SMTL ID : 6yw1.1

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 2OG and RaPID-derived silent allosteric cyclic peptide 3C (14-mer)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.46 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, F.192, H.200 Ligands: AKG.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

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.153, A:V.202 Hydrogen bonds: A:Y.155 Water bridges: A:Y.129, A:Y.136, A:Y.136, A:R.209 Salt bridges: A:R.78, A:H.139, A:R.209

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

BCT.3: 3 residues within 4Å: Chain A: R.138, V.140, P.199 No protein-ligand interaction detected (PLIP)

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Egl nine homolog 1

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

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