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Crystal structure of pseudouridine monophosphate glycosidase complexed with sulfate
Analyse Crystal structure of pseudouridine monophosphate glycosidase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GIJ
- Type
- protein
- Length
- 910 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
- MN, SO4
- Pockets
- 9 · best druggability 0.83
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 | 304 | 50% helix, 17% strand | P33025 |
| B | Pseudouridine-5'-phosphate glycosidase (EC 3.2.-.-) | protein | 304 | 50% helix, 17% strand | P33025 |
| C | Pseudouridine-5'-phosphate glycosidase (EC 3.2.-.-) | protein | 302 | 49% helix, 16% strand | P33025 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.83 | 0.98 | 24 | empty |
| 2 | 605 | 0.80 | 0.85 | 77 | SO4, MN |
| 3 | 497 | 0.79 | 0.86 | 66 | SO4, MN |
| 4 | 692 | 0.72 | 0.79 | 71 | SO4, MN |
| 5 | 446 | 0.66 | 0.78 | 53 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1140 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 1112 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 1058 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4GIJ · Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Sulfate · 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 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 P33025
- Elsewhere: RCSB PDB 4GIJ · PDBe 4GIJ · UniProt P33025
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