Research workbench
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)
Analyse Crystal structure of dimeric biodegradative threonine deaminase (tdcb) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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