MolNFT v1 · #17281 · protein + RNA
Crystal structure of nf-KB(P50)2 complexed to a high- affinity RNA aptamer
1OOA: “Crystal structure of nf-KB(P50)2 complexed to a high- affinity RNA aptamer”. X-ray diffraction, 6 pockets (best druggability 0.70). MolNFT v1 #17281 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1OOA
- Type
- protein + RNA
- Length
- 684 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA aptamer; Nuclear factor nf-kappa-B P105 subunit
- UniProt
- P25799
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | RNA aptamer | rna | 29 | — | — |
| A, B | Nuclear factor nf-kappa-B P105 subunit | protein | 313 | 15% helix, 36% strand | P25799 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.70 | 0.80 | 71 | empty |
| 2 | 595 | 0.66 | 0.77 | 50 | empty |
| 3 | 194 | 0.65 | 0.84 | 34 | empty |
| 4 | 106 | 0.50 | 0.81 | 26 | empty |
| 5 | 81 | 0.40 | 0.79 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–A · 996 Ų buried · 24 hydrogen bonds · protein-nucleic
- D–B · 901 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 779 Ų buried · 13 hydrogen bonds · protein-protein
- D–A · 73 Ų buried · 0 hydrogen bonds · protein-nucleic
- C–B · 60 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 1OOA · CRYSTAL STRUCTURE OF NF-kB(p50)2 COMPLEXED TO A HIGH-AFFINITY RNA APTAMER · the same entry in another collection · chain C against C, TM-score 1.00
- P25799 · AlphaFold monomer V2.0 prediction for nuclear factor nf-kappa-B P105 subunit (P25799) · a predicted model of the same protein · chain A against A, TM-score 0.72
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 P25799
- Elsewhere: RCSB PDB 1OOA · PDBe 1OOA · UniProt P25799
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