SMTL ID : 7q5v.1

HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE (NOG) AND HIF-2 ALPHA CODD (523-542)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.17 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: OGA.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.3

1 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.2: 17 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, T.213, W.215 Chain B: P.9 Ligands: MN.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.155 Water bridges: A:R.78, A:Y.129, A:R.209 Salt bridges: A:R.78, A:H.139, A:R.209

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

PEG.3: 3 residues within 4Å: Chain A: D.159, W.160, D.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.159 PEG.7: 7 residues within 4Å: Chain A: H.31, I.33, V.35, P.173, K.176, A.180, I.182 No protein-ligand interaction detected (PLIP) PEG.8: 6 residues within 4Å: Chain A: Q.47, D.50, E.51, G.91, E.93, T.94 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.50, A:D.50, A:E.51, A:E.93, A:E.93, A:T.94

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: S.115, Y.116, K.117, D.218, D.220, E.221, R.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.224 Water bridges: A:K.117

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

FMT.5: 2 residues within 4Å: Chain A: A.207, T.208 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.208 FMT.6: 3 residues within 4Å: Chain A: L.19, Y.23, V.36 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.37 FMT.12: 7 residues within 4Å: Chain A: K.226, Y.229, L.230 Chain B: M.13, D.14, G.15, E.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.226

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

CL.9: 4 residues within 4Å: Chain A: S.100, D.103, D.104, R.107 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 4 residues within 4Å: Chain A: Q.69, K.70, S.71, D.72 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:K.70, A:D.72 MG.11: 5 residues within 4Å: Chain A: I.106, R.107, C.109, N.110, I.118 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.106, H2O.7 MG.13: 2 residues within 4Å: Chain B: F.18, Q.19 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Q.19, H2O.10

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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