MolNFT v1 · #73816 · protein
Crystal structure of cyclophilin a in complex with voclosporin E- ISA247
3ODI: “Crystal structure of cyclophilin a in complex with voclosporin E- ISA247”. X-ray diffraction, 15 pockets (best druggability 0.74). MolNFT v1 #73816 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ODI
- Type
- protein
- Length
- 1,754 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclophilin a; Voclosporin
- EC
- 5.2.1.8
- UniProt
- A8K220
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G, M, O | Cyclophilin a (EC 5.2.1.8) | protein | 165 | 14% helix, 33% strand | A8K220 |
| B, D, F, H, J, L, N, P, R, T | Voclosporin | protein | 11 | 0% helix, 9% strand | — |
| C | Cyclophilin a (EC 5.2.1.8) | protein | 163 | 14% helix, 32% strand | A8K220 |
| I, K, Q, S | Cyclophilin a (EC 5.2.1.8) | protein | 164 | 14% helix, 32% strand | A8K220 |
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.74 | 0.78 | 81 | empty |
| 2 | 1055 | 0.73 | 0.76 | 121 | empty |
| 3 | 902 | 0.72 | 0.77 | 94 | empty |
| 4 | 832 | 0.70 | 0.76 | 103 | empty |
| 5 | 621 | 0.69 | 0.78 | 65 | empty |
Interfaces
55 interfaces between chains.
- A–B · 540 Ų buried · 8 hydrogen bonds · protein-protein
- M–N · 537 Ų buried · 7 hydrogen bonds · protein-protein
- Q–R · 536 Ų buried · 8 hydrogen bonds · protein-protein
- K–L · 527 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 519 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 80 modified, 10 d-amino (nonstandard, methylation, D-amino acid).
Compared structures
- 3ODI · Crystal structure of cyclophilin A in complex with Voclosporin E-ISA247 · 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 A8K220
- Elsewhere: RCSB PDB 3ODI · PDBe 3ODI · UniProt A8K220
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