Research workbench
Crystal structure of tryptophanyl-tRNA synthetase complexed with ATP in an open conformation
Analyse Crystal structure of tryptophanyl-tRNA synthetase complexed with ATP in an open… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MAW
- Type
- protein
- Length
- 1,956 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan-tRNA ligase
- EC
- 6.1.1.2
- UniProt
- P00953
- Ligands
- ATP
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Tryptophan-tRNA ligase (EC 6.1.1.2) | protein | 326 | 55% helix, 9% strand | P00953 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.75 | 0.80 | 62 | ATP |
| 2 | 791 | 0.74 | 0.79 | 60 | ATP |
| 3 | 648 | 0.74 | 0.80 | 55 | ATP |
| 4 | 650 | 0.74 | 0.80 | 52 | ATP |
| 5 | 671 | 0.74 | 0.80 | 57 | ATP |
Interfaces
4 interfaces between chains.
- A–D · 2187 Ų buried · 30 hydrogen bonds · protein-protein
- C–F · 2175 Ų buried · 30 hydrogen bonds · protein-protein
- B–E · 2138 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 375 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1MAW · Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ATP in an Open… · the same entry in another collection · chain C against C, TM-score 1.00
- P00953 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (P00953) · a predicted model of the same protein · chain A 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 P00953
- Elsewhere: RCSB PDB 1MAW · PDBe 1MAW · UniProt P00953
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