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Structure of azuala

Analyse Structure of azuala in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NSF
Type: protein
Length: 1,222 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine--tRNA ligase
EC: 6.1.1.1
UniProt: Q57834
Ligands: 96Z, CA
Pockets: 12 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, C	Tyrosine--tRNA ligase (EC 6.1.1.1)	protein	306	51% helix, 13% strand	Q57834
A, D	Tyrosine--tRNA ligase (EC 6.1.1.1)	protein	305	52% helix, 13% strand	Q57834

Ligands and binding sites

96Z · (2~{S})-2-azanyl-3-(2,6-dihydroazulen-1-yl)propanoic acid · ligand · 4 copies · chains B, A, C, D
CA · Calcium ion · metal · 3 copies · chains B, A, C
GOL · Glycerol · additive · 2 copies · chains B, A
PG4 · Tetraethylene glycol · additive · chains A

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

Pockets

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1096	0.84	0.85	123	96Z, PG4
2	459	0.82	0.89	51	96Z
3	477	0.78	0.86	58	96Z
4	1197	0.77	0.79	104	96Z
5	641	0.64	0.75	50	empty

Interfaces

6 interfaces between chains.

A–C · 719 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 634 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 438 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 270 Å² buried · 1 hydrogen bond · protein-protein
B–A · 65 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5NSF · Structure of AzuAla · the same entry in another collection · chain B against B, TM-score 1.00
Q57834 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase (Q57834) · 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 Q57834
Elsewhere: RCSB PDB 5NSF · PDBe 5NSF · UniProt Q57834

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