MolNFT v1 · #151310 · protein
Crystal structure of the thiazole synthase from methanothermococcus thermolithotrophicus co-crystallized with tb-XO4
6HK1: “Crystal structure of the thiazole synthase from methanothermococcus thermolithotrophicus co-crystallized with…”. X-ray diffraction, 3 ligands (48F, TB, NA), 14 pockets (best druggability 0.85). MolNFT v1 #151310 on GenesisL1: 3D…
- PDB
- 6HK1
- Type
- protein
- Length
- 1,556 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiazole synthase
- Ligands
- 48F, TB, NA
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Thiazole synthase | protein | 261 | 38% helix, 25% strand | — |
| B | Thiazole synthase | protein | 258 | 39% helix, 26% strand | — |
| C | Thiazole synthase | protein | 257 | 40% helix, 26% strand | — |
| F | Thiazole synthase | protein | 258 | 39% helix, 26% strand | — |
Ligands and binding sites
- 48F · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R)-2,3,5-tris(oxidanyl)-4-oxidanylidene-pentyl] hydrogen phosphate · ligand · 6 copies · chains A, B, F, C, D, E
- TB · Terbium(iii) ion · metal · 49 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · chains A, E
- PGE · Triethylene glycol · additive · 3 copies · chains A, E, F
- GOL · Glycerol · additive · 2 copies · chains A, F
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.85 | 0.96 | 45 | empty |
| 2 | 963 | 0.77 | 0.80 | 107 | 48F |
| 3 | 780 | 0.74 | 0.79 | 80 | empty |
| 4 | 850 | 0.72 | 0.77 | 44 | empty |
| 5 | 582 | 0.72 | 0.80 | 65 | 48F |
Interfaces
9 interfaces between chains.
- B–D · 2723 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 2621 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1278 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1260 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 899 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6HK1 · Crystal structure of the Thiazole synthase from Methanothermococcus thermolithotrophicus… · 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
- Elsewhere: RCSB PDB 6HK1 · PDBe 6HK1
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