SMTL ID : 5lbc.1

HIF prolyl hydroxylase 2 (PHD2/EGLN1) I280V/R281L/I292V variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/FG2216)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.139, D.141, F.192, H.200 Ligands: UN9.3 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 CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: K.30, H.31 Ligand excluded by PLIP

1 x UN9: N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE(Non-covalent)

UN9.3: 17 residues within 4Å: Chain A: D.80, I.82, M.125, A.127, Y.129, Y.136, H.139, D.141, I.153, Y.155, L.169, H.200, V.202, R.209, A.211, W.215 Ligands: MN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.82 Hydrogen bonds: A:Y.129, A:Y.155 Salt bridges: A:R.209 pi-Stacking: A:Y.136, A:Y.136

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

SO4.4: 2 residues within 4Å: Chain A: R.222, K.226 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.222 SO4.7: 5 residues within 4Å: Chain A: K.158, D.159, W.160, K.185, F.186 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.159, A:D.159 Water bridges: A:F.186, A:F.186

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: D.181, I.182, E.183, K.185, R.188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.181, A:E.183, A:E.183, A:R.188 GOL.6: 7 residues within 4Å: Chain A: G.135, Y.136, V.137, E.201, V.202, Q.203, P.204 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.136, A:E.201, A:V.202 Water bridges: A:G.135, A:G.135, A:G.135, A:G.135, A:V.137

1 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.8: 3 residues within 4Å: Chain A: R.138, V.140, P.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.138, A:R.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, R. et al., Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases. Nat Commun (2016)

Release Date

2016-08-31

Peptides

Egl nine homolog 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Egl nine homolog 1