Research workbench
The X-ray structure of L,D-transpeptidase ldta from vibrio cholerae
Analyse The X-ray structure of L,D-transpeptidase ldta from vibrio cholerae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AJ9
- Type
- protein
- Length
- 974 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L,D-transpeptidase ycbb
- UniProt
- A0A655UKB5
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase ycbb | protein | 492 | 39% helix, 17% strand | A0A655UKB5 |
| B | L,D-transpeptidase ycbb | protein | 482 | 39% helix, 17% strand | A0A655UKB5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.70 | 0.84 | 31 | empty |
| 2 | 455 | 0.68 | 0.79 | 51 | empty |
| 3 | 265 | 0.57 | 0.78 | 38 | empty |
| 4 | 286 | 0.55 | 0.76 | 33 | empty |
| 5 | 193 | 0.54 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 190 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 7AJ9 · The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae · 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 A0A655UKB5
- Elsewhere: RCSB PDB 7AJ9 · PDBe 7AJ9 · UniProt A0A655UKB5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.