SMTL ID : 9hpq.4 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

1 x GLY- PRO- ARG- GLY- PRO- PRO: Synthetic peptide PRO-PRO-GLY-PRO-ARG-GLY-PRO-PRO-GLY(Non-covalent)

GLY-PRO-ARG-GLY-PRO-PRO.1: 10 residues within 4Å: Chain A: Y.17, D.51, Y.52, Y.55, Y.58, R.82, N.86, Y.89, F.90 Ligands: MPO.9 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.52, A:Y.58, A:Y.58, A:Y.89 Hydrogen bonds: A:Y.17, A:R.82, A:N.86, A:N.86 Water bridges: A:Y.55

4 x GLY: GLYCINE(Non-covalent)(Non-functional Binders)

GLY.2: 5 residues within 4Å: Chain A: F.3, L.4, T.5, D.8 Ligands: MPD.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:D.8 Water bridges: G.2, G.2 GLY.3: 3 residues within 4Å: Chain A: Y.58, Q.59, G.61 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: G.3, A:Y.58, A:Y.58 GLY.4: 2 residues within 4Å: Chain A: Y.23 Ligands: GLY.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:Y.23, G.5, G.5 GLY.5: 3 residues within 4Å: Chain A: Y.23, L.27 Ligands: GLY.4 1 PLIP interactions: 1 Ligand-Ligand interactions Hydrogen bonds: G.4

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 1 residues within 4Å: Chain A: E.19 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.19, H2O.1, H2O.2

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 7 residues within 4Å: Chain A: L.12, V.15, A.16, E.19, D.21, H.24, W.28 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.12, A:V.15, A:E.19 Hydrogen bonds: A:D.21, A:D.21, A:W.28 MPD.8: 6 residues within 4Å: Chain A: L.4, D.8, E.11, L.12, V.15 Ligands: GLY.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.4, A:E.11

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

MPO.9: 10 residues within 4Å: Chain A: Y.17, T.18, E.19, A.20, Y.22, Y.55 Ligands: GLY-PRO-ARG-GLY-PRO-PRO.1, GLY-PRO-ARG-GLY-PRO-PRO.1, GLY-PRO-ARG-GLY-PRO-PRO.1, GLY-PRO-ARG-GLY-PRO-PRO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.22

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
D

Prolyl 4-hydroxylase subunit alpha-1

Related Entries With Identical Sequence