MolNFT v1 · #21289 · protein
Crystal structure of putative isomerase from bacillus subtilis
1S5A · Hypothetical protein yese: “Crystal structure of putative isomerase from bacillus subtilis”. X-ray diffraction, 8 pockets (best druggability 0.79). MolNFT v1 #21289 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1S5A
- Type
- protein
- Length
- 564 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yese
- UniProt
- O31511
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein yese | protein | 139 | 29% helix, 38% strand | O31511 |
| B | Hypothetical protein yese | protein | 143 | 33% helix, 38% strand | O31511 |
| C | Hypothetical protein yese | protein | 143 | 29% helix, 36% strand | O31511 |
| D | Hypothetical protein yese | protein | 139 | 32% helix, 40% strand | O31511 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B, D, C
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.79 | 0.81 | 92 | GOL |
| 2 | 120 | 0.77 | 0.95 | 24 | ACT, GOL |
| 3 | 76 | 0.77 | 0.98 | 21 | ACT, GOL |
| 4 | 74 | 0.76 | 0.98 | 22 | ACT, GOL |
| 5 | 220 | 0.69 | 0.85 | 30 | ACT, GOL |
Interfaces
6 interfaces between chains.
- A–D · 963 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 958 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 871 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 297 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 120 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified (engineered).
Compared structures
- 1S5A · Crystal Structure of Putative Isomerase from Bacillus subtilis · the same entry in another collection · chain D against D, TM-score 1.00
- O31511 · AlphaFold monomer V2.0 prediction for uncharacterized protein yese (O31511) · a predicted model of the same protein · chain A 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 O31511
- Elsewhere: RCSB PDB 1S5A · PDBe 1S5A · UniProt O31511
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