MolNFT v1 · #92764 · protein
Crystal structure of pseudouridine monophosphate GLYCOSIDASE/LINEAR R5P adduct
4GIK · Pseudouridine-5'-phosphate glycosidase: “Crystal structure of pseudouridine monophosphate GLYCOSIDASE/LINEAR R5P adduct”. X-ray diffraction, 2 ligands (R5P, MN), 11 pockets (best druggability 0.83). MolNFT v1 #92764 on GenesisL1: 3D…
- PDB
- 4GIK
- Type
- protein
- Length
- 919 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
- R5P, MN
- Pockets
- 11 · 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 | 307 | 50% helix, 17% strand | P33025 |
| B | Pseudouridine-5'-phosphate glycosidase (EC 3.2.-.-) | protein | 307 | 51% helix, 17% strand | P33025 |
| C | Pseudouridine-5'-phosphate glycosidase (EC 3.2.-.-) | protein | 305 | 48% helix, 18% strand | P33025 |
Ligands and binding sites
- R5P · Ribose-5-phosphate · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.83 | 0.97 | 25 | empty |
| 2 | 389 | 0.79 | 0.88 | 56 | R5P, MN |
| 3 | 136 | 0.78 | 0.96 | 36 | R5P, MN |
| 4 | 138 | 0.76 | 0.94 | 33 | R5P, MN |
| 5 | 393 | 0.65 | 0.79 | 50 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1164 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 1161 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1133 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4GIK · Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear R5P Adduct · 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 4GIK · PDBe 4GIK · UniProt P33025
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