MolNFT v1 · #162460 · protein
Human cyclophilin D in complex with fragment
6R9U · Peptidyl-prolyl cis-trans isomerase F, mitochondrial: “Human cyclophilin D in complex with fragment”. X-ray diffraction, 2 ligands (JVQ, SO4), 1 pocket (best druggability 0.35). MolNFT v1 #162460 on GenesisL1: 3D structure, binding…
- PDB
- 6R9U
- Type
- protein
- Length
- 164 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase F, mitochondrial
- EC
- 5.2.1.8
- UniProt
- P30405
- Ligands
- JVQ, SO4
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase F, mitochondrial (EC 5.2.1.8) | protein | 164 | 15% helix, 32% strand | P30405 |
Ligands and binding sites
- JVQ · 14-ethyl-4,6-dioxa-10,14-diazatricyclo[7.6.0.0^{3, 7}]pentadeca-1(9),2,7-trien-13-one · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- PGE · Triethylene glycol · additive · 3 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.35 | 0.76 | 21 | JVQ, PGE |
Compared structures
- 6R9U · Human Cyclophilin D in complex with fragment · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P30405
- Elsewhere: RCSB PDB 6R9U · PDBe 6R9U · UniProt P30405
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