MolNFT v1 · #49134 · protein
Crystal structure of putative carboxymuconolactone decarboxylase (YP_555818.1) from burkholderia xenovorans LB400 at 1.65 a resolution
2QEU: “Crystal structure of putative carboxymuconolactone decarboxylase (YP_555818.1) from burkholderia xenovorans…”. X-ray diffraction, 3 pockets (best druggability 0.65). MolNFT v1 #49134 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2QEU
- Type
- protein
- Length
- 397 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative carboxymuconolactone decarboxylase
- UniProt
- Q13HH1
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative carboxymuconolactone decarboxylase | protein | 132 | 80% helix, 0% strand | Q13HH1 |
| B | Putative carboxymuconolactone decarboxylase | protein | 133 | 77% helix, 0% strand | Q13HH1 |
Ligands and binding sites
- ACT · Acetate ion · additive · 7 copies · chains A, B, C
- GOL · Glycerol · additive · 4 copies · chains A, C, B
- CIT · Citric acid · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.65 | 0.81 | 31 | CIT |
| 2 | 412 | 0.64 | 0.78 | 50 | ACT, CIT, GOL |
| 3 | 271 | 0.63 | 0.80 | 32 | ACT, CIT |
Interfaces
3 interfaces between chains.
- A–B · 632 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 627 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 623 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 2QEU · Crystal structure of putative carboxymuconolactone decarboxylase (YP_555818.1) 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 Q13HH1
- Elsewhere: RCSB PDB 2QEU · PDBe 2QEU · UniProt Q13HH1
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