Research workbench
Crystal structure of D-alanine-D-alanine ligase from aeromonas hydrophila
Analyse Crystal structure of D-alanine-D-alanine ligase from aeromonas hydrophila in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LL9
- Type
- protein
- Length
- 563 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--D-alanine ligase
- EC
- 6.3.2.4
- UniProt
- A0A3S8RJF8
- Ligands
- DAL
- Pockets
- 11 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 297 | 28% helix, 23% strand | A0A3S8RJF8 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 266 | 28% helix, 21% strand | A0A3S8RJF8 |
Ligands and binding sites
- DAL · D-alanine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.60 | 0.79 | 33 | empty |
| 2 | 234 | 0.59 | 0.80 | 43 | empty |
| 3 | 212 | 0.50 | 0.76 | 29 | empty |
| 4 | 160 | 0.49 | 0.77 | 32 | empty |
| 5 | 120 | 0.42 | 0.77 | 28 | DAL |
Interfaces
1 interface between chains.
- A–B · 1386 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6LL9 · Crystal structure of D-alanine-D-alanine ligase from Aeromonas hydrophila · 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 A0A3S8RJF8
- Elsewhere: RCSB PDB 6LL9 · PDBe 6LL9 · UniProt A0A3S8RJF8
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