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
- 1ZE1
- Type
- protein
- Length
- 1,208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA pseudouridine synthase B
- EC
- 4.2.1.70
- UniProt
- Q9WZW0
- Ligands
- MG
- Pockets
- 12 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | TRNA pseudouridine synthase B (EC 4.2.1.70) | protein | 308 | 25% helix, 33% strand | Q9WZW0 |
| D | TRNA pseudouridine synthase B (EC 4.2.1.70) | protein | 284 | 25% helix, 34% strand | Q9WZW0 |
Ligands and binding sites
- MG · Magnesium 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
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.58 | 0.84 | 27 | empty |
| 2 | 66 | 0.51 | 0.85 | 20 | empty |
| 3 | 110 | 0.49 | 0.81 | 19 | empty |
| 4 | 114 | 0.49 | 0.80 | 19 | empty |
| 5 | 93 | 0.48 | 0.81 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 578 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 537 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 423 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1ZE1 · Conformational Change of Pseudouridine 55 Synthase upon Its Association with RNA Substrate · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WZW0 · AlphaFold monomer V2.0 prediction for tRNA pseudouridine synthase B (Q9WZW0) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 1ZE1 · PDBe 1ZE1 · UniProt Q9WZW0
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