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Crystal structure of pseudouridine monophosphate GLYCOSIDASE/LINEAR pseudouridine 5'-phosphate adduct
Analyse Crystal structure of pseudouridine monophosphate GLYCOSIDASE/LINEAR… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GIL
- Type
- protein
- Length
- 918 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pseudouridine-5'-phosphate glycosidase
- EC
- 3.2.-.-
- UniProt
- P33025
- Ligands
- KPS, MN
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pseudouridine-5'-phosphate glycosidase (EC 3.2.-.-) | protein | 307 | 50% helix, 17% strand | P33025 |
| B | Pseudouridine-5'-phosphate glycosidase (EC 3.2.-.-) | protein | 307 | 50% helix, 17% strand | P33025 |
| C | Pseudouridine-5'-phosphate glycosidase (EC 3.2.-.-) | protein | 304 | 50% helix, 17% strand | P33025 |
Ligands and binding sites
- KPS · pseudouridine 5'-phosphate, linear · ligand · 3 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.84 | 0.98 | 25 | empty |
| 2 | 209 | 0.82 | 0.96 | 51 | KPS, MN |
| 3 | 191 | 0.81 | 0.96 | 49 | KPS, MN |
| 4 | 127 | 0.78 | 0.96 | 38 | MN, KPS |
| 5 | 468 | 0.66 | 0.78 | 59 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1144 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 1101 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 1011 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4GIL · Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear Pseudouridine… · the same entry in another collection · chain A against A, TM-score 1.00
- P33025 · AlphaFold monomer V2.0 prediction for pseudouridine-5'-phosphate glycosidase (P33025) · a predicted model of the same protein · 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 P33025
- Elsewhere: RCSB PDB 4GIL · PDBe 4GIL · UniProt P33025
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