Research workbench
Crystal structure of the L. plantarum D-alanine ligase dlta
Analyse Crystal structure of the L. plantarum D-alanine ligase dlta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R27
- Type
- protein
- Length
- 792 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--D-alanyl carrier protein ligase
- EC
- 6.2.1.54
- UniProt
- A0A151G8K4
- Ligands
- DAL, AMP
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanyl carrier protein ligase (EC 6.2.1.54) | protein | 394 | 32% helix, 26% strand | A0A151G8K4 |
| B | D-alanine--D-alanyl carrier protein ligase (EC 6.2.1.54) | protein | 398 | 32% helix, 25% strand | A0A151G8K4 |
Ligands and binding sites
- DAL · D-alanine · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.76 | 0.81 | 73 | empty |
| 2 | 356 | 0.64 | 0.79 | 47 | DAL, AMP |
| 3 | 390 | 0.61 | 0.77 | 53 | DAL, AMP |
Interfaces
1 interface between chains.
- A–B · 281 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7R27 · Crystal structure of the L. plantarum D-alanine ligase DltA · 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 A0A151G8K4
- Elsewhere: RCSB PDB 7R27 · PDBe 7R27 · UniProt A0A151G8K4
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