Research workbench
Structure of bacillus cereus PATB1 with sulfonyl adduct
Analyse Structure of bacillus cereus PATB1 with sulfonyl adduct in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V8D
- Type
- protein
- Length
- 1,187 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacillus cereus PATB1
- UniProt
- Q73CU0
- Ligands
- SO4
- Pockets
- 18 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacillus cereus PATB1 | protein | 290 | 35% helix, 23% strand | Q73CU0 |
| B | Bacillus cereus PATB1 | protein | 298 | 34% helix, 23% strand | Q73CU0 |
| C | Bacillus cereus PATB1 | protein | 299 | 33% helix, 22% strand | Q73CU0 |
| D | Bacillus cereus PATB1 | protein | 300 | 33% helix, 22% strand | Q73CU0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.72 | 0.78 | 65 | empty |
| 2 | 710 | 0.65 | 0.74 | 68 | empty |
| 3 | 385 | 0.60 | 0.76 | 53 | empty |
| 4 | 340 | 0.58 | 0.76 | 37 | SO4 |
| 5 | 113 | 0.55 | 0.84 | 24 | SO4 |
Interfaces
5 interfaces between chains.
- A–C · 602 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 567 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 485 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 109 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 5V8D · Structure of Bacillus cereus PatB1 with sulfonyl adduct · 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 Q73CU0
- Elsewhere: RCSB PDB 5V8D · PDBe 5V8D · UniProt Q73CU0
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