MolNFT v1 · #124725 · protein

Evolutionary gain of alanine mischarging to non-cognate trnas with a G4:U69 base pair

5KNN · Alanine--tRNA ligase, cytoplasmic: “Evolutionary gain of alanine mischarging to non-cognate trnas with a G4:U69 base pair”. X-ray diffraction, 1 ligand (A5A), 20 pockets (best druggability 0.78). MolNFT v1 #124725 on GenesisL1: 3D…

PDB: 5KNN
Type: protein
Length: 3,585 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alanine--tRNA ligase, cytoplasmic
EC: 6.1.1.7
UniProt: P49588
Ligands: A5A
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 46% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E	Alanine--tRNA ligase, cytoplasmic (EC 6.1.1.7)	protein	450	46% helix, 18% strand	P49588
C	Alanine--tRNA ligase, cytoplasmic (EC 6.1.1.7)	protein	444	45% helix, 18% strand	P49588
D	Alanine--tRNA ligase, cytoplasmic (EC 6.1.1.7)	protein	447	46% helix, 18% strand	P49588
F, G	Alanine--tRNA ligase, cytoplasmic (EC 6.1.1.7)	protein	449	46% helix, 18% strand	P49588
H	Alanine--tRNA ligase, cytoplasmic (EC 6.1.1.7)	protein	446	46% helix, 17% strand	P49588

Ligands and binding sites

A5A · 5'-O-(N-(L-alanyl)-sulfamoyl)adenosine · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1007	0.78	0.80	86	empty
2	894	0.76	0.79	83	empty
3	1083	0.74	0.77	87	empty
4	1010	0.74	0.77	84	empty
5	333	0.73	0.85	39	A5A

Interfaces

9 interfaces between chains.

A–B · 629 Å² buried · 9 hydrogen bonds · protein-protein
F–H · 545 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 519 Å² buried · 1 hydrogen bond · protein-protein
A–D · 518 Å² buried · 1 hydrogen bond · protein-protein
E–G · 506 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5KNN · Evolutionary gain of alanine mischarging to non-cognate tRNAs with a G4:U69 base pair · the same entry in another collection · chain H against H, TM-score 1.00
P49588 · AlphaFold monomer V2.0 prediction for alanine--tRNA ligase, cytoplasmic (P49588) · a predicted model of the same protein · chain F against A, TM-score 0.98

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 P49588
Elsewhere: RCSB PDB 5KNN · PDBe 5KNN · UniProt P49588

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