MolNFT v1 · #50260 · protein + RNA
Glutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N-(L- glutaminyl)-SULFAMOYL]ADENOSINE
2RD2 · Glutamine tRNA: “Glutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N-(L- glutaminyl)-SULFAMOYL]ADENOSINE”. X-ray diffraction, 2 ligands (QSI, SO4), 7 pockets (best druggability 0.80). MolNFT v1 #50260 on GenesisL1: 3D…
- PDB
- 2RD2
- Type
- protein + RNA
- Length
- 603 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine tRNA; Glutaminyl-tRNA synthetase
- EC
- 6.1.1.18
- UniProt
- P00962
- Ligands
- QSI, SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Glutamine tRNA | rna | 74 | — | — |
| A | Glutaminyl-tRNA synthetase (EC 6.1.1.18) | protein | 529 | 32% helix, 25% strand | P00962 |
Ligands and binding sites
- QSI · 5'-O-[N-(L-glutaminyl)-sulfamoyl]adenosine · ligand · chains B, A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.80 | 0.96 | 25 | empty |
| 2 | 780 | 0.76 | 0.81 | 68 | SO4, QSI |
| 3 | 604 | 0.66 | 0.77 | 36 | empty |
| 4 | 601 | 0.65 | 0.76 | 30 | empty |
| 5 | 178 | 0.63 | 0.84 | 33 | empty |
Interfaces
1 interface between chains.
- B–A · 2643 Ų buried · 61 hydrogen bonds · protein-nucleic
Compared structures
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 P00962
- Elsewhere: RCSB PDB 2RD2 · PDBe 2RD2 · UniProt P00962
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