Research workbench
Quasi-racemic snakin-1 in P1 before radiation damage
Analyse Quasi-racemic snakin-1 in P1 before radiation damage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E5Y
- Type
- protein
- Length
- 251 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Snakin-1; D- snakin-1
- UniProt
- B6E1W5
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Snakin-1 | protein | 63 | 51% helix, 3% strand | B6E1W5 |
| B, D | D- snakin-1 | protein | 63 | 51% helix, 3% strand | — |
| C | Snakin-1 | protein | 62 | 52% helix, 3% strand | B6E1W5 |
Ligands and binding sites
- FMT · Formic acid · additive · 6 copies · chains B, D, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.78 | 0.96 | 24 | EDO |
| 2 | 143 | 0.38 | 0.73 | 26 | EDO |
| 3 | 80 | 0.34 | 0.75 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–C · 514 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 494 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 357 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 114 d-amino, 24 disulfide, 2 modified (D-amino acid, disulfide, nonstandard).
Compared structures
- 5E5Y · Quasi-racemic snakin-1 in P1 before radiation damage · 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 B6E1W5
- Elsewhere: RCSB PDB 5E5Y · PDBe 5E5Y · UniProt B6E1W5
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