SMTL ID : 9htd.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

GLY-PRO-ALA-GLY-PRO-HYP-GLY.1: 12 residues within 4Å: Chain A: R.19, Y.22, N.23, D.56, Y.57, Y.60, F.63, Q.64, R.87, N.91, Y.94, F.95 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.57, A:Y.60, A:F.63, A:R.87, A:F.95, A:F.95 Hydrogen bonds: A:N.23, A:Y.57, A:R.87, A:N.91, A:N.91 Water bridges: A:Y.60, A:R.87 Salt bridges: A:R.19

4 x GLY: GLYCINE(Non-covalent)

GLY.2: 3 residues within 4Å: Chain A: R.76, R.77, S.80 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Water bridges: A:R.77 Hydrogen bonds: G.2 GLY.3: 3 residues within 4Å: Chain A: L.65, G.66, D.67 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.65, A:G.66 Water bridges: A:L.68, A:L.68 GLY.4: 4 residues within 4Å: Chain A: T.50, S.52, Q.53, D.82 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:S.52, A:D.82, G.4 Water bridges: A:S.52 GLY.5: 3 residues within 4Å: Chain A: L.32, W.33, Q.36 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.32, A:Q.36 Water bridges: A:Q.36

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

SO4.6: 5 residues within 4Å: Chain A: L.41, T.49, T.50, K.51, S.52 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:K.51 Water bridges: A:S.52, G.4 Salt bridges: A:K.51

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-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Prolyl 4-hydroxylase subunit alpha-2

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