Research workbench
As grown, untreated co-crystals of the ternary complex containing a T- box stem I RNA, its cognate trnagly, and B. subtilis ybxf protein
Analyse As grown, untreated co-crystals of the ternary complex containing a T- box stem… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TZP
- Type
- protein + RNA
- Length
- 511 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome-associated protein L7AE-like; Engineered tRNA; Glyq T-box stem I
- UniProt
- P46350
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ribosome-associated protein L7AE-like | protein | 81 | 42% helix, 20% strand | P46350 |
| B | Engineered tRNA | rna | 70 | — | — |
| C, F | Glyq T-box stem I | rna | 102 | — | — |
| E | Engineered tRNA | rna | 75 | — | — |
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.75 | 0.80 | 63 | empty |
| 2 | 935 | 0.70 | 0.76 | 56 | empty |
| 3 | 762 | 0.68 | 0.76 | 30 | empty |
| 4 | 728 | 0.67 | 0.76 | 33 | empty |
| 5 | 610 | 0.65 | 0.76 | 36 | empty |
Interfaces
4 interfaces between chains.
- B–C · 560 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- D–F · 552 Ų buried · 34 hydrogen bonds · protein-nucleic
- E–F · 383 Ų buried · 13 hydrogen bonds · nucleic-nucleic
- A–C · 357 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4TZP · As Grown, Untreated Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its… · the same entry in another collection · chain C against C, 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 4TZP · PDBe 4TZP · UniProt P46350
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