MolNFT v1 · #137019 · protein
Human RNA pseudouridylate synthase domain containing 1
5VBB · RNA pseudouridylate synthase domain-containing protein 1: “Human RNA pseudouridylate synthase domain containing 1”. X-ray diffraction, 2 ligands (SO4, CL), 4 pockets (best druggability 0.63). MolNFT v1 #137019 on GenesisL1: 3D…
- PDB
- 5VBB
- Type
- protein
- Length
- 245 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA pseudouridylate synthase domain-containing protein 1
- UniProt
- Q9UJJ7
- Ligands
- SO4, CL
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA pseudouridylate synthase domain-containing protein 1 | protein | 245 | 16% helix, 36% strand | Q9UJJ7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.63 | 0.80 | 31 | SO4, CL, GOL |
| 2 | 131 | 0.47 | 0.78 | 23 | empty |
| 3 | 54 | 0.37 | 0.80 | 11 | empty |
| 4 | 59 | 0.27 | 0.73 | 13 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5VBB · Human RNA Pseudouridylate Synthase Domain Containing 1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UJJ7 · AlphaFold monomer V2.0 prediction for RNA pseudouridylate synthase domain-containing… · 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 Q9UJJ7
- Elsewhere: RCSB PDB 5VBB · PDBe 5VBB · UniProt Q9UJJ7
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