MolNFT v1 · #172951 · protein
The X-ray structure of L,D-transpeptidase ldta from vibrio cholerae in complex with the cross-linking reaction intermediate
7AJO · L,D-transpeptidase ycbb: “The X-ray structure of L,D-transpeptidase ldta from vibrio cholerae in complex with the cross-linking…”. X-ray diffraction, 1 ligand (S2K), 5 pockets (best druggability 0.65). MolNFT v1 #172951 on…
- PDB
- 7AJO
- Type
- protein
- Length
- 492 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L,D-transpeptidase ycbb
- UniProt
- A0A655UKB5
- Ligands
- S2K
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase ycbb | protein | 492 | 42% helix, 18% strand | A0A655UKB5 |
Ligands and binding sites
- S2K · (2~{S},6~{S})-2-azanyl-6-[[(4~{R})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]heptanedioic 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.65 | 0.80 | 24 | empty |
| 2 | 280 | 0.55 | 0.76 | 35 | S2K |
| 3 | 118 | 0.49 | 0.80 | 26 | empty |
| 4 | 171 | 0.43 | 0.74 | 30 | empty |
| 5 | 94 | 0.39 | 0.77 | 19 | empty |
Modifications
Observed in the structure: 11 modified, 1 covalent (engineered, covalent ligand).
Compared structures
- 7AJO · The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with the… · 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 7AJO · PDBe 7AJO · UniProt A0A655UKB5
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