Research workbench
Crystal structure of D-ALANINE:D-alanine ligase with ADP from thermus thermophius HB8
Analyse Crystal structure of D-ALANINE:D-alanine ligase with ADP from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZDG
- Type
- protein
- Length
- 1,228 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
- Pockets
- 13 · best druggability 0.82
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 | 302 | 34% helix, 25% 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 | 319 | 34% helix, 25% strand | Q5SHZ3 |
| D | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 304 | 32% helix, 24% strand | Q5SHZ3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains C, D
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 | 1066 | 0.82 | 0.83 | 84 | empty |
| 2 | 426 | 0.79 | 0.87 | 64 | ADP, MG |
| 3 | 402 | 0.68 | 0.81 | 36 | empty |
| 4 | 383 | 0.68 | 0.81 | 36 | empty |
| 5 | 485 | 0.67 | 0.79 | 48 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1506 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1399 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 439 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 297 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2ZDG · Crystal structure of D-Alanine:D-Alanine Ligase with ADP from Thermus thermophius HB8 · 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 A 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 2ZDG · PDBe 2ZDG · UniProt Q5SHZ3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.