Research workbench
Crystal structure of a putative plp-dependent aminotransferase (LBUL_1103) from lactobacillus delbrueckii subsp. at 1.61 a resolution
Analyse Crystal structure of a putative plp-dependent aminotransferase (LBUL_1103) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DZZ
- Type
- protein
- Length
- 771 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative pyridoxal 5'-phosphate-dependent C-S lyase
- UniProt
- Q04A76
- Ligands
- CA, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative pyridoxal 5'-phosphate-dependent C-S lyase | protein | 386 | 44% helix, 16% strand | Q04A76 |
| B | Putative pyridoxal 5'-phosphate-dependent C-S lyase | protein | 385 | 45% helix, 16% strand | Q04A76 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.73 | 0.80 | 109 | ACT, PEG |
| 2 | 126 | 0.40 | 0.75 | 22 | empty |
| 3 | 61 | 0.37 | 0.79 | 19 | empty |
| 4 | 50 | 0.35 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2210 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered, cofactor).
Compared structures
- 3DZZ · Crystal structure of a putative plp-dependent aminotransferase (LBUL_1103) from… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q04A76
- Elsewhere: RCSB PDB 3DZZ · PDBe 3DZZ · UniProt Q04A76
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