Research workbench
Crystal structures of cyclophilin a complexed with cyclosporin a and N-methyl-4-[(E)-2-butenyl]-4,4-dimethylthreonine cyclosporin a
Analyse Crystal structures of cyclophilin a complexed with cyclosporin a and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RMA
- Type
- protein
- Length
- 1,760 residues
- Chains
- 20
- 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
- P62937
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S | Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 165 | 14% helix, 34% strand | P62937 |
| B, D, F, H, J, L, N, P, R, T | Cyclosporin a | protein | 11 | 0% helix, 9% strand | — |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.73 | 0.77 | 84 | empty |
| 2 | 527 | 0.70 | 0.79 | 63 | empty |
| 3 | 501 | 0.63 | 0.76 | 63 | empty |
| 4 | 498 | 0.63 | 0.76 | 65 | empty |
| 5 | 454 | 0.61 | 0.76 | 53 | empty |
Interfaces
55 interfaces between chains.
- G–H · 527 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 522 Ų buried · 6 hydrogen bonds · protein-protein
- M–N · 521 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 518 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 510 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 80 modified, 10 d-amino (nonstandard, methylation, D-amino acid).
Compared structures
- 2RMA · Crystal structures of cyclophilin A complexed with cyclosporin A and… · 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 P62937
- Elsewhere: RCSB PDB 2RMA · PDBe 2RMA · UniProt P62937
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