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Crystal structure of carboxymuconolactone decarboxylase family protein SMU.961 from streptococcus mutans
Analyse Crystal structure of carboxymuconolactone decarboxylase family protein SMU.961… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LVY
- Type
- protein
- Length
- 1,086 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxymuconolactone decarboxylase family
- UniProt
- Q8DUG8
- Ligands
- CL, SO4
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxymuconolactone decarboxylase family | protein | 184 | 67% helix, 0% strand | Q8DUG8 |
| B, C | Carboxymuconolactone decarboxylase family | protein | 183 | 67% helix, 0% strand | Q8DUG8 |
| D | Carboxymuconolactone decarboxylase family | protein | 179 | 67% helix, 0% strand | Q8DUG8 |
| E | Carboxymuconolactone decarboxylase family | protein | 174 | 69% helix, 0% strand | Q8DUG8 |
| F | Carboxymuconolactone decarboxylase family | protein | 183 | 66% helix, 0% strand | Q8DUG8 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains D
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.78 | 0.81 | 81 | empty |
| 2 | 1077 | 0.77 | 0.79 | 109 | empty |
| 3 | 351 | 0.73 | 0.84 | 30 | empty |
| 4 | 613 | 0.72 | 0.80 | 69 | empty |
| 5 | 333 | 0.71 | 0.84 | 31 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1978 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1963 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1896 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 576 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 520 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3LVY · Crystal Structure of Carboxymuconolactone Decarboxylase Family Protein SMU.961 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 Q8DUG8
- Elsewhere: RCSB PDB 3LVY · PDBe 3LVY · UniProt Q8DUG8
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