MolNFT v1 · #158201 · protein
Threonine synthase from bacillus subtilis atcc 6633 with plp and appa
6NMX: “Threonine synthase from bacillus subtilis atcc 6633 with plp and appa”. X-ray diffraction, 1 ligand (LJS), 12 pockets (best druggability 0.79). MolNFT v1 #158201 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NMX
- Type
- protein
- Length
- 1,396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine synthase
- EC
- 4.2.3.1
- UniProt
- A8HUA2
- Ligands
- LJS
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonine synthase (EC 4.2.3.1) | protein | 350 | 49% helix, 17% strand | A8HUA2 |
| B, C | Threonine synthase (EC 4.2.3.1) | protein | 349 | 48% helix, 17% strand | A8HUA2 |
| D | Threonine synthase (EC 4.2.3.1) | protein | 348 | 48% helix, 17% strand | A8HUA2 |
Ligands and binding sites
- LJS · (2E,3Z)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4(1H)-ylidene}methyl]imino}-5-phosphonopent-3-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
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.79 | 0.98 | 31 | LJS |
| 2 | 110 | 0.79 | 0.98 | 30 | LJS |
| 3 | 363 | 0.79 | 0.88 | 75 | empty |
| 4 | 106 | 0.79 | 0.98 | 29 | LJS |
| 5 | 104 | 0.78 | 0.98 | 30 | LJS |
Interfaces
4 interfaces between chains.
- A–C · 3288 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 3265 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 370 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NMX · Threonine synthase from Bacillus subtilis ATCC 6633 with PLP and APPA · 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 A8HUA2
- Elsewhere: RCSB PDB 6NMX · PDBe 6NMX · UniProt A8HUA2
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