SMTL ID : 4z2w.1

Factor Inhibiting HIF in Complex with Fe, and Alpha-Ketoglutarate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.1: 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: PEG.2, FE.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.191, A:F.210, A:I.284 Hydrogen bonds: A:Y.148, A:T.199, A:T.199, A:N.208, A:N.297 Salt bridges: A:K.217, A:H.282 AKG.9: 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: PEG.10, FE.11 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.191, 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

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 6 residues within 4Å: Chain A: Y.105, Q.150, H.202, R.241, W.299 Ligands: AKG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.242 PEG.10: 6 residues within 4Å: Chain B: Y.105, Q.150, H.202, R.241, W.299 Ligands: AKG.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.242

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

FE.3: 4 residues within 4Å: Chain A: H.202, D.204, H.282 Ligands: AKG.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.202, A:D.204, A:H.282, H2O.1 FE.11: 4 residues within 4Å: Chain B: H.202, D.204, H.282 Ligands: AKG.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.202, B:D.204, B:H.282, H2O.3

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

SO4.4: 2 residues within 4Å: Chain A: K.314, A.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.315 Water bridges: A:H.316 SO4.5: 4 residues within 4Å: Chain A: K.110, D.240, R.323, K.327 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.240, A:D.240, A:R.323 Salt bridges: A:K.110, A:K.327 SO4.6: 4 residues within 4Å: Chain A: R.141, G.143, E.144, E.145 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.144, A:E.145, A:E.145 Salt bridges: A:R.141 SO4.7: 3 residues within 4Å: Chain A: R.20, R.47, T.68 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.47 SO4.8: 6 residues within 4Å: Chain A: D.225, F.227, E.228, A.315, K.318, M.322 No protein-ligand interaction detected (PLIP) SO4.12: 2 residues within 4Å: Chain B: K.314, A.315 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.315 Water bridges: B:H.316 SO4.13: 4 residues within 4Å: Chain B: K.110, D.240, R.323, K.327 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.240, B:R.323 Salt bridges: B:K.110, B:K.327 SO4.14: 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 SO4.15: 3 residues within 4Å: Chain B: R.20, R.47, T.68 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.47 SO4.16: 6 residues within 4Å: Chain B: D.225, F.227, E.228, A.315, K.318, M.322 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taabazuing, C.Y. et al., Substrate Promotes Productive Gas Binding in the alpha-Ketoglutarate-Dependent Oxygenase FIH. Biochemistry (2016)

Release Date

2016-01-13

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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