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Crystal structure of the cyclophilin-like domain from brugia malayi complexed with cyclosporin a
Analyse Crystal structure of the cyclophilin-like domain from brugia malayi complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C5F
- Type
- protein
- Length
- 1,483 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase 1; Cyclosporin a
- EC
- 5.2.1.8
- UniProt
- Q27450
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Peptidyl-prolyl cis-trans isomerase 1 (EC 5.2.1.8) | protein | 177 | 15% helix, 32% strand | Q27450 |
| B, D, F, H, J, L, N, P | Cyclosporin a | protein | 11 | 0% helix, 9% strand | — |
| E | Peptidyl-prolyl cis-trans isomerase 1 (EC 5.2.1.8) | protein | 174 | 13% helix, 34% strand | Q27450 |
| G, O | Peptidyl-prolyl cis-trans isomerase 1 (EC 5.2.1.8) | protein | 172 | 13% helix, 34% strand | Q27450 |
| I | Peptidyl-prolyl cis-trans isomerase 1 (EC 5.2.1.8) | protein | 173 | 13% helix, 33% strand | Q27450 |
| K, M | Peptidyl-prolyl cis-trans isomerase 1 (EC 5.2.1.8) | protein | 175 | 13% helix, 33% strand | Q27450 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.75 | 0.80 | 86 | empty |
| 2 | 231 | 0.68 | 0.85 | 34 | empty |
| 3 | 133 | 0.51 | 0.80 | 23 | empty |
| 4 | 60 | 0.47 | 0.83 | 16 | empty |
| 5 | 52 | 0.34 | 0.78 | 19 | empty |
Interfaces
23 interfaces between chains.
- C–D · 536 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 530 Ų buried · 1 hydrogen bond · protein-protein
- I–J · 516 Ų buried · 5 hydrogen bonds · protein-protein
- K–L · 512 Ų buried · 7 hydrogen bonds · protein-protein
- M–N · 506 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 modified, 8 d-amino (nonstandard, methylation, D-amino acid).
Compared structures
- 1C5F · Crystal structure of the cyclophilin-like domain from brugia malayi complexed with… · the same entry in another collection · chain N against N, 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 Q27450
- Elsewhere: RCSB PDB 1C5F · PDBe 1C5F · UniProt Q27450
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