MolNFT v1 · #124640 · protein + RNA
Crystal structure of the pumilio-nos-hunchback RNA complex
5KL1 · Maternal protein pumilio: “Crystal structure of the pumilio-nos-hunchback RNA complex”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.79). MolNFT v1 #124640 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5KL1
- Type
- protein + RNA
- Length
- 410 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maternal protein pumilio; Protein nanos; RNA (5'-R(*AP*AP*AP*UP*UP*GP*UP*AP*CP*AP*UP*A)-3'…
- UniProt
- P25822, P25724
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maternal protein pumilio | protein | 328 | 66% helix, 0% strand | P25822 |
| B | Protein nanos | protein | 70 | 31% helix, 3% strand | P25724 |
| C | RNA (5'-R(*AP*AP*AP*UP*UP*GP*UP*AP*CP*AP*UP*A)-3') | rna | 12 | — | — |
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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.79 | 0.95 | 25 | empty |
| 2 | 87 | 0.70 | 0.94 | 18 | empty |
| 3 | 136 | 0.67 | 0.88 | 23 | empty |
| 4 | 69 | 0.29 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1432 Ų buried · 40 hydrogen bonds · protein-nucleic
- A–B · 648 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 545 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 5KL1 · Crystal structure of the Pumilio-Nos-hunchback 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 0.98
- P25724 · AlphaFold monomer V2.0 prediction for protein nanos (P25724) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 5KL1 · PDBe 5KL1 · UniProt P25822 · UniProt P25724
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