MolNFT v1 · #20626 · protein + RNA
Solution structure of the complex formed by the two N-terminal RNA- binding domains of nucleolin and a pre-rRNA target
1RKJ · 5'-R(*GP*GP*AP*UP*GP*CP*CP*UP*CP*CP*CP*GP*AP*GP*UP*GP*CP*AP…: “Solution structure of the complex formed by the two N-terminal RNA- binding domains of nucleolin and a…”. Solution nmr, 4 pockets (best druggability 0.43). MolNFT v1…
- PDB
- 1RKJ
- Type
- protein + RNA
- Length
- 196 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*GP*AP*UP*GP*CP*CP*UP*CP*CP*CP*GP*AP*GP*UP*GP*CP*AP *UP*CP*C)-3'; Nucleolin
- UniProt
- P08199
- Pockets
- 4 · best druggability 0.43
Structure
solution nmr · 2 distinct chains · 23% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-R(*GP*GP*AP*UP*GP*CP*CP*UP*CP*CP*CP*GP*AP*GP*UP*GP*CP*AP *UP*CP*C)-3' | rna | 21 | — | — |
| A | Nucleolin | protein | 175 | 23% helix, 22% strand | P08199 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.43 | 0.76 | 23 | empty |
| 2 | 115 | 0.40 | 0.76 | 17 | empty |
| 3 | 59 | 0.35 | 0.77 | 17 | empty |
| 4 | 58 | 0.29 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 1063 Ų buried · 26 hydrogen bonds · protein-nucleic
Compared structures
- 1RKJ · Solution structure of the complex formed by the two N-terminal RNA-binding domains of… · the same entry in another collection · chain B against B, TM-score 1.00
- P08199 · AlphaFold monomer V2.0 prediction for nucleolin (P08199) · a predicted model of the same protein · chain A against A, TM-score 0.50
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 P08199
- Elsewhere: RCSB PDB 1RKJ · PDBe 1RKJ · UniProt P08199
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