MolNFT v1 · #56174 · protein
Crystal structure of human cyclophilin D in complex with cyclosporin a
2Z6W · Peptidyl-prolyl cis-trans isomerase: “Crystal structure of human cyclophilin D in complex with cyclosporin a”. X-ray diffraction, 1 pocket (best druggability 0.45). MolNFT v1 #56174 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2Z6W
- Type
- protein
- Length
- 350 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase; Cyclosporin a
- EC
- 5.2.1.8
- UniProt
- P30405
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 164 | 15% helix, 34% strand | P30405 |
| M, N | Cyclosporin a | protein | 11 | 0% helix, 9% strand | — |
Ligands and binding sites
- CIT · Citric acid · 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 | 144 | 0.45 | 0.77 | 26 | empty |
Interfaces
4 interfaces between chains.
- B–N · 507 Ų buried · 6 hydrogen bonds · protein-protein
- A–M · 493 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 415 Ų buried · 9 hydrogen bonds · protein-protein
- A–N · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 2 d-amino (nonstandard, methylation, D-amino acid).
Compared structures
- 2Z6W · Crystal structure of human cyclophilin D in complex with cyclosporin A · the same entry in another collection · chain A against A, TM-score 1.00
- P30405 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase F… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 2Z6W · PDBe 2Z6W · UniProt P30405
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