SMTL ID : 6evn.1

Crystal structure of peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase complex with Pro-Pro-Gly-Pro-Ala-Gly-Pro-Pro-Gly.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

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

PRO-PRO-GLY-PRO-ALA-GLY-PRO-PRO-GLY.1: 13 residues within 4Å: Chain A: R.19, Y.22, N.23, D.56, Y.57, Y.60, F.63, R.87, N.91, Y.94, F.95 Ligands: SO4.3, DMS.6 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.57, A:F.63, A:F.95 Hydrogen bonds: A:Y.22, A:N.23, A:N.23, A:Y.57, A:R.87, A:N.91, A:N.91 Salt bridges: A:R.19

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

SO4.2: 3 residues within 4Å: Chain A: R.70, E.73, R.77 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.70, A:R.77 SO4.3: 5 residues within 4Å: Chain A: F.15, Q.53, D.56, Y.57 Ligands: PRO-PRO-GLY-PRO-ALA-GLY-PRO-PRO-GLY.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.53, A:D.56, A:Y.57

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 5 residues within 4Å: Chain A: Y.22, N.23, G.25, Y.27 Ligands: DMS.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.27 pi-Cation interactions: A:Y.22 DMS.5: 3 residues within 4Å: Chain A: L.32, W.33, Q.36 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.36 pi-Cation interactions: A:W.33 DMS.6: 8 residues within 4Å: Chain A: Y.22, Y.27, Y.60 Ligands: PRO-PRO-GLY-PRO-ALA-GLY-PRO-PRO-GLY.1, PRO-PRO-GLY-PRO-ALA-GLY-PRO-PRO-GLY.1, PRO-PRO-GLY-PRO-ALA-GLY-PRO-PRO-GLY.1, PRO-PRO-GLY-PRO-ALA-GLY-PRO-PRO-GLY.1, DMS.4 No protein-ligand interaction detected (PLIP) DMS.7: 4 residues within 4Å: Chain A: D.26, Y.27, Y.28, L.65 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.27, A:Y.28 Salt bridges: A:D.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murthy, A.V. et al., Structural enzymology binding studies of the peptide-substrate-binding domain of human collagen prolyl 4-hydroxylase (type-II): High affinity peptides have a PxGP sequence motif. Protein Sci. (2018)

Release Date

2018-09-12

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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