MolNFT v1 · #60965 · protein
Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved in oxygen detoxification (1591455) from methanococcus jannaschii at 1.75 a resolution
3D7I: “Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved in oxygen…”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.53). MolNFT v1 #60965 on GenesisL1: 3D structure, binding sites…
- PDB
- 3D7I
- Type
- protein
- Length
- 291 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxymuconolactone decarboxylase family protein
- UniProt
- Q58152
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxymuconolactone decarboxylase family protein | protein | 97 | 81% helix, 0% strand | Q58152 |
| B | Carboxymuconolactone decarboxylase family protein | protein | 98 | 81% helix, 0% strand | Q58152 |
| C | Carboxymuconolactone decarboxylase family protein | protein | 96 | 80% helix, 0% strand | Q58152 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.53 | 0.74 | 33 | empty |
| 2 | 97 | 0.37 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1412 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 639 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 392 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3D7I · Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58152 · AlphaFold monomer V2.0 prediction for uncharacterized protein MJ0742 (Q58152) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q58152
- Elsewhere: RCSB PDB 3D7I · PDBe 3D7I · UniProt Q58152
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