Research workbench
Crystal structure of D-threonine aldolase from alcaligenes xylosoxidans
Analyse Crystal structure of D-threonine aldolase from alcaligenes xylosoxidans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V15
- Type
- protein
- Length
- 745 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-threonine aldolase
- EC
- 4.1.2.42
- Ligands
- PLP, MN, NA
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-threonine aldolase (EC 4.1.2.42) | protein | 373 | 33% helix, 25% strand | — |
| B | D-threonine aldolase (EC 4.1.2.42) | protein | 372 | 33% helix, 24% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.68 | 0.85 | 32 | PLP, MN |
| 2 | 251 | 0.68 | 0.84 | 35 | PLP, MN |
| 3 | 167 | 0.57 | 0.81 | 23 | empty |
| 4 | 177 | 0.55 | 0.80 | 23 | empty |
| 5 | 122 | 0.43 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2790 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 4V15 · Crystal structure of D-threonine aldolase from Alcaligenes xylosoxidans · 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
- Elsewhere: RCSB PDB 4V15 · PDBe 4V15
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