MolNFT v1 · #55926 · protein
Crystal structure of D-ALA:D-ala ligase from thermus thermophilus HB8
2YZG · D-alanine--D-alanine ligase: “Crystal structure of D-ALA:D-ala ligase from thermus thermophilus HB8”. X-ray diffraction, 11 pockets (best druggability 0.71). MolNFT v1 #55926 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2YZG
- 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
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 319 | 31% helix, 28% strand | Q5SHZ3 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 311 | 31% helix, 25% strand | Q5SHZ3 |
| C | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 309 | 32% helix, 25% strand | Q5SHZ3 |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.71 | 0.80 | 44 | empty |
| 2 | 504 | 0.67 | 0.78 | 65 | empty |
| 3 | 376 | 0.66 | 0.80 | 35 | empty |
| 4 | 453 | 0.66 | 0.78 | 54 | empty |
| 5 | 272 | 0.51 | 0.74 | 37 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1409 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 135 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2YZG · Crystal structure of D-ALA:D-ALA Ligase from Thermus thermophilus HB8 · the same entry in another collection · chain A against A, 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 2YZG · PDBe 2YZG · UniProt Q5SHZ3
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