Research workbench
The LIN28B cold shock domain in complex with heptathymidine
Analyse The LIN28B cold shock domain in complex with heptathymidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A76
- Type
- protein + DNA
- Length
- 368 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*TP)-3'
- UniProt
- B4F6I0
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LIN28 cold shock domain | protein | 86 | 7% helix, 58% strand | B4F6I0 |
| B, D | 5'-D(*TP*TP*TP*TP*TP*TP*TP)-3' | dna | 7 | — | — |
| C | LIN28 cold shock domain | protein | 85 | 7% helix, 59% strand | B4F6I0 |
| E | LIN28 cold shock domain | protein | 87 | 7% helix, 54% strand | B4F6I0 |
| F, H | 5'-D(*TP*TP*TP*TP*TP*TP*TP)-3' | dna | 4 | — | — |
| G | LIN28 cold shock domain | protein | 88 | 7% helix, 55% strand | B4F6I0 |
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 | 1166 | 0.77 | 0.79 | 96 | empty |
| 2 | 187 | 0.57 | 0.81 | 33 | empty |
| 3 | 201 | 0.49 | 0.76 | 24 | empty |
Interfaces
17 interfaces between chains.
- C–D · 864 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 858 Ų buried · 15 hydrogen bonds · protein-nucleic
- G–H · 550 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–F · 540 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–G · 359 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4A76 · The Lin28b Cold shock domain in complex with heptathymidine · 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 4A76 · PDBe 4A76 · UniProt B4F6I0
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