Research workbench
DBR1 in complex with synthetic branched RNA analog
Analyse DBR1 in complex with synthetic branched RNA analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PEI
- Type
- protein + RNA
- Length
- 1,755 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA lariat debranching enzyme, putative; RNA (5'-R(*UP*AP*AP*CP*A)-3')
- UniProt
- C4M1P9
- Ligands
- G46, NI, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RNA lariat debranching enzyme, putative | protein | 349 | 39% helix, 21% strand | C4M1P9 |
| V, W | RNA (5'-R(*UP*AP*AP*CP*A)-3') | rna | 2 | — | — |
| X, Z | RNA (5'-R(*UP*AP*AP*CP*A)-3') | rna | 3 | — | — |
| Y | RNA (5'-R(*UP*AP*AP*CP*A)-3') | rna | 1 | — | — |
| E | RNA lariat debranching enzyme, putative | protein | 348 | 38% helix, 21% strand | C4M1P9 |
Ligands and binding sites
- G46 · Guanosine-5'-monothiophosphate · ligand · 5 copies · chains A, V, B, W, X, D, Y, Z
- NI · Nickel (II) ion · metal · 5 copies · chains A, B, C, X, D, E, Z
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 6 copies · chains A, V, C, D
- PG4 · Tetraethylene glycol · additive · chains 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.77 | 0.80 | 82 | empty |
| 2 | 51 | 0.72 | 0.99 | 16 | empty |
| 3 | 50 | 0.69 | 0.98 | 23 | empty |
| 4 | 591 | 0.67 | 0.77 | 53 | empty |
| 5 | 665 | 0.66 | 0.75 | 71 | SO4 |
Interfaces
11 interfaces between chains.
- B–C · 707 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 650 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 642 Ų buried · 9 hydrogen bonds · protein-protein
- C–X · 468 Ų buried · 14 hydrogen bonds · protein-nucleic
- E–Z · 447 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4PEI · Dbr1 in complex with synthetic branched RNA analog · 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 4PEI · PDBe 4PEI · UniProt C4M1P9
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