MolNFT v1 · #21262 · protein
Crystal structure of a sod-like protein from bacillus subtilis
1S4I · Superoxide dismutase-like protein yojm: “Crystal structure of a sod-like protein from bacillus subtilis”. X-ray diffraction, 2 ligands (ZN, CL), 4 pockets (best druggability 0.41). MolNFT v1 #21262 on GenesisL1: 3D structure…
- PDB
- 1S4I
- Type
- protein
- Length
- 605 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase-like protein yojm
- EC
- 1.15.1.1
- UniProt
- O31851
- Ligands
- ZN, CL
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Superoxide dismutase-like protein yojm (EC 1.15.1.1) | protein | 152 | 0% helix, 40% strand | O31851 |
| A, C, D | Superoxide dismutase-like protein yojm (EC 1.15.1.1) | protein | 151 | 0% helix, 38% strand | O31851 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains B, D, A, C
- CL · Chloride ion · ion · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.41 | 0.76 | 20 | empty |
| 2 | 147 | 0.41 | 0.74 | 25 | empty |
| 3 | 156 | 0.40 | 0.73 | 22 | empty |
| 4 | 96 | 0.39 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–A · 412 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 404 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 396 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1S4I · Crystal structure of a SOD-like protein from Bacillus subtilis · the same entry in another collection · chain B against B, TM-score 1.00
- O31851 · AlphaFold monomer V2.0 prediction for superoxide dismutase-like protein yojm (O31851) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O31851
- Elsewhere: RCSB PDB 1S4I · PDBe 1S4I · UniProt O31851
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