SMTL ID : 8k0m.1

Human collagen prolyl processing enzyme complex, P3H1/CRTAP/PPIB heterotrimer, bound to 2-oxoglutarate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: H.536, L.537, N.540 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.536, A:N.540 NAG.2: 2 residues within 4Å: Chain A: N.316, Q.319 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain B: N.87 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain B: L.323, F.362, N.363, L.367 No protein-ligand interaction detected (PLIP)

1 x FE: FE (III) ION(Non-covalent)

FE.3: 4 residues within 4Å: Chain A: H.587, D.589, H.659 Ligands: AKG.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.587, A:D.589, A:D.589, A:H.659

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

AKG.4: 10 residues within 4Å: Chain A: R.569, H.584, H.587, D.589, F.627, H.659, V.661, R.669, W.675 Ligands: FE.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.661 Salt bridges: A:R.569, A:H.584, A:H.587, A:R.669

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., The structural basis for the collagen processing by human P3H1/CRTAP/PPIB ternary complex. Nat Commun (2024)

Release Date

2024-09-18

Peptides

Prolyl 3-hydroxylase 1: A
Cartilage-associated protein: B
Peptidyl-prolyl cis-trans isomerase B: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Prolyl 3-hydroxylase 1

Cartilage-associated protein

Peptidyl-prolyl cis-trans isomerase B

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