Research workbench
Crystal structure of the pumilio-nos-cyclinb RNA complex
Analyse Crystal structure of the pumilio-nos-cyclinb RNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KL8
- Type
- protein + RNA
- Length
- 389 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maternal protein pumilio; Protein nanos; RNA (5'-R(*UP*AP*UP*UP*UP*GP*UP*AP*AP*UP*U)-3')
- UniProt
- P25822, P25724
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maternal protein pumilio | protein | 309 | 68% helix, 0% strand | P25822 |
| B | Protein nanos | protein | 69 | 35% helix, 3% strand | P25724 |
| C | RNA (5'-R(*UP*AP*UP*UP*UP*GP*UP*AP*AP*UP*U)-3') | rna | 11 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.80 | 0.95 | 27 | empty |
| 2 | 119 | 0.73 | 0.93 | 21 | empty |
| 3 | 204 | 0.69 | 0.86 | 25 | empty |
| 4 | 225 | 0.61 | 0.81 | 30 | empty |
| 5 | 99 | 0.33 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1321 Ų buried · 43 hydrogen bonds · protein-nucleic
- A–B · 688 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 548 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 5KL8 · Crystal structure of the Pumilio-Nos-CyclinB RNA complex · the same entry in another collection · chain A against A, TM-score 1.00
- P25822 · AlphaFold monomer V2.0 prediction for maternal protein pumilio (P25822) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P25724 · AlphaFold monomer V2.0 prediction for protein nanos (P25724) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P25822
- Every structure of UniProt P25724
- Elsewhere: RCSB PDB 5KL8 · PDBe 5KL8 · UniProt P25822 · UniProt P25724
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.