Research workbench
Tryptophan synthase beta-subunit from pyrococcus furiosus with L- threonine non-covalently bound in the active site
Analyse Tryptophan synthase beta-subunit from pyrococcus furiosus with L- threonine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IXJ
- Type
- protein
- Length
- 1,550 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase beta chain 1
- EC
- 4.2.1.20
- UniProt
- Q8U093
- Ligands
- THR, NA
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 384 | 48% helix, 20% strand | Q8U093 |
| B | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 388 | 48% helix, 19% strand | Q8U093 |
| D | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 394 | 48% helix, 19% strand | Q8U093 |
Ligands and binding sites
- THR · Threonine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.78 | 0.97 | 21 | THR |
| 2 | 110 | 0.77 | 0.97 | 20 | THR |
| 3 | 108 | 0.77 | 0.97 | 21 | THR |
| 4 | 123 | 0.77 | 0.96 | 34 | empty |
| 5 | 109 | 0.77 | 0.97 | 21 | THR |
Interfaces
5 interfaces between chains.
- B–C · 1808 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1791 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 409 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 95 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 12 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 5IXJ · Tryptophan Synthase beta-subunit from Pyrococcus furiosus with L-threonine non-covalently… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8U093 · AlphaFold monomer V2.0 prediction for tryptophan synthase beta chain 1 (Q8U093) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q8U093
- Elsewhere: RCSB PDB 5IXJ · PDBe 5IXJ · UniProt Q8U093
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