Research workbench
Crystal structure of an apo form cyclase FILC1 from fischerella sp. tau
Analyse Crystal structure of an apo form cyclase FILC1 from fischerella sp. tau in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YVP
- Type
- protein
- Length
- 794 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclase a
- UniProt
- A0A1P8VSI6
- Ligands
- CA
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclase a | protein | 199 | 0% helix, 43% strand | A0A1P8VSI6 |
| C, D | Cyclase a | protein | 198 | 0% helix, 43% strand | A0A1P8VSI6 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.86 | 0.92 | 61 | PG4 |
| 2 | 119 | 0.67 | 0.90 | 25 | empty |
| 3 | 96 | 0.64 | 0.90 | 23 | empty |
| 4 | 208 | 0.63 | 0.82 | 27 | empty |
| 5 | 98 | 0.62 | 0.89 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 952 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 884 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 877 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5YVP · Crystal structure of an apo form cyclase Filc1 from Fischerella sp. TAU · 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 A0A1P8VSI6
- Elsewhere: RCSB PDB 5YVP · PDBe 5YVP · UniProt A0A1P8VSI6
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