Research workbench
Crystal structure of candida albicans RAI1 in complex with PU5-MN2+
Analyse Crystal structure of candida albicans RAI1 in complex with PU5-MN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BUD
- Type
- protein + RNA
- Length
- 786 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Decapping nuclease RAI1; RNA (5'-R(P*UP*UP*UP*U)-3')
- EC
- 3.6.1.-
- UniProt
- Q5AAT0
- Ligands
- MN
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decapping nuclease RAI1 (EC 3.6.1.-) | protein | 391 | 43% helix, 24% strand | Q5AAT0 |
| B | Decapping nuclease RAI1 (EC 3.6.1.-) | protein | 387 | 43% helix, 24% strand | Q5AAT0 |
| D, E | RNA (5'-R(P*UP*UP*UP*U)-3') | rna | 4 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.82 | 0.83 | 79 | MN |
| 2 | 1090 | 0.81 | 0.83 | 86 | MN |
| 3 | 132 | 0.80 | 0.97 | 24 | empty |
| 4 | 124 | 0.48 | 0.79 | 27 | empty |
| 5 | 163 | 0.46 | 0.76 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 661 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 654 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–D · 629 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 5BUD · Crystal structure of Candida albicans Rai1 in complex with pU5-Mn2+ · the same entry in another collection · chain E against E, TM-score 1.00
- Q5AAT0 · AlphaFold monomer V2.0 prediction for decapping nuclease RAI1 (Q5AAT0) · 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 Q5AAT0
- Elsewhere: RCSB PDB 5BUD · PDBe 5BUD · UniProt Q5AAT0
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