MolNFT v1 · #57275 · protein + RNA

Crystal structure of tils complexed with tRNA

3A2K · TRNA(ILE)-lysidine synthase: “Crystal structure of tils complexed with tRNA”. X-ray diffraction, 18 pockets (best druggability 0.79). MolNFT v1 #57275 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3A2K
Type: protein + RNA
Length: 1,078 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA(ILE)-lysidine synthase; Bacterial tRNA
EC: 6.3.4.-
UniProt: Q5L3T3
Pockets: 18 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	TRNA(ILE)-lysidine synthase (EC 6.3.4.-)	protein	462	39% helix, 21% strand	Q5L3T3
C, D	Bacterial tRNA	rna	77	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	759	0.79	0.83	71	empty
2	765	0.79	0.83	71	empty
3	92	0.78	0.98	23	empty
4	910	0.78	0.81	75	empty
5	91	0.77	0.98	24	empty

Interfaces

5 interfaces between chains.

A–C · 2922 Å² buried · 87 hydrogen bonds · protein-nucleic
B–D · 2910 Å² buried · 96 hydrogen bonds · protein-nucleic
A–B · 1778 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 196 Å² buried · 4 hydrogen bonds · protein-nucleic
A–D · 184 Å² buried · 2 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

3A2K · Crystal structure of TilS complexed with tRNA · the same entry in another collection · chain A against A, TM-score 1.00
Q5L3T3 · AlphaFold monomer V2.0 prediction for TRNA(ILE)-lysidine synthase (Q5L3T3) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q5L3T3
Elsewhere: RCSB PDB 3A2K · PDBe 3A2K · UniProt Q5L3T3

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