UniProt Q5SHZ3
D-alanine--D-alanine ligase (Q5SHZ3)
D-alanine--D-alanine ligase (UniProt Q5SHZ3), EC 6.3.2.4: 23 experimental structures and 1 predicted model on GenesisL1, 9 ligands bound, 6 pockets. Binding sites, druggability and experiment against prediction (TM-score) in GL1X.
- UniProt
- Q5SHZ3
- Protein
- D-alanine--D-alanine ligase
- EC
- 6.3.2.4
- Experimental structures
- 23
- Predicted models
- 1
- Ligands
- 9
- Pockets
- 6 · 1 record with a druggable one
Structures
24 records of Q5SHZ3 in the MolNFT archive: 23 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 2YZG | Crystal structure of D-ALA:D-ALA Ligase from Thermus thermophilus HB8 | x-ray diffraction | A, B, C | — | — |
| 2YZG | Crystal structure of D-ALA:D-ala ligase from thermus thermophilus HB8 | x-ray diffraction | A, B, C | — | — |
| 2YZM | Structure of D-Alanine:D-Alanine Ligase with substrate from Thermus thermophilus HB8 | x-ray diffraction | A, B, C | — | — |
| 2YZM | Structure of D-ALANINE:D-alanine ligase with substrate from thermus thermophilus HB8 | x-ray diffraction | A, B, C | — | — |
| 2YZN | Crystal structure of D-alanine:D-Alanine Ligase with AMPPNP from Thermus thermophilus HB8. | x-ray diffraction | A, B, C | — | — |
| 2YZN | Crystal structure of D-ALANINE:D-alanine ligase with amppnp from thermus thermophilus HB8. | x-ray diffraction | A, B, C | — | — |
| 2ZDG | Crystal structure of D-Alanine:D-Alanine Ligase with ADP from Thermus thermophius HB8 | x-ray diffraction | A, B, C, D | — | — |
| 2ZDG | Crystal structure of D-ALANINE:D-alanine ligase with ADP from thermus thermophius HB8 | x-ray diffraction | A, B, C, D | — | — |
| 2ZDH | Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine from Thermus thermophius HB8 | x-ray diffraction | A, B, C, D | — | — |
| 2ZDH | Crystal structure of D-ALANINE:D-alanine ligase with ADP and D-alanine from thermus thermophius HB8 | x-ray diffraction | A, B, C, D | — | — |
| 2ZDQ | Crystal structure of D-Alanine:D-Alanine Ligase with ATP and D-Alanine:D-Alanine from Thermus… | x-ray diffraction | A, B | — | — |
| 2ZDQ | Crystal structure of D-ALANINE:D-alanine ligase with ATP and D-ALANINE:D-alanine from thermus… | x-ray diffraction | A, B | — | — |
| 6U1C | Apo form of thermus thermophilus D-alanine-D-alanine ligase | x-ray diffraction | A, B, C, D | — | — |
| 6U1D | Thermus thermophilus D-alanine-D-alanine ligase in complex with ATP, D-alanine-D-alanine, MG2+ and… | x-ray diffraction | A, B | MG, RB, ATP | — |
| 6U1E | Thermus thermophilus D-alanine-D-alanine ligase in complex with ATP, D-alanine-D-alanine, Mg2+ and… | x-ray diffraction | A, B | MG, RB, ATP | — |
| 6U1E | Thermus thermophilus D-alanine-D-alanine ligase in complex with ATP, D-alanine-D-alanine, MG2+ and… | x-ray diffraction | A, B | MG, RB, ATP | — |
| 6U1F | Thermus thermophilus D-alanine-D-alanine ligase in complex with ATP, D-alanine-D-alanine, Mg2+ and… | x-ray diffraction | A, B | MG, CS, ATP | 6 (best 0.77) |
| 6U1F | Thermus thermophilus D-alanine-D-alanine ligase in complex with ATP, D-alanine-D-alanine, MG2+ and… | x-ray diffraction | A, B | MG, CS, ATP | — |
| 6U1G | Thermus thermophilus D-alanine-D-alanine ligase in complex with ATP, D-alanine-D-alanine, MG2+ and… | x-ray diffraction | A, B | CS, MG, ATP | — |
| 6U1H | Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphate, MG2+ and K+ | x-ray diffraction | A, B, C, D | MG, PO4, K, ADP | — |
| 6U1I | Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphorylated D-cycloserine… | x-ray diffraction | A, B, C, D | ADP, MG, K, DS0 | — |
| 6U1J | Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphate, D-ala-D-ala, MG2+… | x-ray diffraction | A, B, C, D | MG, PO4, K, ADP | — |
| 6U1K | Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, carbonate… | x-ray diffraction | A, B, C, D | MG, K, ADP, CO3 | — |
| Q5SHZ3 | AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q5SHZ3) | predicted | A | — | — |
Ligands
- MG · Magnesium ion · in 10 records
- ATP · Adenosine-5'-triphosphate · in 6 records
- ADP · Adenosine-5'-diphosphate · in 4 records
- K · Potassium ion · in 4 records
- CS · Cesium ion · in 3 records
- RB · Rubidium ion · in 3 records
- PO4 · Phosphate ion · in 2 records
- CO3 · Carbonate ion · in 1 record
- DS0 · [(4R)-4-azanyl-4,5-dihydro-1,2-oxazol-3-yl] dihydrogen phosphate · in 1 record
Experiment against prediction
- 6U1C chain B against the predicted model Q5SHZ3: TM-score 0.99, RMSD 0.67 Å
- 2ZDG chain A against the predicted model Q5SHZ3: TM-score 0.99, RMSD 0.67 Å
- 2ZDG chain A against the predicted model Q5SHZ3: TM-score 0.99, RMSD 0.67 Å
- 2ZDG chain B against the predicted model Q5SHZ3: TM-score 0.99, RMSD 0.74 Å
- 2ZDG chain B against the predicted model Q5SHZ3: TM-score 0.99, RMSD 0.74 Å
- 2ZDH chain D against the predicted model Q5SHZ3: TM-score 0.99, RMSD 0.70 Å
- 2ZDH chain D against the predicted model Q5SHZ3: TM-score 0.99, RMSD 0.70 Å
- 6U1C chain D against the predicted model Q5SHZ3: TM-score 0.99, RMSD 0.69 Å
- 2ZDG chain D against the predicted model Q5SHZ3: TM-score 0.99, RMSD 0.93 Å
- 2ZDG chain D against the predicted model Q5SHZ3: TM-score 0.99, RMSD 0.93 Å
Elsewhere
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