Research workbench
Crystal structure of the glutamine transamidosome from thermotoga maritima in the glutamylation state.
Analyse Crystal structure of the glutamine transamidosome from thermotoga maritima in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AL0
- Type
- protein + RNA
- Length
- 1,592 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamyl-TRNA(GLN) amidotransferase subunit a; ASPARTYL/GLUTAMYL-TRNA(ASN/GLN)…
- EC
- 6.3.5.7, 6.3.5.-, 6.1.1.17
- UniProt
- Q9X0Z9, Q9X100, Q9WY94, Q9X2I8
- Ligands
- GSU, ZN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamyl-TRNA(GLN) amidotransferase subunit a (EC 6.3.5.7) | protein | 472 | 33% helix, 9% strand | Q9X0Z9 |
| B | ASPARTYL/GLUTAMYL-TRNA(ASN/GLN) amidotransferase subunit B (EC 6.3.5.-) | protein | 482 | 34% helix, 15% strand | Q9X100 |
| C | Glutamyl-TRNA(GLN) amidotransferase subunit C,LINKER, glutamate--tRNA ligase 2 (EC 6.3.5.-, 6.1.1.17) | protein | 564 | 38% helix, 10% strand | Q9WY94, Q9X2I8 |
| E | Trnagln | rna | 74 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.80 | 0.90 | 38 | GSU |
| 2 | 70 | 0.73 | 0.96 | 16 | empty |
| 3 | 256 | 0.71 | 0.85 | 45 | empty |
| 4 | 300 | 0.69 | 0.83 | 44 | empty |
| 5 | 99 | 0.68 | 0.91 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2849 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 2462 Ų buried · 50 hydrogen bonds · protein-nucleic
- B–C · 2083 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1348 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 1250 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 3AL0 · Crystal structure of the glutamine transamidosome from Thermotoga maritima in the… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9X0Z9 · AlphaFold monomer V2.0 prediction for glutamyl-TRNA(GLN) amidotransferase subunit a… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9X2I8 · AlphaFold monomer V2.0 prediction for glutamate--tRNA ligase 2 (Q9X2I8) · a predicted model of the same protein · chain C against A, TM-score 0.81
- Q9X100 · AlphaFold monomer V2.0 prediction for ASPARTYL/GLUTAMYL-TRNA(ASN/GLN) amidotransferase… · a predicted model of the same protein · chain B against A, TM-score 0.81
- Q9WY94 · AlphaFold monomer V2.0 prediction for glutamyl-TRNA(GLN) amidotransferase subunit C… · a predicted model of the same protein · chain C against A, TM-score 0.16
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 Q9X0Z9
- Every structure of UniProt Q9X100
- Every structure of UniProt Q9WY94
- Every structure of UniProt Q9X2I8
- Elsewhere: RCSB PDB 3AL0 · PDBe 3AL0 · UniProt Q9X0Z9 · UniProt Q9X100 · UniProt Q9WY94 · UniProt Q9X2I8
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