Research workbench
Crystal structure of threonine synthase from thermus thermophilus HB8 in complex with a substrate analogue
Analyse Crystal structure of threonine synthase from thermus thermophilus HB8 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V7C
- Type
- protein
- Length
- 1,404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine synthase
- EC
- 4.2.3.1
- UniProt
- P83823
- Ligands
- HEY
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Threonine synthase (EC 4.2.3.1) | protein | 351 | 46% helix, 17% strand | P83823 |
Ligands and binding sites
- HEY · (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-5-phosphonopent-2-enoic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.79 | 0.98 | 30 | HEY |
| 2 | 119 | 0.79 | 0.98 | 30 | HEY |
| 3 | 108 | 0.79 | 0.99 | 30 | HEY |
| 4 | 120 | 0.79 | 0.97 | 30 | HEY |
| 5 | 170 | 0.56 | 0.81 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3459 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 3377 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 354 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1V7C · Crystal structure of threonine synthase from thermus thermophilus hb8 in complex with a… · 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 P83823
- Elsewhere: RCSB PDB 1V7C · PDBe 1V7C · UniProt P83823
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