Research workbench
Structure of D-ALANINE:D-alanine ligase with substrate from thermus thermophilus HB8
Analyse Structure of D-ALANINE:D-alanine ligase with substrate from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YZM
- Type
- protein
- Length
- 939 residues
- Chains
- 3
- 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
- DAL
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 319 | 32% helix, 28% 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 | 308 | 31% helix, 26% strand | Q5SHZ3 |
Ligands and binding sites
- DAL · D-alanine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.74 | 0.78 | 81 | DAL |
| 2 | 385 | 0.68 | 0.81 | 31 | empty |
| 3 | 438 | 0.66 | 0.78 | 57 | DAL |
| 4 | 483 | 0.65 | 0.77 | 56 | DAL |
| 5 | 225 | 0.48 | 0.74 | 30 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1445 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 153 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2YZM · Structure of D-Alanine:D-Alanine Ligase with substrate from Thermus thermophilus HB8 · the same entry in another collection · chain B against B, 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 C 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 2YZM · PDBe 2YZM · UniProt Q5SHZ3
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