MolNFT v1 · #92766 · protein
Crystal structure of pseudouridine monophosphate glycosidase complexed with pseudouridine 5'-phosphate
4GIM · Pseudouridine-5'-phosphate glycosidase: “Crystal structure of pseudouridine monophosphate glycosidase complexed with pseudouridine 5'-phosphate”. X-ray diffraction, 2 ligands (PSU, MN), 11 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 4GIM
- Type
- protein
- Length
- 917 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
- PSU, MN
- Pockets
- 11 · 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 | 306 | 50% helix, 17% strand | P33025 |
| B | Pseudouridine-5'-phosphate glycosidase (EC 3.2.-.-) | protein | 306 | 49% helix, 17% strand | P33025 |
| C | Pseudouridine-5'-phosphate glycosidase (EC 3.2.-.-) | protein | 305 | 50% helix, 17% strand | P33025 |
Ligands and binding sites
- PSU · Pseudouridine-5'-monophosphate · ligand · 3 copies · chains A, C, B
- 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
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.84 | 0.98 | 26 | empty |
| 2 | 213 | 0.82 | 0.96 | 37 | PSU, MN |
| 3 | 208 | 0.82 | 0.96 | 36 | PSU, MN |
| 4 | 205 | 0.82 | 0.96 | 38 | PSU, MN |
| 5 | 463 | 0.66 | 0.78 | 61 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1148 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 1115 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 1084 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4GIM · Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with 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 B 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 4GIM · PDBe 4GIM · UniProt P33025
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.