MolNFT v1 · #38110 · protein
Crystal structure of dimeric biodegradative threonine deaminase (tdcb) from salmonella typhimurium at 2.2A resolution (triclinic form with one dimer of tdcb in the asymmetric unit)
2GN1 · Threonine dehydratase catabolic: “Crystal structure of dimeric biodegradative threonine deaminase (tdcb) from salmonella typhimurium at 2.2A…”. X-ray diffraction, 1 ligand (NA), 5 pockets (best druggability 0.71). MolNFT v1 #38110…
- PDB
- 2GN1
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine dehydratase catabolic
- EC
- 4.3.1.19
- UniProt
- P11954
- Ligands
- NA
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonine dehydratase catabolic (EC 4.3.1.19) | protein | 327 | 52% helix, 15% strand | P11954 |
| B | Threonine dehydratase catabolic (EC 4.3.1.19) | protein | 321 | 51% helix, 15% strand | P11954 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.71 | 0.79 | 60 | empty |
| 2 | 605 | 0.70 | 0.78 | 61 | empty |
| 3 | 289 | 0.56 | 0.76 | 26 | empty |
| 4 | 91 | 0.41 | 0.77 | 13 | empty |
| 5 | 73 | 0.39 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1056 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 2GN1 · Crystal structure of dimeric biodegradative threonine deaminase (TdcB) from Salmonella… · the same entry in another collection · chain A against A, TM-score 1.00
- P11954 · AlphaFold monomer V2.0 prediction for L-threonine dehydratase catabolic tdcb (P11954) · a predicted model of the same protein · chain B 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 P11954
- Elsewhere: RCSB PDB 2GN1 · PDBe 2GN1 · UniProt P11954
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