MolNFT v1 · #161247 · protein

Neisseria gonorrhoeae leucyl-tRNA synthetase in complex with 5'-O-(N- (L-leucyl)-SULFAMOYL)URIDINE

6Q8C · Leucine--tRNA ligase: “Neisseria gonorrhoeae leucyl-tRNA synthetase in complex with 5'-O-(N- (L-leucyl)-SULFAMOYL)URIDINE”. X-ray diffraction, 3 ligands (LSU, ZN, MG), 9 pockets (best druggability 0.70). MolNFT v1 #161247 on…

PDB: 6Q8C
Type: protein
Length: 832 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leucine--tRNA ligase
EC: 6.1.1.4
UniProt: A0A1D3HNX6
Ligands: LSU, ZN, MG
Pockets: 9 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Leucine--tRNA ligase (EC 6.1.1.4)	protein	832	41% helix, 17% strand	A0A1D3HNX6

Ligands and binding sites

LSU · 5'-O-(N-(L-Leucyl)-Sulfamoyl)Uridine · ligand · chains A
ZN · Zinc ion · metal · chains A
MG · Magnesium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

9 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	670	0.70	0.78	79	LSU
2	381	0.62	0.78	29	empty
3	51	0.48	0.86	16	empty
4	154	0.47	0.77	25	empty
5	89	0.43	0.79	23	empty

Compared structures

6Q8C · Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with… · 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 A0A1D3HNX6
Elsewhere: RCSB PDB 6Q8C · PDBe 6Q8C · UniProt A0A1D3HNX6

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