Research workbench
Crystal structure of glycyl radical enzyme with bound substrate
Analyse Crystal structure of glycyl radical enzyme with bound substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YAJ
- Type
- protein
- Length
- 1,912 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, 4HP
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 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 |
| C | 4-hydroxyphenylacetate decarboxylase large subunit (EC 4.1.1.83) | protein | 871 | 50% helix, 12% strand | Q38HX4 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains B, A, D, C
- 4HP · 4-hydroxyphenylacetate · ligand · 2 copies · chains A, 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 | 455 | 0.88 | 0.95 | 65 | empty |
| 2 | 127 | 0.72 | 0.92 | 25 | empty |
| 3 | 126 | 0.71 | 0.92 | 25 | empty |
| 4 | 184 | 0.71 | 0.88 | 42 | empty |
| 5 | 175 | 0.69 | 0.88 | 41 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1978 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1845 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1807 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 10 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2YAJ · CRYSTAL STRUCTURE OF GLYCYL RADICAL ENZYME with bound substrate · 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 C 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 0.93
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 2YAJ · PDBe 2YAJ · UniProt Q38HX4 · UniProt Q38HX3
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