MolNFT v1 · #105562 · protein + RNA
High resolution structure of a mirror-image RNA oligonucleotide aptamer in complex with the chemokine CCL2
4R8I · C-C motif chemokine 2: “High resolution structure of a mirror-image RNA oligonucleotide aptamer in complex with the chemokine CCL2”. X-ray diffraction, 3 ligands (K, NA, SR), 2 pockets (best druggability 0.45). MolNFT v1 #105562 on…
- PDB
- 4R8I
- Type
- protein + RNA
- Length
- 108 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-C motif chemokine 2; Mirror-image RNA oligonucleotide aptamer NOXE36
- UniProt
- P13500
- Ligands
- K, NA, SR
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-C motif chemokine 2 | protein | 68 | 22% helix, 25% strand | P13500 |
| B | Mirror-image RNA oligonucleotide aptamer NOXE36 | rna | 40 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains B
- NA · Sodium ion · metal · chains B
- SR · Strontium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 139 | 0.45 | 0.78 | 15 | NA, K |
| 2 | 87 | 0.32 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 741 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 40 modified, 2 disulfide (nucleotide modification, disulfide).
Compared structures
- 4R8I · High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in Complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P13500 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 2 (P13500) · a predicted model of the same protein · chain A 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 P13500
- Elsewhere: RCSB PDB 4R8I · PDBe 4R8I · UniProt P13500
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