MolNFT v1 · #165632 · protein
Thermus thermophilus D-alanine-D-alanine ligase in complex with ATP, D-alanine-D-alanine, MG2+ and cs+
6U1G · D-alanine--D-alanine ligase: “Thermus thermophilus D-alanine-D-alanine ligase in complex with ATP, D-alanine-D-alanine, MG2+ and cs+”. X-ray diffraction, 3 ligands (ATP, CS, MG), 6 pockets (best druggability 0.75). MolNFT v1 #165632…
- PDB
- 6U1G
- Type
- protein
- Length
- 655 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
- Q5SHZ3
- Ligands
- ATP, CS, MG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 328 | 33% helix, 23% strand | Q5SHZ3 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 327 | 33% helix, 23% strand | Q5SHZ3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- CS · Cesium ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.75 | 0.80 | 52 | empty |
| 2 | 152 | 0.75 | 0.92 | 33 | MG, ATP |
| 3 | 463 | 0.73 | 0.82 | 38 | empty |
| 4 | 176 | 0.71 | 0.89 | 34 | MG, ATP |
| 5 | 92 | 0.45 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1325 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 d-amino (D-amino acid).
Compared structures
- 6U1G · Thermus thermophilus D-alanine-D-alanine ligase in complex with ATP, D-alanine-D-alanine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SHZ3 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q5SHZ3) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q5SHZ3
- Elsewhere: RCSB PDB 6U1G · PDBe 6U1G · UniProt Q5SHZ3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.