MolNFT v1 · #111692 · protein + RNA

Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in complex with the canonical trnathr and threonyl sulfamoyl adenylate

4YYE · Threonine--tRNA ligase, mitochondrial: “Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in complex with the canonical…”. X-ray diffraction, 3 ligands (TSB, ZN, SO4), 13 pockets (best druggability 0.89).…

PDB: 4YYE
Type: protein + RNA
Length: 983 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Threonine--tRNA ligase, mitochondrial; TRNA
EC: 6.1.1.3
UniProt: P07236
Ligands: TSB, ZN, SO4
Pockets: 13 · best druggability 0.89

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Threonine--tRNA ligase, mitochondrial (EC 6.1.1.3)	protein	418	38% helix, 24% strand	P07236
B	Threonine--tRNA ligase, mitochondrial (EC 6.1.1.3)	protein	417	39% helix, 24% strand	P07236
C, D	TRNA	rna	74	—	—

Ligands and binding sites

TSB · 5'-O-(N-(L-threonyl)-sulfamoyl)adenosine · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1044	0.89	0.90	88	empty
2	1081	0.80	0.81	93	empty
3	995	0.75	0.78	83	TSB
4	1019	0.75	0.78	81	TSB
5	796	0.75	0.80	63	empty

Interfaces

5 interfaces between chains.

A–B · 3756 Å² buried · 43 hydrogen bonds · protein-protein
B–D · 1398 Å² buried · 29 hydrogen bonds · protein-nucleic
A–C · 1390 Å² buried · 28 hydrogen bonds · protein-nucleic
A–D · 561 Å² buried · 16 hydrogen bonds · protein-nucleic
B–C · 552 Å² buried · 12 hydrogen bonds · protein-nucleic

Compared structures

4YYE · 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 A 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 4YYE · PDBe 4YYE · UniProt P07236

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