Research workbench
DBR1 in complex with 16-mer branched RNA
Analyse DBR1 in complex with 16-mer branched RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K78
- Type
- protein + RNA
- Length
- 1,759 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA lariat debranching enzyme, putative; Branch 1 of branched RNA…
- UniProt
- C4M1P9
- Ligands
- FE2, ZN, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA lariat debranching enzyme, putative | protein | 347 | 37% helix, 21% strand | C4M1P9 |
| B | RNA lariat debranching enzyme, putative | protein | 351 | 36% helix, 21% strand | C4M1P9 |
| C, D, E | RNA lariat debranching enzyme, putative | protein | 349 | 38% helix, 21% strand | C4M1P9 |
| X | Branch 1 of branched RNA 5'-UACUAA(2'-GUAUGU)CAAGU-3' | rna | 3 | — | — |
| x | Branch 2 of branched RNA 5'-UACUAA(2'-GUAUGU)CAAGU-3' | rna | 5 | — | — |
| Y | Branch 1 of branched RNA 5'-UACUAA(2'-GUAUGU)CAAGU-3' | rna | 2 | — | — |
| y | Branch 2 of branched RNA 5'-UACUAA(2'-GUAUGU)CAAGU-3' | rna | 4 | — | — |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 5 copies · chains A, B, C, x, D, y, E
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, x, D, y, E
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, X, D, E
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 | 1108 | 0.82 | 0.83 | 108 | SO4 |
| 2 | 57 | 0.73 | 0.99 | 20 | empty |
| 3 | 54 | 0.73 | 1.00 | 16 | empty |
| 4 | 57 | 0.73 | 0.99 | 18 | empty |
| 5 | 56 | 0.73 | 0.99 | 18 | empty |
Interfaces
11 interfaces between chains.
- B–C · 672 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 665 Ų buried · 12 hydrogen bonds · protein-protein
- C–x · 644 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 637 Ų buried · 12 hydrogen bonds · protein-protein
- C–X · 542 Ų buried · 7 hydrogen bonds · protein-nucleic
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 5K78 · PDBe 5K78 · UniProt C4M1P9
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