MolNFT v1 · #165634 · protein
Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphorylated D-cycloserine, MG2+ and K+
6U1I · D-alanine--D-alanine ligase: “Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphorylated D-cycloserine, MG2+ and K+”. X-ray diffraction, 4 ligands (ADP, DS0, MG), 13 pockets (best druggability 0.78). MolNFT…
- PDB
- 6U1I
- Type
- protein
- Length
- 1,234 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, DS0, MG, K
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 300 | 34% helix, 24% strand | Q5SHZ3 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 303 | 31% helix, 23% strand | Q5SHZ3 |
| C | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 324 | 33% helix, 24% strand | Q5SHZ3 |
| D | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 307 | 34% helix, 24% strand | Q5SHZ3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
- DS0 · [(4R)-4-azanyl-4,5-dihydro-1,2-oxazol-3-yl] dihydrogen phosphate · ligand · chains C
- MG · Magnesium ion · metal · 2 copies · chains C
- K · Potassium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.78 | 0.81 | 70 | empty |
| 2 | 365 | 0.77 | 0.87 | 56 | MG, ADP, DS0 |
| 3 | 609 | 0.76 | 0.83 | 64 | empty |
| 4 | 525 | 0.75 | 0.83 | 49 | empty |
| 5 | 502 | 0.74 | 0.82 | 47 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1585 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1441 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 291 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 142 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 31 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6U1I · Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphorylated… · 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 B against A, TM-score 0.98
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 6U1I · PDBe 6U1I · UniProt Q5SHZ3
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