MolNFT v1 · #21460 · protein
Crystal structure of the E.COLI pseudouridine synthase trud
1SB7 · TRNA pseudouridine synthase D: “Crystal structure of the E.COLI pseudouridine synthase trud”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.75). MolNFT v1 #21460 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1SB7
- Type
- protein
- Length
- 686 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA pseudouridine synthase D
- EC
- 4.2.1.70
- UniProt
- Q57261
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA pseudouridine synthase D (EC 4.2.1.70) | protein | 342 | 32% helix, 26% strand | Q57261 |
| B | TRNA pseudouridine synthase D (EC 4.2.1.70) | protein | 344 | 33% helix, 26% strand | Q57261 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.75 | 0.80 | 87 | GOL |
| 2 | 236 | 0.63 | 0.82 | 31 | PO4 |
| 3 | 201 | 0.60 | 0.81 | 24 | GOL |
| 4 | 164 | 0.50 | 0.78 | 24 | empty |
| 5 | 126 | 0.45 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 782 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 1SB7 · Crystal structure of the E.coli pseudouridine synthase TruD · the same entry in another collection · chain A against A, TM-score 1.00
- Q57261 · AlphaFold monomer V2.0 prediction for tRNA pseudouridine synthase D (Q57261) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q57261
- Elsewhere: RCSB PDB 1SB7 · PDBe 1SB7 · UniProt Q57261
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