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Cocrystal structure of a tyrosyl-tRNA synthetase splicing factor with a group I intron RNA
Analyse Cocrystal structure of a tyrosyl-tRNA synthetase splicing factor with a group I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RKJ
- Type
- protein + RNA
- Length
- 3,904 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (238-mer); RNA (5'-R(P*GP*CP*UP*U)-3'); Tyrosyl-tRNA synthetase
- EC
- 6.1.1.1
- UniProt
- P12063
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, G, K, O | RNA (238-mer) | rna | 238 | — | — |
| D, H, L, P | RNA (5'-R(P*GP*CP*UP*U)-3') | rna | 4 | — | — |
| A, B, E, F, I, J, M, N | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 367 | 58% helix, 10% strand | P12063 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.77 | 0.87 | 37 | empty |
| 2 | 75 | 0.76 | 0.98 | 22 | empty |
| 3 | 371 | 0.76 | 0.87 | 40 | empty |
| 4 | 67 | 0.75 | 0.98 | 19 | empty |
| 5 | 279 | 0.74 | 0.88 | 30 | empty |
Interfaces
20 interfaces between chains.
- I–J · 1507 Ų buried · 16 hydrogen bonds · protein-protein
- M–N · 1507 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1506 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1504 Ų buried · 16 hydrogen bonds · protein-protein
- G–F · 1219 Ų buried · 25 hydrogen bonds · protein-nucleic
Compared structures
- 2RKJ · Cocrystal structure of a tyrosyl-tRNA synthetase splicing factor with a group I intron RNA · the same entry in another collection · chain M against M, TM-score 1.00
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 P12063
- Elsewhere: RCSB PDB 2RKJ · PDBe 2RKJ · UniProt P12063
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