Research workbench
Crystal structure of the L-tyrosine-bound radical SAM tyrosine lyase thih (2-iminoacetate synthase) from thermosinus carboxydivorans
Analyse Crystal structure of the L-tyrosine-bound radical SAM tyrosine lyase thih… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PD1
- Type
- protein
- Length
- 733 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiazole biosynthesis protein thih
- UniProt
- A1HPQ5
- Ligands
- SF4, 5AD, MET, TYR, K, BR, SO4
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiazole biosynthesis protein thih | protein | 366 | 44% helix, 13% strand | A1HPQ5 |
| B | Thiazole biosynthesis protein thih | protein | 367 | 43% helix, 13% strand | A1HPQ5 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains A, B
- MET · Methionine · ligand · 2 copies · chains A, B
- TYR · Tyrosine · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · chains A
- BR · Bromide ion · ion · 11 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.85 | 0.96 | 51 | SF4, 5AD, MET, TYR, SO4 |
| 2 | 258 | 0.85 | 0.96 | 43 | SF4, 5AD, MET, TYR, SO4 |
| 3 | 1041 | 0.82 | 0.83 | 85 | empty |
| 4 | 150 | 0.56 | 0.82 | 37 | empty |
| 5 | 71 | 0.39 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 553 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7PD1 · Crystal structure of the L-tyrosine-bound radical SAM tyrosine lyase ThiH (2-iminoacetate… · 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 A1HPQ5
- Elsewhere: RCSB PDB 7PD1 · PDBe 7PD1 · UniProt A1HPQ5
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