SMTL ID : 5l9r.1

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 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: 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.2

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

OGA.2: 15 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 Ligands: MN.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.155 Water bridges: A:R.78, A:Y.129, A:Y.129, A:R.209, A:R.209 Salt bridges: A:R.78, A:H.139, A:R.209 OGA.3: 6 residues within 4Å: Chain A: I.33, V.35, A.180, D.181, I.182, R.188 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.181 Water bridges: A:R.188, A:R.188, A:R.188 Salt bridges: A:R.188

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 8 residues within 4Å: Chain A: N.119, G.120, R.121, T.122, K.123, F.217, R.222 Ligands: SO4.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.121

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

SO4.5: 4 residues within 4Å: Chain A: R.138, H.139, V.140, P.199 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.139 Water bridges: A:R.138, A:R.138, A:V.140 SO4.6: 8 residues within 4Å: Chain A: D.103, I.106, R.107, N.110, I.118, N.119, G.120, Y.216 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.107 SO4.7: 4 residues within 4Å: Chain A: T.122, R.148, F.217 Ligands: PG4.4 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.148

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 10 residues within 4Å: Chain A: D.76, I.77, R.78, G.79, G.133, T.134, G.135, Y.136, V.137, P.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.77, A:R.78

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

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