Research workbench
Crystal structure of S. cerevisiae mitochondrial gatfab
Analyse Crystal structure of S. cerevisiae mitochondrial gatfab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N0H
- Type
- protein
- Length
- 856 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
- NO3
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamyl-TRNA(GLN) amidotransferase subunit a, mitochondrial (EC 6.3.5.-) | protein | 446 | 38% helix, 16% strand | Q03557 |
| B | Glutamyl-TRNA(GLN) amidotransferase subunit B, mitochondrial (EC 6.3.5.-) | protein | 285 | 21% helix, 28% strand | P33893 |
| F | Glutamyl-TRNA(GLN) amidotransferase subunit F, mitochondrial (EC 6.3.5.-) | protein | 125 | 42% helix, 7% strand | P53260 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.79 | 0.80 | 76 | empty |
| 2 | 525 | 0.70 | 0.79 | 45 | empty |
| 3 | 346 | 0.52 | 0.73 | 31 | empty |
| 4 | 156 | 0.46 | 0.77 | 25 | empty |
| 5 | 115 | 0.40 | 0.75 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–F · 3176 Ų buried · 28 hydrogen bonds · protein-protein
- B–F · 1713 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1381 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4N0H · Crystal structure of S. cerevisiae mitochondrial GatFAB · the same entry in another collection · chain A against A, TM-score 1.00
- 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
- 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
- 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 0.95
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 4N0H · PDBe 4N0H · UniProt Q03557 · UniProt P33893 · UniProt P53260
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