MolNFT v1 · #134519 · protein
Structure of the tryptophan synthase B-subunit from pyroccus furiosus with B-methyltryptophan non-covalently bound
5T6M · Tryptophan synthase beta chain 1: “Structure of the tryptophan synthase B-subunit from pyroccus furiosus with B-methyltryptophan non-covalently…”. X-ray diffraction, 3 ligands (78U, NA, PO4), 15 pockets (best druggability 0.82).…
- PDB
- 5T6M
- Type
- protein
- Length
- 1,542 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
- 78U, NA, PO4
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 383 | 49% helix, 20% strand | Q8U093 |
| B | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 386 | 49% helix, 21% strand | Q8U093 |
| C | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 391 | 49% helix, 19% strand | Q8U093 |
| D | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 382 | 50% helix, 20% strand | Q8U093 |
Ligands and binding sites
- 78U · (betaS)-beta-methyl-L-tryptophan · ligand · 3 copies · chains B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.82 | 0.96 | 43 | empty |
| 2 | 735 | 0.78 | 0.82 | 79 | PO4, 78U |
| 3 | 1035 | 0.78 | 0.80 | 92 | empty |
| 4 | 109 | 0.78 | 0.97 | 26 | 78U |
| 5 | 101 | 0.77 | 0.98 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1981 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1828 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 358 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 320 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 106 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 5T6M · Structure of the tryptophan synthase b-subunit from Pyroccus furiosus with… · 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 A 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 5T6M · PDBe 5T6M · UniProt Q8U093
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