Research workbench
Structural analysis of a probable eukaryotic D-amino acid tRNA deacylase
Analyse Structural analysis of a probable eukaryotic D-amino acid tRNA deacylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TC5
- Type
- protein
- Length
- 746 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA
- UniProt
- P84066
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA | protein | 187 | 20% helix, 30% strand | P84066 |
| C, D | Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA | protein | 186 | 19% helix, 30% strand | P84066 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.75 | 0.78 | 88 | empty |
| 2 | 291 | 0.54 | 0.76 | 42 | empty |
| 3 | 198 | 0.53 | 0.78 | 29 | empty |
| 4 | 207 | 0.52 | 0.77 | 29 | empty |
| 5 | 146 | 0.44 | 0.75 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1409 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 260 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 193 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 69 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1TC5 · Structural Analysis of a probable eukaryotic D-amino acid tRNA deacylase · the same entry in another collection · chain D against D, TM-score 1.00
- P84066 · AlphaFold monomer V2.0 prediction for putative D-tyrosyl-TRNA(TYR) deacylase 2 (P84066) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P84066
- Elsewhere: RCSB PDB 1TC5 · PDBe 1TC5 · UniProt P84066
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