SMTL ID : 7q5x.1

HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH 2-OXOGLUTARATE (2OG) AND HIF-2 ALPHA CODD (523-542)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.21 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: H.139, D.141, H.200 Chain B: P.9 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.139, A:D.141, A:H.200, H2O.2

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

AKG.2: 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: MN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.153, A:V.202 Hydrogen bonds: A:Y.155 Water bridges: A:R.78, A:R.209 Salt bridges: A:R.78, A:H.139, A:R.209

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

PEG.3: 8 residues within 4Å: Chain A: F.172, P.173, E.174, G.175, K.176, A.177, Q.178, F.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.175, A:K.176, A:Q.178

11 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 6 residues within 4Å: Chain A: K.75, G.79, T.134, G.135, V.137 Ligands: FMT.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.135 FMT.6: 6 residues within 4Å: Chain A: G.135, Y.136, V.137, V.202, P.204 Ligands: FMT.4 No protein-ligand interaction detected (PLIP) FMT.7: 3 residues within 4Å: Chain A: E.174, R.196, R.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.174 FMT.8: 4 residues within 4Å: Chain A: L.14, L.19, Y.23, V.36 No protein-ligand interaction detected (PLIP) FMT.9: 5 residues within 4Å: Chain A: T.62, Q.65, I.82, W.84 Chain B: Y.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.62, A:T.62, A:W.84 FMT.10: 6 residues within 4Å: Chain A: W.160, D.161, A.162, E.183, P.184, K.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.162, A:E.183 FMT.11: 3 residues within 4Å: Chain A: S.73, K.75, D.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.75 FMT.12: 7 residues within 4Å: Chain A: E.86, G.87, G.96, M.99, S.100, R.121 Chain B: F.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.87, A:R.121 FMT.13: 4 residues within 4Å: Chain A: K.60, T.62, T.83 Ligands: MG.15 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.83 FMT.14: 3 residues within 4Å: Chain A: A.177, Q.178, F.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.179, A:F.179 FMT.21: 3 residues within 4Å: Chain B: D.17, F.18, Q.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.19

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: P.13, L.14, L.19, V.36, D.37, D.38, F.39 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.14

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

MG.15: 3 residues within 4Å: Chain A: T.83, W.84 Ligands: FMT.13 No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain A: A.162, K.163, V.164, G.166, Y.206 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain A: L.55, K.60, E.89 No protein-ligand interaction detected (PLIP)

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

CL.18: 5 residues within 4Å: Chain A: M.28, N.29, G.32, W.193, R.197 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: R.138, P.199 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain A: N.110, G.111, Y.116, K.117, I.118 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Figg Jr., W.D. et al., Structural basis for binding of the renal carcinoma target hypoxia-inducible factor 2 alpha to prolyl hydroxylase domain 2. Proteins (2023)

Release Date

2022-11-16

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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