Research workbench
Crystal structure of Scheffersomyces stipitis Rai1 in complex with (3'-NADP)+ and calcium ion
Analyse Crystal structure of Scheffersomyces stipitis Rai1 in complex with (3'-NADP)+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ULJ
- Type
- protein
- Length
- 1,527 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.911
- Source
- Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL…
- Molecule
- RAI1
- UniProt
- A3LNL5
- Ligands
- 0WD, PPV, CA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.911 · 4 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAI1 | protein | 381 | 39% helix, 25% strand | A3LNL5 |
| B | RAI1 | protein | 386 | 39% helix, 25% strand | A3LNL5 |
| C | RAI1 | protein | 381 | 41% helix, 25% strand | A3LNL5 |
| D | RAI1 | protein | 379 | 41% helix, 25% strand | A3LNL5 |
Ligands and binding sites
- 0WD · [[(2R,3S,4R,5R)-5-(3-aminocarbonyl-4H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate · ligand · 2 copies · chains A, B
- PPV · Pyrophosphate · ligand · 2 copies · chains C, D
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.77 | 0.79 | 85 | CA, 0WD |
| 2 | 1181 | 0.77 | 0.79 | 82 | PPV |
| 3 | 917 | 0.76 | 0.79 | 76 | PPV |
| 4 | 880 | 0.76 | 0.79 | 65 | CA, 0WD |
| 5 | 827 | 0.74 | 0.78 | 73 | empty |
Interfaces
5 interfaces between chains.
- A–C · 593 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 380 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 303 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 167 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 102 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5ULJ · Crystal structure of scheffersomyces stipitis RAI1 in complex with (3'-NADP)+ and calcium… · the same entry in another collection · chain D against D, TM-score 1.00
- A3LNL5 · AlphaFold monomer V2.0 prediction for decapping nuclease RAI1 (A3LNL5) · a predicted model of the same protein · chain D 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 A3LNL5
- Elsewhere: RCSB PDB 5ULJ · PDBe 5ULJ · UniProt A3LNL5
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