SMTL ID : 8q6e.1

Aerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with Fe(III), 2-oxoglutarate (2OG) and HIF2alpha-CODD peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

hetero-1-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: T.83, W.84 No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain A: A.162, K.163, V.164, G.166, Y.206 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: L.55, K.60, E.89 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: M.28, N.29, G.32, W.193, R.197 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: N.110, G.111, Y.116, K.117, I.118 Ligand excluded by PLIP

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

FE.6: 6 residues within 4Å: Chain A: H.139, D.141, F.192, H.200 Chain B: P.9 Ligands: AKG.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.139, A:D.141, A:H.200, H2O.1

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

AKG.7: 16 residues within 4Å: Chain A: R.78, M.125, Y.129, Y.136, H.139, D.141, I.153, Y.155, L.169, H.200, V.202, R.209, A.211, W.215 Chain B: P.9 Ligands: FE.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.153, A:V.202 Hydrogen bonds: A:Y.155 Water bridges: A:Y.129, A:R.209 Salt bridges: A:R.78, A:H.139, A:R.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fiorini, G. et al., HIF prolyl hydroxylase 2 in complex with HIF2alpha-CODD. To Be Published

Release Date

2024-08-21

Peptides

Egl nine homolog 1: A
Endothelial PAS domain-containing protein 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Egl nine homolog 1

Endothelial PAS domain-containing protein 1

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