Research workbench
DBR1 in complex with synthetic linear RNA
Analyse DBR1 in complex with synthetic linear RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PEH
- Type
- protein + RNA
- Length
- 1,762 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA lariat debranching enzyme, putative; RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')
- UniProt
- C4M1P9
- Ligands
- MN, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | RNA lariat debranching enzyme, putative | protein | 349 | 35% helix, 21% strand | C4M1P9 |
| V, Z | RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3') | rna | 3 | — | — |
| W | RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3') | rna | 3 | — | — |
| X, Y | RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 5 copies · chains A, V, B, W, C, X, D, Y, E, Z
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, X, D, E
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.77 | 0.80 | 83 | SO4 |
| 2 | 52 | 0.72 | 0.99 | 19 | empty |
| 3 | 51 | 0.72 | 0.99 | 17 | empty |
| 4 | 536 | 0.70 | 0.79 | 51 | empty |
| 5 | 51 | 0.69 | 0.98 | 21 | empty |
Interfaces
11 interfaces between chains.
- B–C · 724 Ų buried · 8 hydrogen bonds · protein-protein
- C–X · 711 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–Y · 677 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–E · 655 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 648 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (nucleotide modification).
Compared structures
- 4PEH · Dbr1 in complex with synthetic linear RNA · the same entry in another collection · 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 C4M1P9
- Elsewhere: RCSB PDB 4PEH · PDBe 4PEH · UniProt C4M1P9
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