Research workbench
The LIN28B cold shock domain in complex with hexathymidine.
Analyse The LIN28B cold shock domain in complex with hexathymidine. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A75
- Type
- protein + DNA
- Length
- 372 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LIN28 cold shock domain; 5'-D(*TP*TP*TP*TP*TP*TP)-3'
- UniProt
- B4F6I0
- Ligands
- SCN
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LIN28 cold shock domain | protein | 89 | 7% helix, 56% strand | B4F6I0 |
| B, F | 5'-D(*TP*TP*TP*TP*TP*TP)-3' | dna | 4 | — | — |
| C | LIN28 cold shock domain | protein | 87 | 7% helix, 57% strand | B4F6I0 |
| D, H | 5'-D(*TP*TP*TP*TP*TP*TP)-3' | dna | 6 | — | — |
| E, G | LIN28 cold shock domain | protein | 88 | 7% helix, 57% strand | B4F6I0 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.74 | 0.77 | 120 | empty |
| 2 | 72 | 0.31 | 0.74 | 21 | empty |
Interfaces
10 interfaces between chains.
- G–H · 813 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 800 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–G · 641 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 606 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 552 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 4A75 · The Lin28b Cold shock domain in complex with hexathymidine. · 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 4A75 · PDBe 4A75 · UniProt B4F6I0
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