SMTL ID : 5jwp.1

Crystal structure of human FIH D201E variant in complex with Zn, alpha-ketoglutarate, and HIF1 alpha peptide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

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

AKG.1: 13 residues within 4Å: Chain A: Y.148, L.191, T.199, H.202, E.204, N.208, F.210, K.217, H.282, I.284, N.297, W.299 Ligands: ZN.3 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.199, A:F.210 Hydrogen bonds: A:T.199, A:T.199, A:N.208, A:N.297 Salt bridges: A:K.217, A:H.282 Water bridges: B:N.16 AKG.8: 13 residues within 4Å: Chain C: Y.148, L.191, T.199, H.202, E.204, N.208, F.210, K.217, H.282, I.284, N.297, W.299 Ligands: ZN.10 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.199, C:F.210 Hydrogen bonds: C:Y.148, C:T.199, C:N.208, C:N.297 Salt bridges: C:K.217, C:H.282 Water bridges: D:N.16

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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:S.243 Water bridges: A:F.247 GOL.9: 7 residues within 4Å: Chain C: K.102, L.104, Y.233, S.243, Q.244, V.245, D.246 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.243 Water bridges: C:F.247

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.202, E.204, H.282 Ligands: AKG.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.202, A:E.204, A:E.204, A:H.282 ZN.10: 4 residues within 4Å: Chain C: H.202, E.204, H.282 Ligands: AKG.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.202, C:E.204, C:E.204, C:H.282

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

SO4.4: 5 residues within 4Å: Chain A: R.146, E.195, G.196, L.288, N.289 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.289, A:N.289 Salt bridges: A:R.146 SO4.5: 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 SO4.6: 6 residues within 4Å: Chain A: P.224, D.225, F.227, E.228, A.315, K.318 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.315 SO4.7: 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, A:H.316 SO4.11: 5 residues within 4Å: Chain C: R.146, E.195, G.196, L.288, N.289 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.289, C:N.289 Salt bridges: C:R.146 SO4.12: 4 residues within 4Å: Chain C: R.141, G.143, E.144, E.145 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.144, C:E.145 Salt bridges: C:R.141 SO4.13: 6 residues within 4Å: Chain C: P.224, D.225, F.227, E.228, A.315, K.318 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.315 SO4.14: 3 residues within 4Å: Chain C: D.225, K.314, A.315 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.315 Water bridges: C:H.316, C:H.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hangasky, J.A. et al., The facial triad in the alpha-ketoglutarate dependent oxygenase FIH: A role for sterics in linking substrate binding to O2 activation. J.Inorg.Biochem. (2016)

Release Date

2016-11-23

Peptides

Hypoxia-inducible factor 1-alpha inhibitor: AC
Hypoxia-inducible factor 1-alpha: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Hypoxia-inducible factor 1-alpha inhibitor

Hypoxia-inducible factor 1-alpha

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