Research workbench
Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, carbonate, D-alanine-D-alanine, MG2+ and K+
Analyse Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, carbonate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U1K
- Type
- protein
- Length
- 1,297 residues
- Chains
- 4
- 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
- ADP, MG, K, CO3
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 326 | 33% helix, 24% strand | Q5SHZ3 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 324 | 34% helix, 25% strand | Q5SHZ3 |
| C | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 325 | 34% helix, 24% strand | Q5SHZ3 |
| D | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 322 | 33% helix, 25% strand | Q5SHZ3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- CO3 · Carbonate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 823 | 0.82 | 0.85 | 73 | empty |
| 2 | 139 | 0.75 | 0.94 | 33 | MG, ADP, CO3 |
| 3 | 150 | 0.74 | 0.92 | 34 | MG, ADP |
| 4 | 141 | 0.74 | 0.92 | 30 | MG, ADP |
| 5 | 312 | 0.73 | 0.86 | 40 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1529 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 1412 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 320 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 60 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 d-amino (D-amino acid).
Compared structures
- 6U1K · Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, carbonate… · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.96
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 6U1K · PDBe 6U1K · UniProt Q5SHZ3
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