MolNFT v1 · #191467 · protein + RNA
DBR1 in complex with 5-mer cleavage product
8DZK · RNA lariat debranching enzyme, putative: “DBR1 in complex with 5-mer cleavage product”. X-ray diffraction, 3 ligands (FE2, ZN, SO4), 20 pockets (best druggability 0.77). MolNFT v1 #191467 on GenesisL1: 3D structure, binding sites…
- PDB
- 8DZK
- 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(P*(G46)P*UP*GP*UP*U)-3')
- UniProt
- C4M1P9
- Ligands
- FE2, ZN, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | RNA lariat debranching enzyme, putative | protein | 349 | 37% helix, 21% strand | C4M1P9 |
| F, N | RNA (5'-R(P*(G46)P*UP*GP*UP*U)-3') | rna | 4 | — | — |
| G, O, P | RNA (5'-R(P*(G46)P*UP*GP*UP*U)-3') | rna | 3 | — | — |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 5 copies · chains A, F, B, G, C, N, D, O, E, P
- ZN · Zinc ion · metal · 5 copies · chains A, F, B, G, C, N, D, O, E, P
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.77 | 0.81 | 81 | SO4 |
| 2 | 1110 | 0.74 | 0.77 | 89 | SO4 |
| 3 | 54 | 0.73 | 1.00 | 19 | empty |
| 4 | 618 | 0.68 | 0.77 | 80 | SO4 |
| 5 | 231 | 0.63 | 0.82 | 24 | empty |
Interfaces
11 interfaces between chains.
- B–C · 804 Ų buried · 10 hydrogen bonds · protein-protein
- C–N · 636 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–F · 631 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–E · 630 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 588 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (nucleotide modification).
Compared structures
- 8DZK · Dbr1 in complex with 5-mer cleavage product · 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 8DZK · PDBe 8DZK · UniProt C4M1P9
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