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Crystal structure of E. COLI threonyl-tRNA synthetase interacting with the essential domain of its mRNA operator
Analyse Crystal structure of E. COLI threonyl-tRNA synthetase interacting with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KOG
- Type
- protein + RNA
- Length
- 3,504 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonyl-tRNA synthetase mRNA; Threonyl-tRNA synthetase
- EC
- 6.1.1.3
- UniProt
- P0A8M3
- Ligands
- TSB, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, J, K, L, M, N, O, P | Threonyl-tRNA synthetase mRNA | rna | 37 | — | — |
| A, B, C, D, E, F, G, H | Threonyl-tRNA synthetase (EC 6.1.1.3) | protein | 401 | 37% helix, 24% strand | P0A8M3 |
Ligands and binding sites
- TSB · 5'-O-(N-(L-threonyl)-sulfamoyl)adenosine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 342 | 0.85 | 0.94 | 49 | empty |
| 2 | 354 | 0.85 | 0.94 | 51 | empty |
| 3 | 337 | 0.85 | 0.94 | 47 | empty |
| 4 | 1131 | 0.79 | 0.81 | 87 | empty |
| 5 | 1120 | 0.79 | 0.81 | 84 | empty |
Interfaces
27 interfaces between chains.
- A–B · 2143 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2139 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2123 Ų buried · 26 hydrogen bonds · protein-protein
- O–G · 979 Ų buried · 25 hydrogen bonds · protein-nucleic
- M–E · 973 Ų buried · 26 hydrogen bonds · protein-nucleic
Compared structures
- 1KOG · Crystal structure of E. coli threonyl-tRNA synthetase interacting with the essential… · the same entry in another collection · chain G against G, TM-score 1.00
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 P0A8M3
- Elsewhere: RCSB PDB 1KOG · PDBe 1KOG · UniProt P0A8M3
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