SMTL ID : 2wwu.1

Crystal structure of the catalytic domain of PHD finger protein 8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: D.55, G.56, L.57, G.58, M.59 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.56, A:G.58, A:M.59 Water bridges: A:L.57, A:L.57 Salt bridges: A:K.54 SO4.2: 5 residues within 4Å: Chain A: H.319, K.322 Chain B: H.319, K.322 Ligands: SO4.17 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Water bridges: A:E.265, A:H.319, A:A.323, A:E.365, B:H.319 Salt bridges: A:H.319, B:H.319 SO4.3: 2 residues within 4Å: Chain A: R.69, H.73 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.69 Salt bridges: A:R.69, A:H.73 SO4.4: 5 residues within 4Å: Chain A: T.196, N.197 Chain B: A.314, S.315, Y.316 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.197, B:S.315, B:Y.316 Water bridges: A:T.196, A:A.198 SO4.5: 3 residues within 4Å: Chain A: R.18, T.19, F.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.19, A:F.20 Salt bridges: A:R.18 SO4.6: 3 residues within 4Å: Chain A: H.73, Y.74, R.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.74 Salt bridges: A:H.73, A:R.123 SO4.7: 5 residues within 4Å: Chain A: T.67, V.68, Y.103, Y.104, K.185 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.68, A:Y.103, A:Y.104 Salt bridges: A:K.185 SO4.16: 5 residues within 4Å: Chain B: D.55, G.56, L.57, G.58, M.59 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.56, B:G.58, B:M.59 Water bridges: B:L.57, B:L.57 Salt bridges: B:K.54 SO4.17: 5 residues within 4Å: Chain A: H.319, K.322 Chain B: H.319, K.322 Ligands: SO4.2 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Water bridges: B:E.265, B:H.319, B:A.323, B:E.365, A:H.319 Salt bridges: B:H.319, A:H.319 SO4.18: 2 residues within 4Å: Chain B: R.69, H.73 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.69 Salt bridges: B:R.69, B:H.73 SO4.19: 5 residues within 4Å: Chain A: A.314, S.315, Y.316 Chain B: T.196, N.197 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.197, A:S.315, A:Y.316 Water bridges: B:T.196, B:A.198 SO4.20: 3 residues within 4Å: Chain B: R.18, T.19, F.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.19, B:F.20 Salt bridges: B:R.18 SO4.21: 3 residues within 4Å: Chain B: H.73, Y.74, R.123 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.74 Salt bridges: B:H.73, B:R.123 SO4.22: 5 residues within 4Å: Chain B: T.67, V.68, Y.103, Y.104, K.185 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.68, B:Y.103, B:Y.104 Salt bridges: B:K.185

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

ACT.8: 3 residues within 4Å: Chain A: G.58, K.132, R.135 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.132 Salt bridges: A:R.135 ACT.9: 4 residues within 4Å: Chain A: D.82, D.91, D.281, L.282 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.91, A:D.91, A:D.281, A:L.282 ACT.10: 4 residues within 4Å: Chain A: R.304, D.356, R.359, E.360 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.360 Salt bridges: A:R.304, A:R.359 ACT.11: 3 residues within 4Å: Chain A: F.11, E.14, F.216 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.11, A:F.216 ACT.12: 2 residues within 4Å: Chain A: D.301, I.302 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.301 ACT.23: 3 residues within 4Å: Chain B: G.58, K.132, R.135 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.132 Salt bridges: B:R.135 ACT.24: 4 residues within 4Å: Chain B: D.82, D.91, D.281, L.282 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.91, B:D.91, B:D.281, B:L.282 ACT.25: 4 residues within 4Å: Chain B: R.304, D.356, R.359, E.360 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.360 Salt bridges: B:R.304, B:R.359 ACT.26: 3 residues within 4Å: Chain B: F.11, E.14, F.216 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.11, B:F.216 ACT.27: 2 residues within 4Å: Chain B: D.301, I.302 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.301

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

NI.13: 4 residues within 4Å: Chain A: H.171, D.173, Y.181, H.243 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.171, A:D.173, A:H.243 NI.28: 4 residues within 4Å: Chain B: H.171, D.173, Y.181, H.243 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.171, B:D.173, B:H.243

4 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.14: 11 residues within 4Å: Chain A: F.170, H.171, I.172, F.203, W.206, S.207, Q.212, E.274, L.277, S.278, T.279 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.172, A:I.172, A:Q.212, A:T.279, A:T.279 BGC.15: 5 residues within 4Å: Chain A: Y.103, Y.104, G.106, R.108, D.250 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.104, A:G.106, A:R.108 Water bridges: A:R.108, A:D.250 Salt bridges: A:R.108 BGC.29: 11 residues within 4Å: Chain B: F.170, H.171, I.172, F.203, W.206, S.207, Q.212, E.274, L.277, S.278, T.279 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.172, B:I.172, B:Q.212, B:T.279, B:T.279 BGC.30: 5 residues within 4Å: Chain B: Y.103, Y.104, G.106, R.108, D.250 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.104, B:G.106, B:R.108 Water bridges: B:R.108, B:D.250 Salt bridges: B:R.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yue, W.W. et al., Crystal structure of the PHF8 Jumonji domain, an Nepsilon-methyl lysine demethylase. FEBS Lett. (2010)

Release Date

2009-11-17

Peptides

PHD FINGER PROTEIN 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PHD FINGER PROTEIN 8