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The X-ray structure of L,D-transpeptidase ldta from vibrio cholerae in complex with meropenem
Analyse The X-ray structure of L,D-transpeptidase ldta from vibrio cholerae in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AJX
- Type
- protein
- Length
- 490 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L,D-transpeptidase ycbb
- UniProt
- A0A655UKB5
- Ligands
- MXR
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase ycbb | protein | 490 | 40% helix, 17% strand | A0A655UKB5 |
Ligands and binding sites
- MXR · (2S,3R,4S)-4-{[(3S,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.68 | 0.83 | 26 | empty |
| 2 | 266 | 0.53 | 0.75 | 35 | MXR |
| 3 | 180 | 0.45 | 0.75 | 26 | empty |
| 4 | 100 | 0.45 | 0.79 | 16 | empty |
| 5 | 72 | 0.39 | 0.78 | 21 | EDO |
Modifications
Observed in the structure: 11 modified, 1 covalent (engineered, covalent ligand).
Compared structures
- 7AJX · The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with… · 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 7AJX · PDBe 7AJX · UniProt A0A655UKB5
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