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Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in complex with seryl sulfamoyl adenylate
Analyse Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EO4
- Type
- protein
- Length
- 1,660 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Threonine--tRNA ligase, mitochondrial
- EC
- 6.1.1.3
- UniProt
- P07236
- Ligands
- SSA, ZN
- Pockets
- 15 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Threonine--tRNA ligase, mitochondrial (EC 6.1.1.3) | protein | 417 | 34% helix, 24% strand | P07236 |
| B | Threonine--tRNA ligase, mitochondrial (EC 6.1.1.3) | protein | 413 | 34% helix, 24% strand | P07236 |
| C | Threonine--tRNA ligase, mitochondrial (EC 6.1.1.3) | protein | 416 | 35% helix, 24% strand | P07236 |
| D | Threonine--tRNA ligase, mitochondrial (EC 6.1.1.3) | protein | 414 | 34% helix, 23% strand | P07236 |
Ligands and binding sites
- SSA · 5'-O-(N-(L-seryl)-sulfamoyl)adenosine · ligand · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.89 | 0.90 | 100 | empty |
| 2 | 1114 | 0.88 | 0.89 | 103 | empty |
| 3 | 246 | 0.69 | 0.85 | 40 | SSA, ZN |
| 4 | 348 | 0.68 | 0.82 | 41 | SSA, ZN |
| 5 | 298 | 0.66 | 0.82 | 38 | SSA, ZN |
Interfaces
3 interfaces between chains.
- A–C · 3721 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 3617 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 524 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4EO4 · Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- P07236 · AlphaFold monomer V2.0 prediction for threonine--tRNA ligase, mitochondrial (P07236) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P07236
- Elsewhere: RCSB PDB 4EO4 · PDBe 4EO4 · UniProt P07236
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