SMTL ID : 5lbb.1

HIF prolyl hydroxylase 2 (PHD2/EGLN1) R396T variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-trimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.139, D.141, F.192, H.200 Ligands: UN9.2 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 MN.4: 5 residues within 4Å: Chain B: H.139, D.141, F.192, H.200 Ligands: UN9.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.139, B:D.141, B:H.200, H2O.7 MN.7: 5 residues within 4Å: Chain C: H.139, D.141, F.192, H.200 Ligands: UN9.8 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.139, C:D.141, C:H.200, H2O.11

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

UN9.2: 19 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 Chain B: R.224, V.227 Ligands: MN.1 5 PLIP interactions: 5 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 UN9.5: 19 residues within 4Å: Chain B: 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 Chain C: R.224, V.227 Ligands: MN.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.82 Hydrogen bonds: B:Y.129, B:Y.155 Salt bridges: B:R.209 pi-Stacking: B:Y.136 UN9.8: 19 residues within 4Å: Chain A: R.224, V.227 Chain C: 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.7 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.82 Hydrogen bonds: C:Y.129, C:Y.155 Salt bridges: C:R.209 pi-Stacking: C:Y.136

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

BCT.3: 4 residues within 4Å: Chain A: R.138, V.140, R.196, P.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.138, A:R.138 BCT.6: 4 residues within 4Å: Chain B: R.138, V.140, R.196, P.199 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.138, B:R.138 BCT.9: 4 residues within 4Å: Chain C: R.138, V.140, R.196, P.199 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.138, C: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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Egl nine homolog 1