MolNFT v1 · #83376 · protein
Crystal structure of aeromonas jandaei L-allo-threonine aldolase
3WGB: “Crystal structure of aeromonas jandaei L-allo-threonine aldolase”. X-ray diffraction, 2 ligands (PLG, GLY), 12 pockets (best druggability 0.69). MolNFT v1 #83376 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3WGB
- Type
- protein
- Length
- 1,294 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-allo-threonine aldolase
- EC
- 4.1.2.49
- UniProt
- O07051
- Ligands
- PLG, GLY
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-allo-threonine aldolase (EC 4.1.2.49) | protein | 324 | 44% helix, 16% strand | O07051 |
| B | L-allo-threonine aldolase (EC 4.1.2.49) | protein | 319 | 45% helix, 17% strand | O07051 |
| C | L-allo-threonine aldolase (EC 4.1.2.49) | protein | 327 | 45% helix, 17% strand | O07051 |
| D | L-allo-threonine aldolase (EC 4.1.2.49) | protein | 324 | 42% helix, 17% strand | O07051 |
Ligands and binding sites
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 4 copies · chains A, B, C, D
- GLY · Glycine · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.69 | 0.84 | 42 | PLG |
| 2 | 341 | 0.68 | 0.82 | 43 | PLG |
| 3 | 278 | 0.67 | 0.83 | 36 | PLG |
| 4 | 299 | 0.66 | 0.82 | 40 | PLG |
| 5 | 318 | 0.61 | 0.79 | 38 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1895 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1874 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 857 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 809 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 765 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3WGB · Crystal structure of aeromonas jandaei L-allo-threonine aldolase · the same entry in another collection · chain D against D, TM-score 1.00
- O07051 · AlphaFold monomer V2.0 prediction for L-allo-threonine aldolase (O07051) · a predicted model of the same protein · 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 O07051
- Elsewhere: RCSB PDB 3WGB · PDBe 3WGB · UniProt O07051
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