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Crystal structure of an alpha subunit of tryptophan synthase from vibrio cholerae O1 biovar el tor str. N16961
Analyse Crystal structure of an alpha subunit of tryptophan synthase from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NAV
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase alpha chain
- EC
- 4.2.1.20
- UniProt
- C3LLL5
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 261 | 53% helix, 15% strand | C3LLL5 |
| B | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 258 | 51% helix, 14% strand | C3LLL5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.80 | 0.83 | 97 | EDO |
| 2 | 388 | 0.65 | 0.79 | 51 | empty |
| 3 | 71 | 0.37 | 0.78 | 16 | empty |
| 4 | 57 | 0.26 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 944 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3NAV · Crystal structure of an alpha subunit of tryptophan synthase from Vibrio cholerae O1… · the same entry in another collection · chain A against A, TM-score 1.00
- C3LLL5 · AlphaFold monomer V2.0 prediction for tryptophan synthase alpha chain (C3LLL5) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 C3LLL5
- Elsewhere: RCSB PDB 3NAV · PDBe 3NAV · UniProt C3LLL5
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