Research workbench
Crystal structure of peptidyl-tRNA hydrolase from escherichia COLI in complex with the cca-acceptor-T[PSI]C domain of tRNA
Analyse Crystal structure of peptidyl-tRNA hydrolase from escherichia COLI in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VJR
- Type
- protein + RNA
- Length
- 458 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-tRNA hydrolase; TRNA cca-acceptor
- EC
- 3.1.1.29
- UniProt
- P0A7D1
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 193 | 44% helix, 21% strand | P0A7D1 |
| B, D | TRNA cca-acceptor | rna | 36 | — | — |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.76 | 0.83 | 49 | empty |
| 2 | 373 | 0.70 | 0.83 | 26 | empty |
| 3 | 244 | 0.66 | 0.84 | 36 | empty |
| 4 | 278 | 0.63 | 0.81 | 39 | empty |
| 5 | 55 | 0.26 | 0.73 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 706 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 695 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–D · 566 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- A–D · 38 Ų buried · 1 hydrogen bond · protein-nucleic
- B–C · 36 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 3VJR · Crystal structure of Peptidyl-tRNA hydrolase from Escherichia coli in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A7D1 · AlphaFold monomer V2.0 prediction for peptidyl-tRNA hydrolase (P0A7D1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0A7D1
- Elsewhere: RCSB PDB 3VJR · PDBe 3VJR · UniProt P0A7D1
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