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Crystal structure of arylmalonate decarboxylase
Analyse Crystal structure of arylmalonate decarboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EIS
- Type
- protein
- Length
- 931 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arylmalonate decarboxylase
- EC
- 4.1.1.76
- UniProt
- Q05115
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arylmalonate decarboxylase (EC 4.1.1.76) | protein | 224 | 49% helix, 17% strand | Q05115 |
| B | Arylmalonate decarboxylase (EC 4.1.1.76) | protein | 234 | 46% helix, 18% strand | Q05115 |
| C | Arylmalonate decarboxylase (EC 4.1.1.76) | protein | 236 | 48% helix, 16% strand | Q05115 |
| D | Arylmalonate decarboxylase (EC 4.1.1.76) | protein | 237 | 49% helix, 16% strand | Q05115 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.79 | 0.83 | 81 | empty |
| 2 | 96 | 0.71 | 0.94 | 22 | empty |
| 3 | 262 | 0.57 | 0.78 | 29 | empty |
| 4 | 229 | 0.56 | 0.79 | 39 | empty |
| 5 | 255 | 0.55 | 0.77 | 34 | GOL |
Interfaces
4 interfaces between chains.
- B–C · 569 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 502 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 341 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 294 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (artifact).
Compared structures
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 Q05115
- Elsewhere: RCSB PDB 3EIS · PDBe 3EIS · UniProt Q05115
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