SMTL ID : 2yde.1

FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH S-2-HYDROXYGLUTARATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: H.202, D.204, H.282 Ligands: S2G.2, GOL.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.202, A:D.204, A:H.282 FE.10: 5 residues within 4Å: Chain B: H.202, D.204, H.282 Ligands: S2G.11, GOL.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.202, B:D.204, B:H.282

4 x S2G: (2S)-2-HYDROXYPENTANEDIOIC ACID(Non-covalent)

S2G.2: 14 residues within 4Å: Chain A: Y.148, L.191, T.199, H.202, D.204, N.208, F.210, K.217, H.282, I.284, N.297, W.299 Ligands: FE.1, GOL.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.191, A:T.199, A:F.210, A:I.284 Hydrogen bonds: A:T.199, A:T.199, A:N.208, A:N.297 Salt bridges: A:K.217, A:H.282 S2G.3: 2 residues within 4Å: Chain A: Q.151, T.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.151, A:T.152 S2G.11: 14 residues within 4Å: Chain B: Y.148, L.191, T.199, H.202, D.204, N.208, F.210, K.217, H.282, I.284, N.297, W.299 Ligands: FE.10, GOL.14 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.191, B:T.199, B:F.210, B:I.284 Hydrogen bonds: B:Y.148, B:T.199, B:N.208, B:N.297 Salt bridges: B:K.217, B:H.282 S2G.12: 2 residues within 4Å: Chain B: Q.151, T.152 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.151

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: K.102, L.104, Y.233, S.243, Q.244, V.245, D.246 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.233, A:Y.233 Water bridges: A:F.247 GOL.5: 8 residues within 4Å: Chain A: Y.105, Q.150, T.199, H.202, D.204, W.299 Ligands: FE.1, S2G.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.150 Water bridges: A:Q.150, A:T.199 GOL.13: 7 residues within 4Å: Chain B: K.102, L.104, Y.233, S.243, Q.244, V.245, D.246 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.233 Water bridges: B:F.247 GOL.14: 8 residues within 4Å: Chain B: Y.105, Q.150, T.199, H.202, D.204, W.299 Ligands: FE.10, S2G.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.150 Water bridges: B:Q.150, B:T.199

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

SO4.6: 3 residues within 4Å: Chain A: D.225, K.314, A.315 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.315 Water bridges: A:H.316 Salt bridges: A:K.314 SO4.7: 4 residues within 4Å: Chain A: R.141, G.143, E.144, E.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.144, A:E.145 Salt bridges: A:R.141 SO4.8: 4 residues within 4Å: Chain A: K.110, D.240, R.323, K.327 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.240, A:D.240 Water bridges: A:R.323 Salt bridges: A:K.110, A:R.323, A:K.327 SO4.9: 5 residues within 4Å: Chain A: R.146, E.195, G.196, L.288, N.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.289 Salt bridges: A:R.146 SO4.15: 3 residues within 4Å: Chain B: D.225, K.314, A.315 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.225, B:A.315 Water bridges: B:H.316 Salt bridges: B:K.314 SO4.16: 4 residues within 4Å: Chain B: R.141, G.143, E.144, E.145 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.144, B:E.145 Salt bridges: B:R.141 SO4.17: 4 residues within 4Å: Chain B: K.110, D.240, R.323, K.327 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.240 Water bridges: B:R.323 Salt bridges: B:K.110, B:R.323, B:K.327 SO4.18: 5 residues within 4Å: Chain B: R.146, E.195, G.196, L.288, N.289 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.289 Salt bridges: B:R.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, R. et al., The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep. (2011)

Release Date

2011-03-30

Peptides

HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR

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