Research workbench
Crystal structure of Weissella viridescens FemXVv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate
Analyse Crystal structure of Weissella viridescens FemXVv non-ribosomal amino acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4II9
- Type
- protein + RNA
- Length
- 345 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.66
- Source
- Weissella viridescens; SYNTHETIC CONSTRUCT
- Molecule
- FemX; 5-mer peptide; RNA (5'-R(P*CP*CP*(A9Z))-3')
- EC
- 2.3.2.10
- UniProt
- Q9EY50
- Ligands
- UDP, MUB
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · resolution 1.66 · 3 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FemX (EC 2.3.2.10) | protein | 337 | 38% helix, 27% strand | Q9EY50 |
| B | 5-mer peptide | protein | 5 | 0% helix, 0% strand | — |
| C | RNA (5'-R(P*CP*CP*(A9Z))-3') | rna | 3 | — | — |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A, B
- MUB · N-acetyl-alpha-muramic acid · sugar · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.56 | 0.83 | 24 | empty |
| 2 | 200 | 0.52 | 0.77 | 40 | UDP, MUB |
| 3 | 50 | 0.43 | 0.84 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 555 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 403 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 99 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 d-amino, 2 modified, 1 glycan (D-amino acid, glycosylation, nonstandard, nucleotide modification).
Compared structures
- 4II9 · Crystal structure of weissella viridescens femxvv non-ribosomal amino acid transferase in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9EY50 · AlphaFold monomer V2.0 prediction for udp-N- acetylmuramoylpentapeptide-lysine… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9EY50
- Elsewhere: RCSB PDB 4II9 · PDBe 4II9 · UniProt Q9EY50
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.