SMTL ID : 4do0.1

Crystal Structure of human PHF8 in complex with Daminozide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

2 x DZA: DAMINOZIDE

DZA.1: 12 residues within 4Å: Chain A: N.116, I.118, L.163, T.171, H.174, D.176, F.177, Y.184, K.191, H.246, V.248 Ligands: ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.118, A:V.248 Hydrogen bonds: A:N.116, A:T.171, A:T.171, A:Y.184 Salt bridges: A:D.176, A:K.191 DZA.14: 12 residues within 4Å: Chain B: N.116, I.118, L.163, T.171, H.174, D.176, F.177, Y.184, K.191, H.246, V.248 Ligands: ZN.15 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.118, B:V.248 Hydrogen bonds: B:N.116, B:T.171 Salt bridges: B:D.176, B:K.191

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.174, D.176, H.246 Ligands: DZA.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.174, A:D.176, A:H.246, H2O.1 ZN.15: 4 residues within 4Å: Chain B: H.174, D.176, H.246 Ligands: DZA.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.174, B:D.176, B:H.246, H2O.2

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: T.70, V.71, Y.106, Y.107, K.188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.71, A:Y.107, A:Y.107 Salt bridges: A:K.188 SO4.4: 5 residues within 4Å: Chain A: H.322, K.325 Chain B: H.322, K.325 Ligands: SO4.17 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.322, A:H.322 SO4.5: 6 residues within 4Å: Chain A: K.57, D.58, G.59, L.60, G.61, M.62 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.59, A:G.59, A:G.61 Salt bridges: A:K.57 SO4.6: 2 residues within 4Å: Chain A: R.72, H.76 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.72, A:H.76 SO4.7: 2 residues within 4Å: Chain A: K.135, R.138 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.138 SO4.8: 5 residues within 4Å: Chain A: T.199, N.200 Chain B: A.317, S.318, Y.319 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.318, B:Y.319, A:N.200 Salt bridges: A:K.272 SO4.16: 5 residues within 4Å: Chain B: T.70, V.71, Y.106, Y.107, K.188 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.71, B:Y.106, B:Y.107 Salt bridges: B:K.188 SO4.17: 5 residues within 4Å: Chain A: H.322, K.325 Chain B: H.322, K.325 Ligands: SO4.4 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.322, A:H.322 SO4.18: 6 residues within 4Å: Chain B: K.57, D.58, G.59, L.60, G.61, M.62 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.59, B:G.59, B:G.61 Salt bridges: B:K.57 SO4.19: 2 residues within 4Å: Chain B: R.72, H.76 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.72, B:H.76 SO4.20: 2 residues within 4Å: Chain B: K.135, R.138 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.138 SO4.21: 5 residues within 4Å: Chain A: A.317, S.318, Y.319 Chain B: T.199, N.200 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.200, A:S.318, A:Y.319 Salt bridges: B:K.272

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

EDO.9: 6 residues within 4Å: Chain A: L.31, K.32, P.33, F.42 Chain B: D.27, E.28 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.32, B:D.27 EDO.11: 2 residues within 4Å: Chain A: S.66, S.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.66, A:S.66, A:S.68 EDO.12: 2 residues within 4Å: Chain A: K.229, S.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.231, A:K.233, A:K.233 EDO.22: 6 residues within 4Å: Chain A: D.27, E.28 Chain B: L.31, K.32, P.33, F.42 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.32, A:D.27 EDO.24: 2 residues within 4Å: Chain B: S.66, S.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.66, B:S.66, B:S.68 EDO.25: 2 residues within 4Å: Chain B: K.229, S.231 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.231, B:K.233, B:K.233

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 3 residues within 4Å: Chain A: F.177, A.283, R.287 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.287 ACT.13: 2 residues within 4Å: Chain A: Q.37 Chain B: K.226 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.226 Hydrogen bonds: A:Q.37 ACT.23: 3 residues within 4Å: Chain B: F.177, A.283, R.287 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.287 ACT.26: 2 residues within 4Å: Chain A: K.226 Chain B: Q.37 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.226 Hydrogen bonds: B:Q.37

Links

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Citation

 - 

Release Date

2012-03-14

Peptides

Histone lysine demethylase PHF8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histone lysine demethylase PHF8