MolNFT v1 · #102368 · protein
Crystal structure of a C-terminally truncated cyt-18 protein including N-terminal residues
4OJM · Tyrosine--tRNA ligase, mitochondrial: “Crystal structure of a C-terminally truncated cyt-18 protein including N-terminal residues”. X-ray diffraction, 1 ligand (TYR), 7 pockets (best druggability 0.69). MolNFT v1 #102368 on…
- PDB
- 4OJM
- Type
- protein
- Length
- 382 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine--tRNA ligase, mitochondrial
- EC
- 6.1.1.1
- UniProt
- P12063
- Ligands
- TYR
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Tyrosine--tRNA ligase, mitochondrial (EC 6.1.1.1) | protein | 382 | 58% helix, 9% strand | P12063 |
Ligands and binding sites
- TYR · Tyrosine · ligand · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.69 | 0.80 | 29 | empty |
| 2 | 370 | 0.67 | 0.80 | 36 | TYR |
| 3 | 80 | 0.55 | 0.86 | 20 | empty |
| 4 | 148 | 0.47 | 0.76 | 22 | empty |
| 5 | 68 | 0.32 | 0.75 | 15 | empty |
Compared structures
- 4OJM · Crystal structure of a C-terminally truncated CYT-18 protein including N-terminal residues · the same entry in another collection · chain X against X, TM-score 1.00
- P12063 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase, mitochondrial (P12063) · a predicted model of the same protein · chain X 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 P12063
- Elsewhere: RCSB PDB 4OJM · PDBe 4OJM · UniProt P12063
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