Research workbench
Crystal structure of glycyl radical enzyme
Analyse Crystal structure of glycyl radical enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y8N
- Type
- protein
- Length
- 1,910 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxyphenylacetate decarboxylase large subunit; 4-hydroxyphenylacetate decarboxylase…
- EC
- 4.1.1.83
- UniProt
- Q38HX4, Q38HX3
- Ligands
- SF4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 4-hydroxyphenylacetate decarboxylase large subunit (EC 4.1.1.83) | protein | 869 | 50% helix, 11% strand | Q38HX4 |
| B, D | 4-hydroxyphenylacetate decarboxylase small subunit (EC 4.1.1.83) | protein | 86 | 7% helix, 33% strand | Q38HX3 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains B, A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.88 | 0.95 | 66 | empty |
| 2 | 193 | 0.71 | 0.89 | 49 | empty |
| 3 | 145 | 0.71 | 0.91 | 40 | empty |
| 4 | 115 | 0.70 | 0.92 | 26 | empty |
| 5 | 122 | 0.69 | 0.91 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1974 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1842 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1832 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2Y8N · Crystal structure of glycyl radical enzyme · the same entry in another collection · chain A against A, TM-score 1.00
- Q38HX4 · AlphaFold monomer V2.0 prediction for 4-hydroxyphenylacetate decarboxylase glycyl radical… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q38HX3 · AlphaFold monomer V2.0 prediction for 4-hydroxyphenylacetate decarboxylase small subunit… · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q38HX4
- Every structure of UniProt Q38HX3
- Elsewhere: RCSB PDB 2Y8N · PDBe 2Y8N · UniProt Q38HX4 · UniProt Q38HX3
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