MolNFT v1 · #81935 · protein + RNA
Crystal structure of ybxf bound to the SAM-I riboswitch aptamer
3V7E · Ribosome-associated protein L7AE-like: “Crystal structure of ybxf bound to the SAM-I riboswitch aptamer”. X-ray diffraction, 3 ligands (NCO, SAM, MG), 12 pockets (best druggability 0.79). MolNFT v1 #81935 on GenesisL1: 3D structure…
- PDB
- 3V7E
- Type
- protein + RNA
- Length
- 410 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome-associated protein L7AE-like; SAM-I riboswitch aptamer with an engineered helix…
- UniProt
- P46350
- Ligands
- NCO, SAM, MG
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosome-associated protein L7AE-like | protein | 81 | 44% helix, 25% strand | P46350 |
| B | Ribosome-associated protein L7AE-like | protein | 77 | 25% helix, 8% strand | P46350 |
| C, D | SAM-I riboswitch aptamer with an engineered helix P3 | rna | 126 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 18 copies · chains C, D
- SAM · S-adenosylmethionine · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 22 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.79 | 0.82 | 55 | NCO, SAM, MG |
| 2 | 901 | 0.78 | 0.82 | 56 | NCO, SAM, MG |
| 3 | 746 | 0.68 | 0.77 | 49 | NCO |
| 4 | 742 | 0.63 | 0.74 | 33 | NCO |
| 5 | 304 | 0.59 | 0.79 | 36 | NCO |
Interfaces
5 interfaces between chains.
- A–C · 437 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 384 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–D · 167 Ų buried · 1 hydrogen bond · nucleic-nucleic
- B–C · 77 Ų buried · 0 hydrogen bonds · protein-nucleic
- A–D · 72 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 3V7E · Crystal structure of YbxF bound to the SAM-I riboswitch aptamer · the same entry in another collection · chain A against A, TM-score 1.00
- P46350 · AlphaFold monomer V2.0 prediction for ribosome-associated protein L7AE-like (P46350) · 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 P46350
- Elsewhere: RCSB PDB 3V7E · PDBe 3V7E · UniProt P46350
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