Research workbench
Conformational change of pseudouridine 55 synthase upon its association with RNA substrate
Analyse Conformational change of pseudouridine 55 synthase upon its association with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZE2
- Type
- protein + RNA
- Length
- 562 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*GP*CP*CP*AP*CP*GP*GP*UP*(FHU) P*CP*GP*AP*AP*UP*CP*CP*GP*UP*GP*GP*C)-3'; TRNA…
- EC
- 4.2.1.70
- UniProt
- Q9WZW0
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-R(*GP*GP*CP*CP*AP*CP*GP*GP*UP*(FHU) P*CP*GP*AP*AP*UP*CP*CP*GP*UP*GP*GP*C)-3' | rna | 22 | — | — |
| A | TRNA pseudouridine synthase B (EC 4.2.1.70) | protein | 300 | 21% helix, 35% strand | Q9WZW0 |
| B | TRNA pseudouridine synthase B (EC 4.2.1.70) | protein | 218 | 18% helix, 17% strand | Q9WZW0 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.78 | 0.81 | 49 | empty |
| 2 | 66 | 0.45 | 0.82 | 16 | empty |
| 3 | 116 | 0.43 | 0.78 | 21 | empty |
| 4 | 175 | 0.41 | 0.73 | 23 | empty |
| 5 | 71 | 0.34 | 0.76 | 22 | empty |
Interfaces
5 interfaces between chains.
- D–B · 1484 Ų buried · 45 hydrogen bonds · protein-nucleic
- C–A · 1469 Ų buried · 43 hydrogen bonds · protein-nucleic
- C–B · 375 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–A · 353 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–D · 250 Ų buried · 13 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1ZE2 · Conformational change of pseudouridine 55 synthase upon its association with RNA substrate · the same entry in another collection · chain C against C, TM-score 1.00
- Q9WZW0 · AlphaFold monomer V2.0 prediction for tRNA pseudouridine synthase B (Q9WZW0) · a predicted model of the same protein · chain A 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 Q9WZW0
- Elsewhere: RCSB PDB 1ZE2 · PDBe 1ZE2 · UniProt Q9WZW0
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