MolNFT v1 · #144354 · protein

Crystal structure of tyrosine-tRNA synthetase from acinetobacter baumannii

6BQY · Tyrosine--tRNA ligase: “Crystal structure of tyrosine-tRNA synthetase from acinetobacter baumannii”. X-ray diffraction, 3 pockets (best druggability 0.62). MolNFT v1 #144354 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6BQY
Type: protein
Length: 434 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine--tRNA ligase
EC: 6.1.1.1
UniProt: A0A086HYS2
Pockets: 3 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine--tRNA ligase (EC 6.1.1.1)	protein	215	51% helix, 14% strand	A0A086HYS2
B	Tyrosine--tRNA ligase (EC 6.1.1.1)	protein	219	51% helix, 14% strand	A0A086HYS2

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 7 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	342	0.62	0.78	37	EDO
2	283	0.59	0.78	35	EDO
3	61	0.33	0.76	11	empty

Interfaces

1 interface between chains.

A–B · 470 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6BQY · Crystal Structure of Tyrosine-tRNA Synthetase from Acinetobacter baumannii · 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
Every structure of UniProt A0A086HYS2
Elsewhere: RCSB PDB 6BQY · PDBe 6BQY · UniProt A0A086HYS2

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