Research workbench
Crystal structure of a putative L-allo-threonine aldolase (LMO0305) from listeria monocytogenes egd-E at 1.80 a resolution
Analyse Crystal structure of a putative L-allo-threonine aldolase (LMO0305) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PJ0
- Type
- protein
- Length
- 1,430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LMO0305 protein
- UniProt
- Q8YA56
- Ligands
- NA, CL
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | LMO0305 protein | protein | 359 | 47% helix, 18% strand | Q8YA56 |
| C | LMO0305 protein | protein | 353 | 46% helix, 19% strand | Q8YA56 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 6 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.70 | 0.78 | 52 | empty |
| 2 | 639 | 0.69 | 0.77 | 60 | empty |
| 3 | 612 | 0.68 | 0.77 | 55 | MRD |
| 4 | 603 | 0.68 | 0.78 | 59 | empty |
| 5 | 566 | 0.67 | 0.77 | 55 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2181 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2181 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 345 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified (engineered, cofactor).
Compared structures
- 3PJ0 · Crystal structure of a putative L-allo-threonine aldolase (lmo0305) from Listeria… · 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 Q8YA56
- Elsewhere: RCSB PDB 3PJ0 · PDBe 3PJ0 · UniProt Q8YA56
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