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Crystal structure of 5-carboxyvanillate decarboxylase from sphingomonas paucimobilis complexed with 4-hydroxy-3-methoxy-5- nitrobenzoic acid
Analyse Crystal structure of 5-carboxyvanillate decarboxylase from sphingomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NG3
- Type
- protein
- Length
- 2,680 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-carboxyvanillate decarboxylase
- UniProt
- Q8RJ47
- Ligands
- 1DF, MN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | 5-carboxyvanillate decarboxylase | protein | 335 | 51% helix, 11% strand | Q8RJ47 |
Ligands and binding sites
- 1DF · 4-hydroxy-3-methoxy-5-nitrobenzoic acid · ligand · 8 copies · chains A, H, B, G, C, F, D, E
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, C, D, E, F, G, H
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains B, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.78 | 0.80 | 72 | empty |
| 2 | 1087 | 0.78 | 0.80 | 67 | EDO |
| 3 | 1022 | 0.78 | 0.80 | 54 | empty |
| 4 | 1122 | 0.78 | 0.80 | 70 | EDO |
| 5 | 91 | 0.72 | 0.95 | 24 | 1DF |
Interfaces
12 interfaces between chains.
- A–H · 2893 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 2892 Ų buried · 27 hydrogen bonds · protein-protein
- C–F · 2887 Ų buried · 27 hydrogen bonds · protein-protein
- B–G · 2878 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 632 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4NG3 · Crystal structure of 5-carboxyvanillate decarboxylase from Sphingomonas paucimobilis… · 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 Q8RJ47
- Elsewhere: RCSB PDB 4NG3 · PDBe 4NG3 · UniProt Q8RJ47
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