MolNFT v1 · #56381 · protein
Crystal structure of D-ALANINE:D-alanine ligase with ADP and D-alanine from thermus thermophius HB8
2ZDH · D-alanine--D-alanine ligase: “Crystal structure of D-ALANINE:D-alanine ligase with ADP and D-alanine from thermus thermophius HB8”. X-ray diffraction, 3 ligands (ADP, DAL, MG), 18 pockets (best druggability 0.79). MolNFT v1 #56381…
- PDB
- 2ZDH
- Type
- protein
- Length
- 1,266 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, DAL, MG
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 319 | 34% helix, 24% strand | Q5SHZ3 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 312 | 32% helix, 25% strand | Q5SHZ3 |
| C | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 316 | 31% helix, 26% strand | Q5SHZ3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- DAL · D-alanine · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.79 | 0.88 | 63 | ADP, DAL, MG |
| 2 | 347 | 0.79 | 0.89 | 55 | ADP, DAL, MG |
| 3 | 593 | 0.74 | 0.81 | 59 | ADP, MG |
| 4 | 644 | 0.73 | 0.80 | 65 | ADP, MG |
| 5 | 453 | 0.71 | 0.81 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1417 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1397 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 1010 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2ZDH · Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine from Thermus… · 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 0.99
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 2ZDH · PDBe 2ZDH · UniProt Q5SHZ3
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