Research workbench
Crystal structure of the tRNA modifier tias from pyrococcus furiosus, northeast structural genomics consortium target PFR225
Analyse Crystal structure of the tRNA modifier tias from pyrococcus furiosus, northeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U02
- Type
- protein
- Length
- 933 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative transcription-associated protein tfiis
- UniProt
- Q8TZX0
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative transcription-associated protein tfiis | protein | 240 | 33% helix, 26% strand | Q8TZX0 |
| B | Putative transcription-associated protein tfiis | protein | 244 | 34% helix, 26% strand | Q8TZX0 |
| C | Putative transcription-associated protein tfiis | protein | 226 | 34% helix, 27% strand | Q8TZX0 |
| D | Putative transcription-associated protein tfiis | protein | 223 | 35% helix, 27% strand | Q8TZX0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, C, B, D
- CIT · Citric acid · additive · 3 copies · chains A, B, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B, D
- ACY · Acetic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.78 | 0.85 | 67 | SO4 |
| 2 | 453 | 0.75 | 0.84 | 63 | SO4, ACY |
| 3 | 285 | 0.68 | 0.83 | 39 | empty |
| 4 | 169 | 0.68 | 0.87 | 28 | empty |
| 5 | 206 | 0.59 | 0.81 | 40 | SO4 |
Interfaces
6 interfaces between chains.
- C–D · 1934 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1879 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1485 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1484 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 284 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered, phosphorylation).
Compared structures
- 3U02 · Crystal Structure of the tRNA modifier TiaS from Pyrococcus furiosus, Northeast… · 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 Q8TZX0
- Elsewhere: RCSB PDB 3U02 · PDBe 3U02 · UniProt Q8TZX0
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