Research workbench
Crystal structure of 5-carboxyvanillate decarboxylase LIGW2 from novosphingobium aromaticivorans dsm 12444 (target efi-505250) with bound manganese and 3-methoxy-4-hydroxy-5-nitrobenzoic acid, the D314N mutant
Analyse Crystal structure of 5-carboxyvanillate decarboxylase LIGW2 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QS5
- Type
- protein
- Length
- 1,394 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LIGW2 decarboxylase
- UniProt
- Q2GA79
- Ligands
- 1DF, MN, CL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | LIGW2 decarboxylase | protein | 349 | 51% helix, 10% strand | Q2GA79 |
| C, D | LIGW2 decarboxylase | protein | 348 | 52% helix, 10% strand | Q2GA79 |
Ligands and binding sites
- 1DF · 4-hydroxy-3-methoxy-5-nitrobenzoic acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.79 | 0.94 | 40 | 1DF |
| 2 | 186 | 0.79 | 0.94 | 48 | MN, 1DF |
| 3 | 157 | 0.76 | 0.93 | 33 | 1DF |
| 4 | 155 | 0.75 | 0.92 | 38 | 1DF |
| 5 | 337 | 0.59 | 0.77 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2897 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2888 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 177 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4QS5 · CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 FROM NOVOSPHINGOBIUM… · 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 Q2GA79
- Elsewhere: RCSB PDB 4QS5 · PDBe 4QS5 · UniProt Q2GA79
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.