Research workbench
Crystal structure of MBNL1 tandem zinc finger 3 and 4 domain in complex with cgcugu RNA
Analyse Crystal structure of MBNL1 tandem zinc finger 3 and 4 domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D2S
- Type
- protein + RNA
- Length
- 286 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Muscleblind-like protein 1; 5'-R(*CP*GP*CP*UP*GP*U)-3'
- UniProt
- Q9NR56
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Muscleblind-like protein 1 | protein | 67 | 21% helix, 18% strand | Q9NR56 |
| B, D | Muscleblind-like protein 1 | protein | 68 | 19% helix, 16% strand | Q9NR56 |
| E, G | 5'-R(*CP*GP*CP*UP*GP*U)-3' | rna | 5 | — | — |
| F, H | 5'-R(*CP*GP*CP*UP*GP*U)-3' | rna | 3 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, E, B, F, C, G, D, H
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 | 706 | 0.72 | 0.78 | 76 | empty |
| 2 | 140 | 0.42 | 0.75 | 20 | empty |
Interfaces
9 interfaces between chains.
- C–D · 774 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 740 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 457 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 295 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–H · 292 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 3D2S · Crystal structure of MBNL1 tandem zinc finger 3 and 4 domain in complex with CGCUGU RNA · the same entry in another collection · chain H against H, TM-score 1.00
- Q9NR56 · AlphaFold monomer V2.0 prediction for muscleblind-like protein 1 (Q9NR56) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 Q9NR56
- Elsewhere: RCSB PDB 3D2S · PDBe 3D2S · UniProt Q9NR56
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