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Crystal structure of mycobacterium tuberculosis methionyl-tRNA synthetase bound by methionyl-adenylate (met-AMP)
Analyse Crystal structure of mycobacterium tuberculosis methionyl-tRNA synthetase bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XET
- Type
- protein
- Length
- 505 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine--tRNA ligase
- EC
- 6.1.1.10
- UniProt
- A5U150
- Ligands
- ME8, MG
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Methionine--tRNA ligase (EC 6.1.1.10) | protein | 505 | 52% helix, 15% strand | A5U150 |
Ligands and binding sites
- ME8 · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] (2S)-2-azanyl-4-methylsulfanyl-butanoate · ligand · chains C
- MG · Magnesium ion · metal · 5 copies · chains C
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.77 | 0.82 | 54 | ME8 |
| 2 | 145 | 0.50 | 0.78 | 22 | empty |
Compared structures
- 5XET · Crystal structure of Mycobacterium tuberculosis methionyl-tRNA synthetase bound by… · the same entry in another collection · chain C against C, 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 A5U150
- Elsewhere: RCSB PDB 5XET · PDBe 5XET · UniProt A5U150
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