MolNFT v1 · #11301 · protein

Crystal structure of S. aureus tyrrs in complex with sb-239629

1JIJ · Tyrosyl-tRNA synthetase: “Crystal structure of S. aureus tyrrs in complex with sb-239629”. X-ray diffraction, 1 ligand (629), 3 pockets (best druggability 0.70). MolNFT v1 #11301 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1JIJ
Type: protein
Length: 319 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosyl-tRNA synthetase
EC: 6.1.1.1
Ligands: 629
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosyl-tRNA synthetase (EC 6.1.1.1)	protein	319	50% helix, 9% strand	—

Ligands and binding sites

629 · [2-amino-3-(4-hydroxy-phenyl)-propionylamino]-(1,3,4,5-tetrahydroxy-4-hydroxymethyl-piperidin-2-yl)- acetic acid · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	367	0.70	0.83	46	629
2	91	0.36	0.74	16	empty
3	51	0.33	0.78	14	empty

Compared structures

1JIJ · Crystal structure of S. aureus TyrRS in complex with SB-239629 · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 1JIJ · PDBe 1JIJ

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