SMTL ID : 9ibn.1

Crystal structure of the peptidyl-prolyl isomerase (PPIase) from E. faecium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: R.63, I.66, Y.67, F.122, I.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.67 GOL.6: 5 residues within 4Å: Chain B: Q.62, R.63, Y.67, N.119, F.122 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.62, B:Y.67, B:N.119 GOL.7: 4 residues within 4Å: Chain B: D.134, D.249, D.251, K.254 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.251, B:D.251, B:D.251

15 x CD: CADMIUM ION(Non-covalent)

CD.2: 1 residues within 4Å: Chain A: E.50 No protein-ligand interaction detected (PLIP) CD.3: 1 residues within 4Å: Chain A: D.49 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.49, A:D.49, H2O.1 CD.4: 1 residues within 4Å: Chain A: D.173 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.173, A:D.173, H2O.1 CD.5: 2 residues within 4Å: Chain A: H.129, D.131 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.129 CD.8: 1 residues within 4Å: Chain B: D.49 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.49, B:D.49 CD.9: 1 residues within 4Å: Chain B: E.50 No protein-ligand interaction detected (PLIP) CD.10: 1 residues within 4Å: Chain B: E.114 No protein-ligand interaction detected (PLIP) CD.11: 2 residues within 4Å: Chain B: D.80, D.84 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.80, B:D.80, B:D.84, B:D.84 CD.12: 3 residues within 4Å: Chain B: H.129, E.278 Ligands: CD.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.129, B:E.278 CD.13: 4 residues within 4Å: Chain B: H.129, D.131 Ligands: CD.12, CD.14 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.129, B:D.131 CD.14: 2 residues within 4Å: Chain B: D.131 Ligands: CD.13 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.131, B:D.131, H2O.3 CD.15: 2 residues within 4Å: Chain B: D.173, S.175 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.173, B:D.173, B:S.175, H2O.3 CD.16: 1 residues within 4Å: Chain B: D.268 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.268 CD.17: 1 residues within 4Å: Chain B: D.290 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.290 CD.18: 1 residues within 4Å: Chain B: D.46 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Napolitano, V. et al., Crystal structure and biophysical characterisation of the enterococcal foldase PpiC, a cross-opsonic antigen against gram-positive nosocomial pathogens. Febs J. (2025)

Release Date

2025-07-16

Peptides

Foldase protein PrsA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Foldase protein PrsA