SMTL ID : 2yc0.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

FE2.1: 5 residues within 4Å: Chain A: H.202, D.204, H.282 Ligands: 2HG.2, GOL.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.202, A:D.204, A:H.282 FE2.10: 5 residues within 4Å: Chain B: H.202, D.204, H.282 Ligands: 2HG.11, GOL.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.202, B:D.204, B:H.282

2 x 2HG: (2R)-2-hydroxypentanedioic acid(Non-covalent)

2HG.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: FE2.1, GOL.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.199, A:F.210, A:I.284 Hydrogen bonds: A:Y.148, A:T.199, A:N.208, A:N.297 Salt bridges: A:K.217, A:H.282 2HG.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: FE2.10, GOL.14 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:T.199, B:F.210, B:I.284 Hydrogen bonds: B:Y.148, B:N.208, B:N.297 Salt bridges: B:K.217, B:H.282

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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.4: 6 residues within 4Å: Chain A: D.225, E.228, A.315, K.318, M.322 Chain B: T.345 No protein-ligand interaction detected (PLIP) GOL.5: 8 residues within 4Å: Chain A: Y.105, Q.150, T.199, H.202, D.204, W.299 Ligands: FE2.1, 2HG.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.150, A:Q.150, A:T.199, A:D.204 Water bridges: A:R.241, A:Q.242 GOL.12: 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.13: 6 residues within 4Å: Chain A: T.345 Chain B: D.225, E.228, A.315, K.318, M.322 No protein-ligand interaction detected (PLIP) GOL.14: 8 residues within 4Å: Chain B: Y.105, Q.150, T.199, H.202, D.204, W.299 Ligands: FE2.10, 2HG.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.150, B:Q.150, B:D.204 Water bridges: B:R.241, B:Q.242

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

SO4.6: 3 residues within 4Å: Chain A: D.225, K.314, A.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.315 Water bridges: A:H.316 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: 2 residues within 4Å: Chain A: R.123, E.125 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.123 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.225, B:A.315 Water bridges: B:H.316 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: 2 residues within 4Å: Chain B: R.123, E.125 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.123 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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