Research workbench
Crystal structure of the pumilio-homology domain from human PUMILIO1 in complex with NRE1-19 RNA
Analyse Crystal structure of the pumilio-homology domain from human PUMILIO1 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M8W
- Type
- protein + RNA
- Length
- 711 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(P*UP*UP*GP*UP*AP*UP*AP*U)-3'; 5'-R(P*UP*GP*UP*AP*UP*AP*U)-3'…
- UniProt
- Q14671
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 6 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-R(P*UP*UP*GP*UP*AP*UP*AP*U)-3' | rna | 8 | — | — |
| D | 5'-R(P*UP*GP*UP*AP*UP*AP*U)-3' | rna | 7 | — | — |
| E | 5'-R(P*UP*UP*GP*UP*CP*CP*AP*G)-3' | rna | 8 | — | — |
| F | 5'-R(P*UP*GP*UP*CP*CP*AP*G)-3' | rna | 7 | — | — |
| A | Pumilio 1 | protein | 340 | 73% helix, 1% strand | Q14671 |
| B | Pumilio 1 | protein | 341 | 71% helix, 1% strand | Q14671 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.49 | 0.76 | 33 | empty |
| 2 | 190 | 0.47 | 0.75 | 27 | empty |
Interfaces
7 interfaces between chains.
- C–E · 1293 Ų buried · 327 hydrogen bonds · nucleic-nucleic
- D–F · 1150 Ų buried · 278 hydrogen bonds · nucleic-nucleic
- D–B · 1108 Ų buried · 34 hydrogen bonds · protein-nucleic
- C–A · 1085 Ų buried · 33 hydrogen bonds · protein-nucleic
- F–B · 1077 Ų buried · 28 hydrogen bonds · protein-nucleic
Compared structures
- 1M8W · Crystal structure of the pumilio-homology domain from human PUMILIO1 in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- Q14671 · AlphaFold monomer V2.0 prediction for pumilio homolog 1 (Q14671) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q14671
- Elsewhere: RCSB PDB 1M8W · PDBe 1M8W · UniProt Q14671
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