SMTL ID : 3kv4.1

Structure of PHF8 in complex with histone H3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.8, C.10, H.31, C.34 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.8, A:C.10, A:H.31, A:C.34 ZN.2: 4 residues within 4Å: Chain A: C.23, C.26, C.50, C.53 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.23, A:C.26, A:C.50, A:C.53

1 x FE2: FE (II) ION(Non-covalent)

FE2.3: 4 residues within 4Å: Chain A: H.247, D.249, H.319 Ligands: OGA.18 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.247, A:D.249, A:H.319, H2O.4

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

NI.4: 5 residues within 4Å: Chain A: S.214, W.215, V.216, F.334, L.335 No protein-ligand interaction detected (PLIP)

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

EDO.5: 6 residues within 4Å: Chain A: C.10, L.12, R.18, H.31, C.34 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.18, A:R.18 EDO.6: 3 residues within 4Å: Chain A: R.92, I.265, K.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.92, A:K.302 EDO.7: 3 residues within 4Å: Chain A: F.96, D.97, S.98 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.96, A:K.302 EDO.8: 2 residues within 4Å: Chain A: V.123, R.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.270, A:R.270 EDO.9: 2 residues within 4Å: Chain A: F.115, E.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.118, A:E.118 EDO.10: 7 residues within 4Å: Chain A: K.212, L.213, S.214, W.215, L.219, H.374 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.212 EDO.11: 5 residues within 4Å: Chain A: K.130, D.131, G.132, L.133, G.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.132 Water bridges: A:M.135 EDO.12: 5 residues within 4Å: Chain A: S.337, H.374, I.378, L.393 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.337 EDO.13: 5 residues within 4Å: Chain A: D.44, I.45, S.60, I.61, M.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.61 EDO.14: 7 residues within 4Å: Chain A: V.35, V.37, Y.48, H.49, C.50, P.51, E.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.35, A:Y.48, A:E.54 Water bridges: A:S.60 EDO.15: 2 residues within 4Å: Chain A: N.52, V.55 No protein-ligand interaction detected (PLIP) EDO.16: 3 residues within 4Å: Chain A: Y.7, S.354, T.355 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.354 Water bridges: A:S.354 EDO.17: 5 residues within 4Å: Chain A: D.161, C.168, M.170, K.186, L.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.161, A:K.186

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

OGA.18: 12 residues within 4Å: Chain A: N.189, I.191, T.244, H.247, D.249, V.255, Y.257, K.264, H.319, V.321 Chain B: K.9 Ligands: FE2.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.189, A:T.244, A:T.244, A:D.249, A:Y.257 Water bridges: A:T.244 Salt bridges: A:K.264, A:H.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nat.Struct.Mol.Biol. (2010)

Release Date

2009-12-22

Peptides

PHD finger protein 8: A
Histone H3-like: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PHD finger protein 8

Histone H3-like

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