Research workbench

1.7 ångström crystal structure of leukotoxin lukd from staphylococcus aureus.

Analyse 1.7 ångström crystal structure of leukotoxin lukd from staphylococcus aureus. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Q7G
Type: protein
Length: 300 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leucotoxin lukdv
UniProt: Q6G8A9
Pockets: 2 · best druggability 0.38

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Leucotoxin lukdv	protein	300	3% helix, 59% strand	Q6G8A9

Ligands and binding sites

BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	102	0.38	0.75	19	empty
2	63	0.29	0.74	20	empty

Compared structures

4Q7G · 1.7 Angstrom Crystal Structure of leukotoxin LukD from Staphylococcus aureus. · the same entry in another collection · chain A against A, TM-score 1.00
Q6G8A9 · AlphaFold monomer V2.0 prediction for leucotoxin lukdv (Q6G8A9) · 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 Q6G8A9
Elsewhere: RCSB PDB 4Q7G · PDBe 4Q7G · UniProt Q6G8A9

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