Research workbench
Crystal structure of alfalfa mosaic virus RNA 3'UTR in complex with coat protein N terminal peptide
Analyse Crystal structure of alfalfa mosaic virus RNA 3'UTR in complex with coat… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XOK
- Type
- protein + RNA
- Length
- 69 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alfalfa mosaic virus RNA 3' utr; Coat protein
- UniProt
- P24264
- Ligands
- BR
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alfalfa mosaic virus RNA 3' utr | rna | 27 | — | — |
| B | Alfalfa mosaic virus RNA 3' utr | rna | 9 | — | — |
| C | Coat protein | protein | 15 | 67% helix, 0% strand | P24264 |
| D | Coat protein | protein | 18 | 50% helix, 0% strand | P24264 |
Ligands and binding sites
- BR · Bromide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.52 | 0.75 | 22 | empty |
| 2 | 212 | 0.46 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–D · 493 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 415 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 298 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- B–D · 209 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 66 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1XOK · crystal structure of alfalfa mosaic virus RNA 3'UTR in complex with coat protein N… · the same entry in another collection · chain A against A, TM-score 1.00
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 P24264
- Elsewhere: RCSB PDB 1XOK · PDBe 1XOK · UniProt P24264
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