Research workbench
Crystal structure of cyclophilin AQUACYP300 from hirschia baltica
Analyse Crystal structure of cyclophilin AQUACYP300 from hirschia baltica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EX1
- Type
- protein
- Length
- 1,630 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase cyclophilin type
- UniProt
- C6XII3
- Ligands
- MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidyl-prolyl cis-trans isomerase cyclophilin type | protein | 271 | 17% helix, 28% strand | C6XII3 |
| C, D | Peptidyl-prolyl cis-trans isomerase cyclophilin type | protein | 272 | 18% helix, 29% strand | C6XII3 |
| E, F | Peptidyl-prolyl cis-trans isomerase cyclophilin type | protein | 272 | 18% helix, 28% strand | C6XII3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains B, D, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.78 | 0.81 | 95 | MG |
| 2 | 837 | 0.77 | 0.80 | 67 | empty |
| 3 | 801 | 0.75 | 0.79 | 75 | empty |
| 4 | 631 | 0.74 | 0.81 | 55 | empty |
| 5 | 77 | 0.68 | 0.94 | 22 | MG |
Interfaces
7 interfaces between chains.
- B–D · 1834 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 1793 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 571 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 552 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 224 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5EX1 · Crystal structure of cyclophilin AquaCyp300 from Hirschia baltica · 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 C6XII3
- Elsewhere: RCSB PDB 5EX1 · PDBe 5EX1 · UniProt C6XII3
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