SMTL ID : 9ht8.2 (1 other biounit)

Peptide-substrate-binding (PSB) domain of human type I collagen prolyl 4-hydroxylase complexed with Pro-Pro-Gly-Pro-Ala-Gly-Pro-Pro-Gly.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x PRO- PRO- GLY- PRO- ALA- GLY- PRO- PRO: GLY-PRO-ALA-GLY-PRO-PRO(Non-covalent)

PRO-PRO-GLY-PRO-ALA-GLY-PRO-PRO.1: 11 residues within 4Å: Chain A: Y.17, D.51, Y.52, Y.55, Y.58, R.82, N.86, Y.89, F.90, Y.92 Ligands: MPO.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.52, A:Y.58, A:Y.89, A:Y.92 Hydrogen bonds: A:R.82, A:N.86, A:N.86

3 x GLY: GLYCINE(Non-covalent)

GLY.2: 3 residues within 4Å: Chain A: Y.58, Q.59, G.61 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.2, G.2 GLY.3: 5 residues within 4Å: Chain A: F.3, L.4, W.28, Q.31 Ligands: GLY.4 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: G.3, A:L.4 GLY.4: 4 residues within 4Å: Chain A: L.27, W.28, Q.31 Ligands: GLY.3 1 PLIP interactions: 1 Ligand-Ligand interactions Hydrogen bonds: G.4

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: T.18, E.19 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.19, H2O.1, H2O.1, H2O.1, H2O.1

1 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.6: 10 residues within 4Å: Chain A: Y.17, T.18, E.19, A.20, Y.22, Y.55 Ligands: PRO-PRO-GLY-PRO-ALA-GLY-PRO-PRO.1, PRO-PRO-GLY-PRO-ALA-GLY-PRO-PRO.1, PRO-PRO-GLY-PRO-ALA-GLY-PRO-PRO.1, PRO-PRO-GLY-PRO-ALA-GLY-PRO-PRO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.22, A:Y.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rahman, M.M. et al., Binding Differences of the Peptide-Substrate-Binding Domain of Collagen Prolyl 4-Hydroxylases I and II for Proline- and Hydroxyproline-Rich Peptides. Proteins (2025)

Release Date

2025-09-24

Peptides

Prolyl 4-hydroxylase subunit alpha-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Prolyl 4-hydroxylase subunit alpha-1

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