Research workbench
Crystal structure of human mitochondrial phers complexed with trnaphe in the active open state
Analyse Crystal structure of human mitochondrial phers complexed with trnaphe in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TUP
- Type
- protein + RNA
- Length
- 478 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanyl-tRNA synthetase, mitochondrial; Thermus thermophilus trnaphe
- EC
- 6.1.1.20
- UniProt
- O95363
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanyl-tRNA synthetase, mitochondrial (EC 6.1.1.20) | protein | 404 | 29% helix, 24% strand | O95363 |
| T | Thermus thermophilus trnaphe | rna | 74 | — | — |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.72 | 0.77 | 51 | empty |
| 2 | 428 | 0.66 | 0.79 | 48 | empty |
| 3 | 435 | 0.60 | 0.77 | 29 | empty |
| 4 | 160 | 0.45 | 0.75 | 28 | empty |
| 5 | 134 | 0.44 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–T · 1227 Ų buried · 28 hydrogen bonds · protein-nucleic
Compared structures
- 3TUP · Crystal structure of human mitochondrial PheRS complexed with tRNAPhe in the active open… · the same entry in another collection · chain A against A, TM-score 1.00
- O95363 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase, mitochondrial (O95363) · a predicted model of the same protein · chain A against A, TM-score 0.76
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 O95363
- Elsewhere: RCSB PDB 3TUP · PDBe 3TUP · UniProt O95363
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