Research workbench
DBR1 in complex with 7-mer branched RNA
Analyse DBR1 in complex with 7-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
- 5K77
- Type
- protein + RNA
- Length
- 1,765 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA lariat debranching enzyme, putative; Branch 1 of branched RNA 5'-uaa(-2'GU)CA-3'…
- UniProt
- C4M1P9
- Ligands
- ZN, FE2, SO4, OH
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | RNA lariat debranching enzyme, putative | protein | 349 | 36% helix, 22% strand | C4M1P9 |
| V, W, X, Y, Z | Branch 1 of branched RNA 5'-uaa(-2'GU)CA-3' | rna | 3 | — | — |
| v, w, x, y, z | Brnch 2 of branched RNA 5'-uaa(-2'GU)CA-3' | rna | 1 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, v, B, w, C, x, D, y, E, z
- FE2 · Fe (II) ion · metal · 5 copies · chains A, v, B, w, C, x, D, y, E, z
- SO4 · Sulfate ion · ion · 25 copies · chains A, V, B, W, C, X, D, Y, E, Z
- OH · Hydroxide ion · ion · 5 copies · chains A, v, B, w, C, x, D, y, E, z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.78 | 0.81 | 79 | SO4 |
| 2 | 863 | 0.77 | 0.80 | 82 | empty |
| 3 | 51 | 0.73 | 0.99 | 19 | empty |
| 4 | 50 | 0.72 | 0.99 | 19 | empty |
| 5 | 640 | 0.67 | 0.77 | 65 | SO4 |
Interfaces
22 interfaces between chains.
- B–C · 787 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 668 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 647 Ų buried · 12 hydrogen bonds · protein-protein
- B–W · 531 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–X · 530 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 5K77 · Dbr1 in complex with 7-mer branched 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 5K77 · PDBe 5K77 · UniProt C4M1P9
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