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The crystal structure of D-alanyl-alanine synthetase a from vibrio cholerae O1 biovar eltor str. N16961
Analyse The crystal structure of D-alanyl-alanine synthetase a from vibrio cholerae O1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DGI
- Type
- protein
- Length
- 661 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
- Q9KM17
- Ligands
- MG
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 333 | 34% helix, 28% strand | Q9KM17 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 328 | 33% helix, 27% strand | Q9KM17 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.68 | 0.79 | 80 | GOL |
| 2 | 558 | 0.66 | 0.77 | 51 | ACT, MG |
| 3 | 464 | 0.65 | 0.78 | 52 | GOL, MG |
| 4 | 61 | 0.36 | 0.78 | 15 | empty |
| 5 | 56 | 0.29 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1654 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 6DGI · The crystal structure of D-alanyl-alanine synthetase A from Vibrio cholerae O1 biovar… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KM17 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q9KM17) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9KM17
- Elsewhere: RCSB PDB 6DGI · PDBe 6DGI · UniProt Q9KM17
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