SMTL ID : 5cbt.1

Human Cyclophilin D Complexed with Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x 4ZL: ethyl N-(benzylcarbamoyl)glycinate(Non-covalent)

4ZL.1: 11 residues within 4Å: Chain A: R.55, F.60, M.61, Q.63, G.72, A.101, N.102, T.107, Q.111, F.113, H.126 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.60, A:F.113 Hydrogen bonds: A:Q.63, A:N.102, A:N.102, A:N.102 Salt bridges: A:R.55, A:H.126

2 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.2: 1 residues within 4Å: Ligands: PGE.7 No protein-ligand interaction detected (PLIP) K.3: 4 residues within 4Å: Chain A: Y.7, D.160, C.161 Ligands: FMT.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.160, A:C.161, H2O.1

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 6 residues within 4Å: Chain A: C.40, T.41, G.42, K.49, C.161 Ligands: K.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:C.40, A:G.47

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 4 residues within 4Å: Chain A: V.93, G.94, P.95, H.131 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.93

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 3 residues within 4Å: Chain A: P.84, D.85, E.86 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.85

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 5 residues within 4Å: Chain A: P.58, S.59, F.60, W.121 Ligands: K.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gibson, R.P. et al., Human Cyclophilin D Complexed with Inhibitor. To Be Published

Release Date

2016-07-20

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptidyl-prolyl cis-trans isomerase F, mitochondrial

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