MolNFT v1 · #141171 · protein
Crystal structures of E.COLI arginyl-tRNA synthetase (argrs) in complex with substrate arg
5YYM · Arginine--tRNA ligase: “Crystal structures of E.COLI arginyl-tRNA synthetase (argrs) in complex with substrate arg”. X-ray diffraction, 1 ligand (ARG), 19 pockets (best druggability 0.76). MolNFT v1 #141171 on GenesisL1: 3D…
- PDB
- 5YYM
- Type
- protein
- Length
- 1,154 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine--tRNA ligase
- EC
- 6.1.1.19
- UniProt
- P11875
- Ligands
- ARG
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine--tRNA ligase (EC 6.1.1.19) | protein | 581 | 54% helix, 12% strand | P11875 |
| B | Arginine--tRNA ligase (EC 6.1.1.19) | protein | 573 | 53% helix, 12% strand | P11875 |
Ligands and binding sites
- ARG · Arginine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.76 | 0.97 | 24 | empty |
| 2 | 428 | 0.67 | 0.80 | 45 | empty |
| 3 | 394 | 0.64 | 0.78 | 49 | ARG |
| 4 | 355 | 0.64 | 0.79 | 41 | empty |
| 5 | 409 | 0.62 | 0.77 | 50 | ARG |
Interfaces
1 interface between chains.
- A–B · 1127 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5YYM · Crystal structures of E.coli arginyl-trna synthetase (argrs) in complex with substrate Arg · the same entry in another collection · chain B against B, TM-score 1.00
- P11875 · AlphaFold monomer V2.0 prediction for arginine--tRNA ligase (P11875) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P11875
- Elsewhere: RCSB PDB 5YYM · PDBe 5YYM · UniProt P11875
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