MolNFT v1 · #107102 · protein + RNA
Co-crystals of the ternary complex containing a T-box stem I RNA, its cognate trnagly, and B. subtilis ybxf protein, treated by removing lithium sulfate and replacing MG2+ with SR2+ post crystallization
4TZW · Ribosome-associated protein L7AE-like: “Co-crystals of the ternary complex containing a T-box stem I RNA, its cognate trnagly, and B. subtilis ybxf…”. X-ray diffraction, 1 ligand (SR), 7 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 4TZW
- Type
- protein + RNA
- Length
- 258 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome-associated protein L7AE-like; Engineered tRNA; T-box stem I
- UniProt
- P46350
- Ligands
- SR
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosome-associated protein L7AE-like | protein | 81 | 41% helix, 20% strand | P46350 |
| B | Engineered tRNA | rna | 75 | — | — |
| C | T-box stem I | rna | 102 | — | — |
Ligands and binding sites
- SR · Strontium ion · metal · 36 copies · chains B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.70 | 0.76 | 60 | SR |
| 2 | 669 | 0.64 | 0.75 | 31 | SR |
| 3 | 237 | 0.62 | 0.82 | 24 | empty |
| 4 | 385 | 0.57 | 0.76 | 23 | SR |
| 5 | 344 | 0.53 | 0.75 | 21 | SR |
Interfaces
2 interfaces between chains.
- B–C · 574 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- A–C · 433 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 4TZW · Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly… · the same entry in another collection · chain B against B, 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 0.96
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 4TZW · PDBe 4TZW · UniProt P46350
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