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Crystal structure of thermovibrio ammonificans THI4
Analyse Crystal structure of thermovibrio ammonificans THI4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RK0
- Type
- protein
- Length
- 1,043 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamine thiazole synthase
- EC
- 2.4.2.59
- UniProt
- E8T346
- Ligands
- 48H, FE
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine thiazole synthase (EC 2.4.2.59) | protein | 261 | 42% helix, 27% strand | E8T346 |
| B, D | Thiamine thiazole synthase (EC 2.4.2.59) | protein | 262 | 42% helix, 27% strand | E8T346 |
| C | Thiamine thiazole synthase (EC 2.4.2.59) | protein | 258 | 43% helix, 28% strand | E8T346 |
Ligands and binding sites
- 48H · 2-[(E)-[(4R)-5-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-3-oxidanylidene-pentan-2-ylidene]amino]ethanoic acid · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) 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
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.71 | 0.82 | 54 | FE, 48H |
| 2 | 407 | 0.71 | 0.82 | 57 | 48H |
| 3 | 548 | 0.68 | 0.78 | 55 | FE, 48H |
| 4 | 527 | 0.68 | 0.78 | 68 | FE, 48H |
| 5 | 59 | 0.46 | 0.83 | 14 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2670 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2638 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 1168 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1049 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1037 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7RK0 · Crystal structure of Thermovibrio ammonificans THI4 · 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 E8T346
- Elsewhere: RCSB PDB 7RK0 · PDBe 7RK0 · UniProt E8T346
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