MolNFT v1 · #25049 · protein
Crystal structure of T.TH. HB8 threonine deaminase
1VE5: “Crystal structure of T.TH. HB8 threonine deaminase”. X-ray diffraction, 2 ligands (PLP, CA), 8 pockets (best druggability 0.80). MolNFT v1 #25049 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1VE5
- Type
- protein
- Length
- 1,159 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine deaminase
- EC
- 4.3.1.19
- UniProt
- Q5SLL4
- Ligands
- PLP, CA
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonine deaminase (EC 4.3.1.19) | protein | 308 | 50% helix, 16% strand | Q5SLL4 |
| B | Threonine deaminase (EC 4.3.1.19) | protein | 297 | 52% helix, 16% strand | Q5SLL4 |
| C | Threonine deaminase (EC 4.3.1.19) | protein | 274 | 51% helix, 15% strand | Q5SLL4 |
| D | Threonine deaminase (EC 4.3.1.19) | protein | 280 | 50% helix, 16% strand | Q5SLL4 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.80 | 0.93 | 31 | empty |
| 2 | 251 | 0.80 | 0.92 | 28 | empty |
| 3 | 633 | 0.72 | 0.79 | 67 | PLP |
| 4 | 650 | 0.67 | 0.76 | 60 | empty |
| 5 | 632 | 0.66 | 0.76 | 63 | empty |
Interfaces
4 interfaces between chains.
- A–B · 946 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 935 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 930 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 898 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1VE5 · Crystal Structure of T.th. HB8 Threonine deaminase · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5SLL4
- Elsewhere: RCSB PDB 1VE5 · PDBe 1VE5 · UniProt Q5SLL4
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