Research workbench
Crystal structure of bacillus anthracis transpeptidase enzyme capd
Analyse Crystal structure of bacillus anthracis transpeptidase enzyme capd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G9K
- Type
- protein
- Length
- 894 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsule biosynthesis protein capd
- UniProt
- Q51693
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Capsule biosynthesis protein capd | protein | 280 | 55% helix, 13% strand | Q51693 |
| S | Capsule biosynthesis protein capd | protein | 168 | 22% helix, 33% strand | Q51693 |
| D | Capsule biosynthesis protein capd | protein | 280 | 55% helix, 13% strand | Q51693 |
| F | Capsule biosynthesis protein capd | protein | 166 | 20% helix, 34% strand | Q51693 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.74 | 0.77 | 99 | empty |
| 2 | 341 | 0.62 | 0.78 | 41 | empty |
| 3 | 94 | 0.56 | 0.85 | 21 | empty |
| 4 | 112 | 0.55 | 0.83 | 20 | empty |
| 5 | 218 | 0.54 | 0.78 | 34 | empty |
Interfaces
4 interfaces between chains.
- L–S · 4783 Ų buried · 94 hydrogen bonds · protein-protein
- D–F · 4478 Ų buried · 88 hydrogen bonds · protein-protein
- L–F · 243 Ų buried · 2 hydrogen bonds · protein-protein
- L–D · 239 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 25 modified (engineered).
Compared structures
- 3G9K · Crystal structure of Bacillus anthracis transpeptidase enzyme CapD · the same entry in another collection · chain D against D, TM-score 1.00
- Q51693 · AlphaFold monomer V2.0 prediction for capsule biosynthesis protein capd proenzyme (Q51693) · a predicted model of the same protein · chain L 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 Q51693
- Elsewhere: RCSB PDB 3G9K · PDBe 3G9K · UniProt Q51693
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