SMTL ID : 8uc5.1 (2 other biounits)

Apo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

6 x DMS: DIMETHYL SULFOXIDE

DMS.1: 8 residues within 4Å: Chain A: R.56, F.61, M.62, Q.64, F.114, L.123, H.127 Ligands: CL.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.56, A:R.56 pi-Cation interactions: A:F.114 DMS.2: 5 residues within 4Å: Chain A: V.133, I.134, E.135, G.136, M.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.136, A:M.137 Water bridges: A:D.138 DMS.3: 3 residues within 4Å: Chain A: G.73, N.103, Q.112 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.110, A:Q.112 DMS.4: 6 residues within 4Å: Chain A: H.55, N.72, S.150, G.151, R.152 Ligands: DMS.5 No protein-ligand interaction detected (PLIP) DMS.5: 3 residues within 4Å: Chain A: H.71, N.72 Ligands: DMS.4 No protein-ligand interaction detected (PLIP) DMS.6: 3 residues within 4Å: Chain A: Q.164, L.165, S.166 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION

NA.7: 3 residues within 4Å: Chain A: Y.8, D.161, C.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.161, A:C.162

2 x CL: CHLORIDE ION

CL.8: 4 residues within 4Å: Chain A: A.102, N.103, H.127 Ligands: DMS.1 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: R.152 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kreitler, D.F. et al., Apo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I). To Be Published

Release Date

2024-09-04

Peptides

Peptidyl-prolyl cis-trans isomerase F, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

Peptidyl-prolyl cis-trans isomerase F, mitochondrial

Related Entries With Identical Sequence