, W.271, I.325, H.331, V.333, N.341, A.343 Ligands: FE.1 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.333 Hydrogen bonds: A:T.248, A:T.248, A:S.259, A:N.261 Water bridges: A:T.248, A:N.345, B:K.11 Salt bridges: A:K.242, A:H.331, B:K.11

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

TBU.4: 7 residues within 4Å: Chain A: I.49, L.51, D.56, S.59, V.61, L.62, F.65 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.49, A:L.62, A:F.65 TBU.5: 6 residues within 4Å: Chain A: T.92, Q.145, A.146, F.149, P.266, W.338 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.149, A:P.266 Water bridges: A:Q.145 TBU.6: 6 residues within 4Å: Chain A: T.103, V.104, E.105, H.135, D.194 Chain B: R.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.103, A:E.105 Water bridges: A:D.194, A:D.194, A:D.194

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

2018-10-17

Peptides

Lysine-specific demethylase 6B: A
Histone 3 peptide H3(17-33)K18IA21M: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine-specific demethylase 6B

Histone 3 peptide H3(17-33)K18IA21M

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