Research workbench
Crystal structure of glu-TRNA(GLN) amidotransferase in the complex with TRNA(GLN)
Analyse Crystal structure of glu-TRNA(GLN) amidotransferase in the complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D6F
- Type
- protein + RNA
- Length
- 2,001 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA; Glutamyl-TRNA(GLN) amidotransferase subunit D; Glutamyl-TRNA(GLN) amidotransferase…
- EC
- 6.3.5.-
- UniProt
- O26802, O26803
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | TRNA | rna | 72 | — | — |
| F | TRNA | rna | 74 | — | — |
| A | Glutamyl-TRNA(GLN) amidotransferase subunit D (EC 6.3.5.-) | protein | 424 | 27% helix, 22% strand | O26802 |
| B | Glutamyl-TRNA(GLN) amidotransferase subunit D (EC 6.3.5.-) | protein | 424 | 28% helix, 21% strand | O26802 |
| C | Glutamyl-TRNA(GLN) amidotransferase subunit E (EC 6.3.5.-) | protein | 485 | 32% helix, 27% strand | O26803 |
| D | Glutamyl-TRNA(GLN) amidotransferase subunit E (EC 6.3.5.-) | protein | 522 | 33% helix, 24% strand | O26803 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.77 | 0.81 | 91 | empty |
| 2 | 802 | 0.77 | 0.81 | 74 | empty |
| 3 | 755 | 0.74 | 0.79 | 80 | empty |
| 4 | 437 | 0.71 | 0.82 | 47 | empty |
| 5 | 178 | 0.71 | 0.89 | 33 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2835 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 1976 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 1883 Ų buried · 33 hydrogen bonds · protein-protein
- F–D · 1122 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–C · 679 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 2D6F · Crystal structure of Glu-tRNA(Gln) amidotransferase in the complex with tRNA(Gln) · the same entry in another collection · chain D against D, TM-score 1.00
- O26802 · AlphaFold monomer V2.0 prediction for glutamyl-TRNA(GLN) amidotransferase subunit D… · a predicted model of the same protein · chain B against A, TM-score 0.99
- O26803 · AlphaFold monomer V2.0 prediction for glutamyl-TRNA(GLN) amidotransferase subunit E… · a predicted model of the same protein · chain D against A, TM-score 0.94
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 O26802
- Every structure of UniProt O26803
- Elsewhere: RCSB PDB 2D6F · PDBe 2D6F · UniProt O26802 · UniProt O26803
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.