MolNFT v1 · #33783 · protein + RNA
Glutamyl-tRNA synthetase from thermus thermophilus in complex with TRNA(GLU), ATP, and an analog of L-glutamate: a quaternary complex
2CV1: “Glutamyl-tRNA synthetase from thermus thermophilus in complex with TRNA(GLU), ATP, and an analog of…”. X-ray diffraction, 3 ligands (ATP, GAU, MG), 13 pockets (best druggability 0.74). MolNFT v1 #33783 on GenesisL1: 3D structure…
- PDB
- 2CV1
- Type
- protein + RNA
- Length
- 1,086 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA; Glutamyl-tRNA synthetase
- EC
- 6.1.1.17
- UniProt
- P27000
- Ligands
- ATP, GAU, MG
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | TRNA | rna | 75 | — | — |
| A, B | Glutamyl-tRNA synthetase (EC 6.1.1.17) | protein | 468 | 52% helix, 12% strand | P27000 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C, A, D, B
- GAU · (4S)-4-amino-5-hydroxypentanoic acid · ligand · 2 copies · chains C, A, D, B
- MG · Magnesium ion · metal · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.74 | 0.85 | 39 | ATP, GAU |
| 2 | 446 | 0.74 | 0.83 | 42 | GAU, ATP |
| 3 | 1150 | 0.72 | 0.77 | 51 | MG |
| 4 | 240 | 0.72 | 0.87 | 41 | empty |
| 5 | 823 | 0.68 | 0.76 | 43 | empty |
Interfaces
2 interfaces between chains.
- C–A · 2349 Ų buried · 51 hydrogen bonds · protein-nucleic
- D–B · 2338 Ų buried · 57 hydrogen bonds · protein-nucleic
Compared structures
- 2CV1 · Glutamyl-tRNA synthetase from Thermus thermophilus in complex with tRNA(Glu), ATP, and an… · the same entry in another collection · chain D against D, TM-score 1.00
- P27000 · AlphaFold monomer V2.0 prediction for glutamate--tRNA ligase (P27000) · 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 P27000
- Elsewhere: RCSB PDB 2CV1 · PDBe 2CV1 · UniProt P27000
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