Research workbench
apo Dbr1
Analyse apo Dbr1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K71
- Type
- protein
- Length
- 1,745 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.57
- Source
- Entamoeba histolytica
- Molecule
- RNA lariat debranching enzyme, putative
- UniProt
- C4M1P9
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.57 · 1 distinct chain · 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 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 16 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 | 930 | 0.78 | 0.80 | 95 | SO4 |
| 2 | 1076 | 0.75 | 0.77 | 79 | empty |
| 3 | 51 | 0.72 | 0.99 | 20 | empty |
| 4 | 50 | 0.71 | 0.99 | 20 | empty |
| 5 | 64 | 0.71 | 0.97 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–C · 821 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 700 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 630 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 342 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 205 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5K71 · APO DBR1 · 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 5K71 · PDBe 5K71 · UniProt C4M1P9
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