MolNFT v1 · #25263 · protein
Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response (TM1620) from thermotoga maritima at 1.56 a resolution
1VKE: “Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved in antioxidative…”. X-ray diffraction, 1 ligand (UNL), 10 pockets (best druggability 0.82). MolNFT v1 #25263 on GenesisL1: 3D structure…
- PDB
- 1VKE
- Type
- protein
- Length
- 635 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxymuconolactone decarboxylase family protein
- EC
- 4.1.-.-
- UniProt
- Q9X1V5
- Ligands
- UNL
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxymuconolactone decarboxylase family protein (EC 4.1.-.-) | protein | 117 | 75% helix, 0% strand | Q9X1V5 |
| B | Carboxymuconolactone decarboxylase family protein (EC 4.1.-.-) | protein | 101 | 75% helix, 0% strand | Q9X1V5 |
| C | Carboxymuconolactone decarboxylase family protein (EC 4.1.-.-) | protein | 100 | 76% helix, 0% strand | Q9X1V5 |
| D | Carboxymuconolactone decarboxylase family protein (EC 4.1.-.-) | protein | 101 | 75% helix, 0% strand | Q9X1V5 |
| E | Carboxymuconolactone decarboxylase family protein (EC 4.1.-.-) | protein | 119 | 76% helix, 0% strand | Q9X1V5 |
| F | Carboxymuconolactone decarboxylase family protein (EC 4.1.-.-) | protein | 97 | 79% helix, 0% strand | Q9X1V5 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 12 copies · chains A, E, D, B, C, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.82 | 0.84 | 76 | UNL |
| 2 | 310 | 0.73 | 0.85 | 38 | UNL |
| 3 | 222 | 0.70 | 0.86 | 30 | UNL |
| 4 | 56 | 0.55 | 0.88 | 18 | empty |
| 5 | 133 | 0.51 | 0.80 | 21 | MPD |
Interfaces
15 interfaces between chains.
- E–F · 1206 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1189 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1186 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 670 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 657 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1VKE · Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved… · 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 Q9X1V5
- Elsewhere: RCSB PDB 1VKE · PDBe 1VKE · UniProt Q9X1V5
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