Research workbench
As-isolated DBR1 with FE(II) and ZN(II)
Analyse As-isolated DBR1 with FE(II) and ZN(II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K73
- Type
- protein
- Length
- 1,746 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA lariat debranching enzyme, putative
- UniProt
- C4M1P9
- Ligands
- FE2, ZN, SO4, OH
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | RNA lariat debranching enzyme, putative | protein | 349 | 37% helix, 22% strand | C4M1P9 |
| D | RNA lariat debranching enzyme, putative | protein | 350 | 37% helix, 21% strand | C4M1P9 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 5 copies · chains A, B, C, D, E
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D, E
- OH · Hydroxide ion · ion · 5 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.77 | 0.81 | 83 | SO4 |
| 2 | 692 | 0.75 | 0.80 | 66 | empty |
| 3 | 55 | 0.73 | 0.99 | 19 | empty |
| 4 | 54 | 0.73 | 0.99 | 20 | empty |
| 5 | 53 | 0.72 | 0.99 | 18 | empty |
Interfaces
6 interfaces between chains.
- B–C · 812 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 630 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 613 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 371 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 251 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5K73 · as-isolated Dbr1 with Fe(II) and Zn(II) · 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 5K73 · PDBe 5K73 · UniProt C4M1P9
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