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Thiazole synthase THI4 from methanocaldococcus jannaschii
Analyse Thiazole synthase THI4 from methanocaldococcus jannaschii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y4M
- Type
- protein
- Length
- 2,065 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ribose 1,5-bisphosphate isomerase
- EC
- 5.3.1.29
- UniProt
- Q58018
- Ligands
- 48F
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ribose 1,5-bisphosphate isomerase (EC 5.3.1.29) | protein | 260 | 38% helix, 27% strand | Q58018 |
| B, E | Putative ribose 1,5-bisphosphate isomerase (EC 5.3.1.29) | protein | 256 | 39% helix, 27% strand | Q58018 |
| C, D | Putative ribose 1,5-bisphosphate isomerase (EC 5.3.1.29) | protein | 255 | 39% helix, 27% strand | Q58018 |
| F, G | Putative ribose 1,5-bisphosphate isomerase (EC 5.3.1.29) | protein | 262 | 39% helix, 27% strand | Q58018 |
| H | Putative ribose 1,5-bisphosphate isomerase (EC 5.3.1.29) | protein | 259 | 40% helix, 27% strand | Q58018 |
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 · 8 copies · chains A, D, B, F, C, E, G, H
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 5 copies · chains A, C, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.84 | 0.96 | 42 | empty |
| 2 | 249 | 0.84 | 0.95 | 41 | empty |
| 3 | 246 | 0.83 | 0.95 | 42 | empty |
| 4 | 1022 | 0.83 | 0.84 | 114 | 48F |
| 5 | 226 | 0.83 | 0.95 | 40 | empty |
Interfaces
20 interfaces between chains.
- E–F · 2790 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 2781 Ų buried · 19 hydrogen bonds · protein-protein
- B–G · 2761 Ų buried · 19 hydrogen bonds · protein-protein
- D–H · 2758 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1357 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
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 Q58018
- Elsewhere: RCSB PDB 4Y4M · PDBe 4Y4M · UniProt Q58018
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