Research workbench
Structure of tRNA-dependent amidotransferase gatcab complexed with MN2+
Analyse Structure of tRNA-dependent amidotransferase gatcab complexed with MN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DF4
- Type
- protein
- Length
- 983 residues
- Chains
- 3
- 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.-
- UniProt
- P63488, P64201, P68807
- Ligands
- MN
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamyl-TRNA(GLN) amidotransferase subunit a (EC 6.3.5.-) | protein | 485 | 43% helix, 15% strand | P63488 |
| B | ASPARTYL/GLUTAMYL-TRNA(ASN/GLN) amidotransferase subunit B (EC 6.3.5.-) | protein | 399 | 33% helix, 25% strand | P64201 |
| C | ASPARTYL/GLUTAMYL-TRNA(ASN/GLN) amidotransferase subunit C (EC 6.3.5.-) | protein | 99 | 39% helix, 7% strand | P68807 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.73 | 0.78 | 70 | MN |
| 2 | 367 | 0.58 | 0.76 | 28 | empty |
| 3 | 89 | 0.48 | 0.82 | 15 | empty |
| 4 | 82 | 0.46 | 0.81 | 12 | empty |
| 5 | 88 | 0.42 | 0.79 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2607 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1854 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1418 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2DF4 · Structure of tRNA-Dependent Amidotransferase GatCAB complexed with Mn2+ · the same entry in another collection · chain A against A, TM-score 1.00
- P63488 · 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 1.00
- P64201 · 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 0.97
- P68807 · AlphaFold monomer V2.0 prediction for ASPARTYL/GLUTAMYL-TRNA(ASN/GLN) amidotransferase… · a predicted model of the same protein · chain C against A, TM-score 0.88
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 P63488
- Every structure of UniProt P64201
- Every structure of UniProt P68807
- Elsewhere: RCSB PDB 2DF4 · PDBe 2DF4 · UniProt P63488 · UniProt P64201 · UniProt P68807
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