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Crystal structure of dimeric biodegradative threonine deaminase (tdcb) from salmonella typhimurium at 1.7 a resolution (triclinic form with one complete subunit built in alternate conformation)
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
- 2GN0
- Type
- protein
- Length
- 1,295 residues
- Chains
- 4
- 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
- 10 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonine dehydratase catabolic (EC 4.3.1.19) | protein | 327 | 53% helix, 15% strand | P11954 |
| B, D | Threonine dehydratase catabolic (EC 4.3.1.19) | protein | 320 | 52% helix, 15% strand | P11954 |
| C | Threonine dehydratase catabolic (EC 4.3.1.19) | protein | 328 | 53% helix, 15% strand | P11954 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.72 | 0.79 | 76 | empty |
| 2 | 622 | 0.72 | 0.79 | 62 | empty |
| 3 | 622 | 0.69 | 0.77 | 64 | empty |
| 4 | 576 | 0.69 | 0.78 | 61 | empty |
| 5 | 399 | 0.62 | 0.77 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1097 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1027 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 563 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 2GN0 · 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 2GN0 · PDBe 2GN0 · UniProt P11954
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