Research workbench
The LIN28B cold shock domain in complex with hexauridine
Analyse The LIN28B cold shock domain in complex with hexauridine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ALP
- Type
- protein + RNA
- Length
- 349 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LIN28 isoform B; Hexa uridine
- UniProt
- B4F6I0
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LIN28 isoform B | protein | 87 | 7% helix, 57% strand | B4F6I0 |
| B, C | LIN28 isoform B | protein | 86 | 7% helix, 58% strand | B4F6I0 |
| D | LIN28 isoform B | protein | 84 | 7% helix, 60% strand | B4F6I0 |
| E | Hexa uridine | rna | 6 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.60 | 0.75 | 45 | empty |
| 2 | 125 | 0.55 | 0.83 | 32 | empty |
| 3 | 68 | 0.28 | 0.73 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 512 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 365 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 199 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–E · 173 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–D · 72 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ALP · The Lin28b Cold shock domain in complex with hexauridine · 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 B4F6I0
- Elsewhere: RCSB PDB 4ALP · PDBe 4ALP · UniProt B4F6I0
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