MolNFT v1 · #117359 · protein
Quasi-racemic snakin-1 in P1 after radiation damage
5E5T: “Quasi-racemic snakin-1 in P1 after radiation damage”. X-ray diffraction, 1 pocket (best druggability 0.72). MolNFT v1 #117359 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5E5T
- 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
- 1 · best druggability 0.72
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 · 4 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.72 | 0.88 | 32 | EDO |
Interfaces
4 interfaces between chains.
- B–D · 516 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 417 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 355 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 41 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
- 5E5T · Quasi-racemic snakin-1 in P1 after 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 5E5T · PDBe 5E5T · UniProt B6E1W5
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