SMTL ID : 6y3e.1

Scaffold-ligand complex with ligand unmodelled

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: N.13, K.15, K.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.15, A:K.154, A:K.154 EDO.2: 4 residues within 4Å: Chain A: R.37, Q.163, S.165 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.163 Water bridges: A:Q.163 EDO.3: 3 residues within 4Å: Chain A: Q.163, S.165 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.163 EDO.4: 3 residues within 4Å: Chain A: R.19, E.134, L.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.19 EDO.5: 4 residues within 4Å: Chain A: E.134, G.135, M.136, D.137 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.135, A:M.136, A:D.137, A:D.137

2 x 12P: DODECAETHYLENE GLYCOL(Non-covalent)

12P.6: 4 residues within 4Å: Chain A: V.93, G.94, P.95, H.131 No protein-ligand interaction detected (PLIP) 12P.7: 5 residues within 4Å: Chain A: G.50, T.52, H.70, K.155, V.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.155

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 2 residues within 4Å: Chain A: S.147, K.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.148 Water bridges: A:G.146, A:S.149

3 x NA: SODIUM ION(Non-functional Binders)

NA.9: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.106 NA.10: 1 residues within 4Å: Chain A: F.60 No protein-ligand interaction detected (PLIP) NA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zacharchenko, T. et al., Human Cyclophilin D Complexed with Inhibitor. To Be Published

Release Date

2020-03-04

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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