MolNFT v1 · #165635 · protein
Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphate, D-ala-D-ala, MG2+ and K+
6U1J · D-alanine--D-alanine ligase: “Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphate, D-ala-D-ala, MG2+ and K+”. X-ray diffraction, 4 ligands (ADP, MG, K), 14 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 6U1J
- Type
- protein
- Length
- 1,260 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, PO4
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 326 | 34% helix, 23% strand | Q5SHZ3 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 304 | 34% helix, 25% strand | Q5SHZ3 |
| D | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 304 | 34% helix, 23% strand | Q5SHZ3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 4 copies · chains A, C
- K · Potassium ion · metal · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.83 | 0.84 | 97 | empty |
| 2 | 541 | 0.75 | 0.82 | 50 | empty |
| 3 | 534 | 0.74 | 0.82 | 50 | empty |
| 4 | 151 | 0.73 | 0.91 | 33 | MG, PO4, ADP |
| 5 | 152 | 0.73 | 0.91 | 40 | MG, PO4, ADP |
Interfaces
4 interfaces between chains.
- C–D · 1504 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1435 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 205 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 71 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 d-amino (D-amino acid).
Compared structures
- 6U1J · Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphate… · 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 6U1J · PDBe 6U1J · UniProt Q5SHZ3
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