Research workbench
Crystal structure of petrobactin biosynthesis protein asbb from bacillus anthracis str. sterne
Analyse Crystal structure of petrobactin biosynthesis protein asbb from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TO3
- Type
- protein
- Length
- 1,188 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Petrobactin biosynthesis protein asbb
- UniProt
- Q81RQ8
- Ligands
- ATP, MG, CL
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Petrobactin biosynthesis protein asbb | protein | 593 | 47% helix, 21% strand | Q81RQ8 |
| B | Petrobactin biosynthesis protein asbb | protein | 595 | 45% helix, 21% strand | Q81RQ8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.80 | 0.82 | 91 | ATP, MG |
| 2 | 879 | 0.77 | 0.80 | 72 | empty |
| 3 | 926 | 0.73 | 0.77 | 88 | empty |
| 4 | 499 | 0.69 | 0.80 | 43 | empty |
| 5 | 227 | 0.59 | 0.80 | 37 | EDO |
Interfaces
1 interface between chains.
- A–B · 1966 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 3TO3 · Crystal Structure of Petrobactin Biosynthesis Protein AsbB from Bacillus anthracis str.… · the same entry in another collection · chain A against A, TM-score 1.00
- Q81RQ8 · AlphaFold monomer V2.0 prediction for citryl- SPERMIDINE/3,4-dihydroxybenzoyl-citryl-SPERM… · a predicted model of the same protein · chain B 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 Q81RQ8
- Elsewhere: RCSB PDB 3TO3 · PDBe 3TO3 · UniProt Q81RQ8
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