Research workbench
The X-ray structure of L,D-transpeptidase ldta from vibrio cholerae in complex with nag-NAM(TETRAPEPTIDE)
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
- 7AJZ
- Type
- protein
- Length
- 977 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L,D-transpeptidase ycbb; Nag-NAM(TETRAPEPTIDE)
- UniProt
- A0A655UKB5
- Ligands
- AMV, API, DAL
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase ycbb | protein | 484 | 40% helix, 18% strand | A0A655UKB5 |
| B | L,D-transpeptidase ycbb | protein | 491 | 40% helix, 17% strand | A0A655UKB5 |
| C | Nag-NAM(TETRAPEPTIDE) | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- AMV · methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside · ligand · chains A, C
- API · 2,6-diaminopimelic acid · ligand · chains A, C
- DAL · D-alanine · ligand · chains C
- 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
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 | 898 | 0.80 | 0.82 | 92 | empty |
| 2 | 490 | 0.71 | 0.80 | 53 | empty |
| 3 | 229 | 0.69 | 0.85 | 27 | EDO |
| 4 | 134 | 0.56 | 0.83 | 21 | empty |
| 5 | 240 | 0.54 | 0.77 | 31 | empty |
Interfaces
2 interfaces between chains.
- A–B · 540 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 148 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 d-amino (covalent ligand, D-amino acid).
Compared structures
- 7AJZ · The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with… · the same entry in another collection · chain B against B, 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 7AJZ · PDBe 7AJZ · UniProt A0A655UKB5
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