Research workbench
Crystal structure of S. cerevisiae mitochondrial gatfab in complex with glutamine
Analyse Crystal structure of S. cerevisiae mitochondrial gatfab in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N0I
- Type
- protein
- Length
- 860 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamyl-TRNA(GLN) amidotransferase subunit a, mitochondrial; Glutamyl-TRNA(GLN)…
- EC
- 6.3.5.-
- UniProt
- Q03557, P33893, P53260
- Ligands
- GLN, NO3
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamyl-TRNA(GLN) amidotransferase subunit a, mitochondrial (EC 6.3.5.-) | protein | 450 | 40% helix, 15% strand | Q03557 |
| B | Glutamyl-TRNA(GLN) amidotransferase subunit B, mitochondrial (EC 6.3.5.-) | protein | 285 | 21% helix, 29% strand | P33893 |
| F | Glutamyl-TRNA(GLN) amidotransferase subunit F, mitochondrial (EC 6.3.5.-) | protein | 125 | 44% helix, 7% strand | P53260 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.76 | 0.78 | 72 | empty |
| 2 | 403 | 0.56 | 0.74 | 37 | empty |
| 3 | 121 | 0.52 | 0.82 | 25 | empty |
| 4 | 164 | 0.48 | 0.77 | 25 | empty |
| 5 | 71 | 0.41 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–F · 3374 Ų buried · 32 hydrogen bonds · protein-protein
- B–F · 1713 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1378 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4N0I · Crystal structure of S. cerevisiae mitochondrial GatFAB in complex with glutamine · the same entry in another collection · chain F against F, TM-score 1.00
- Q03557 · 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
- P33893 · AlphaFold monomer V2.0 prediction for glutamyl-TRNA(GLN) amidotransferase subunit B… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P53260 · AlphaFold monomer V2.0 prediction for glutamyl-TRNA(GLN) amidotransferase subunit F… · a predicted model of the same protein · chain F against A, TM-score 0.96
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 Q03557
- Every structure of UniProt P33893
- Every structure of UniProt P53260
- Elsewhere: RCSB PDB 4N0I · PDBe 4N0I · UniProt Q03557 · UniProt P33893 · UniProt P53260
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