MolNFT v1 · #141083 · protein
Crystal structure of an apo form cyclase FILC1 from fischerella sp. tau
5YVP · Cyclase a: “Crystal structure of an apo form cyclase FILC1 from fischerella sp. tau”. X-ray diffraction, 1 ligand (CA), 11 pockets (best druggability 0.86). MolNFT v1 #141083 on GenesisL1: 3D structure, binding sites and pockets in…
- 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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