Research workbench
Crystal Structure of human epimerase family protein SDR39U1 (isoform2) with NADPH
Analyse Crystal Structure of human epimerase family protein SDR39U1 (isoform2) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B4O
- Type
- protein
- Length
- 2,359 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- HOMO SAPIENS
- Molecule
- Epimerase family protein SDR39U1
- UniProt
- Q9NRG7
- Ligands
- NDP
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.7 · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H | Epimerase family protein SDR39U1 | protein | 295 | 43% helix, 17% strand | Q9NRG7 |
| G | Epimerase family protein SDR39U1 | protein | 294 | 43% helix, 17% strand | Q9NRG7 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.82 | 0.84 | 73 | NDP, PE4 |
| 2 | 857 | 0.82 | 0.84 | 73 | NDP, PE4 |
| 3 | 795 | 0.82 | 0.85 | 68 | NDP, PE4 |
| 4 | 885 | 0.81 | 0.83 | 77 | NDP, PE4 |
| 5 | 892 | 0.81 | 0.83 | 73 | NDP, PE4 |
Interfaces
15 interfaces between chains.
- A–C · 458 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 457 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 456 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 440 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 378 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 4B4O · Crystal structure of human epimerase family protein SDR39U1 (ISOFORM2) with NADPH · the same entry in another collection · chain H against H, TM-score 1.00
- Q9NRG7 · AlphaFold monomer V2.0 prediction for epimerase family protein SDR39U1 (Q9NRG7) · a predicted model of the same protein · chain G 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 Q9NRG7
- Elsewhere: RCSB PDB 4B4O · PDBe 4B4O · UniProt Q9NRG7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.