MolNFT v1 · #61721 · protein
Crystal structure of arylmalonate decarboxylase
3DTV: “Crystal structure of arylmalonate decarboxylase”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.78). MolNFT v1 #61721 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DTV
- Type
- protein
- Length
- 915 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 0.78
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 | 217 | 48% helix, 18% strand | Q05115 |
| B | Arylmalonate decarboxylase (EC 4.1.1.76) | protein | 234 | 47% helix, 16% strand | Q05115 |
| C | Arylmalonate decarboxylase (EC 4.1.1.76) | protein | 228 | 49% helix, 17% strand | Q05115 |
| D | Arylmalonate decarboxylase (EC 4.1.1.76) | protein | 236 | 49% helix, 16% strand | Q05115 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.78 | 0.82 | 77 | SO4, GOL |
| 2 | 487 | 0.71 | 0.81 | 69 | empty |
| 3 | 211 | 0.52 | 0.77 | 34 | empty |
| 4 | 170 | 0.51 | 0.78 | 30 | empty |
| 5 | 152 | 0.43 | 0.75 | 21 | empty |
Interfaces
4 interfaces between chains.
- B–C · 544 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 482 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 345 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 334 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 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 3DTV · PDBe 3DTV · UniProt Q05115
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.