SMTL ID : 6yw3.1

HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) in complex with N-Oxalyl Glycine (NOG), HIF-1ALPHA CODD (556-574) and a RaPID-derived cyclic peptide 3C (14-mer)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-1-1-1-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 C: 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.1

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

OGA.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 C: P.9 Ligands: MN.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.129, A:Y.129, A:Y.155 Water bridges: A:R.78, A:R.209 Salt bridges: A:R.78, A:H.139, A:R.209

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: K.75, D.76, I.77, R.78, G.79, T.134, G.135, Y.136, V.137, P.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.79, A:G.135 Water bridges: A:Y.136

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

SO4.4: 2 residues within 4Å: Chain A: Q.46, D.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, R. et al., Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2. Sci Rep (2020)

Release Date

2020-12-30

Peptides

Egl nine homolog 1: A
PHD2-SPECIFIC RaPID CYCLIC PEPTIDE 3C (14-MER): B
Hypoxia-inducible factor 1-alpha: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
S

Egl nine homolog 1

PHD2-SPECIFIC RaPID CYCLIC PEPTIDE 3C (14-MER)

Hypoxia-inducible factor 1-alpha

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