MolNFT v1 · #34887 · protein
Crystal structure of methanococcus jannacshii O-phosphoseryl-tRNA synthetase
2DU7: “Crystal structure of methanococcus jannacshii O-phosphoseryl-tRNA synthetase”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #34887 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DU7
- Type
- protein
- Length
- 2,156 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-phosphoseryl-tRNA synthetase
- EC
- 6.1.1.-
- UniProt
- Q59054
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | O-phosphoseryl-tRNA synthetase (EC 6.1.1.-) | protein | 539 | 22% helix, 12% strand | Q59054 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.79 | 0.84 | 56 | empty |
| 2 | 344 | 0.76 | 0.87 | 52 | empty |
| 3 | 70 | 0.75 | 0.99 | 17 | empty |
| 4 | 70 | 0.75 | 0.99 | 17 | empty |
| 5 | 413 | 0.75 | 0.85 | 56 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3504 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 3502 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 3398 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 3381 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 215 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2DU7 · Crystal structure of Methanococcus jannacshii O-phosphoseryl-tRNA synthetase · the same entry in another collection · chain B against B, TM-score 1.00
- Q59054 · AlphaFold monomer V2.0 prediction for O-phosphoserine--TRNA(CYS) ligase (Q59054) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q59054
- Elsewhere: RCSB PDB 2DU7 · PDBe 2DU7 · UniProt Q59054
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