MolNFT v1 · #157789 · protein

Crystal structure of gram negative toxin

6NAL · Thiol-activated cytolysin: “Crystal structure of gram negative toxin”. X-ray diffraction, 6 pockets (best druggability 0.67). MolNFT v1 #157789 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6NAL
Type: protein
Length: 947 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thiol-activated cytolysin
UniProt: E8RGW2
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thiol-activated cytolysin	protein	474	22% helix, 43% strand	E8RGW2
B	Thiol-activated cytolysin	protein	473	20% helix, 42% strand	E8RGW2

Ligands and binding sites

IMD · Imidazole · additive · 2 copies · chains A, B
PG4 · Tetraethylene glycol · additive · chains A

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

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	443	0.67	0.79	58	empty
2	237	0.61	0.81	39	empty
3	299	0.61	0.79	43	IMD
4	270	0.59	0.79	36	IMD
5	343	0.57	0.76	43	empty

Interfaces

1 interface between chains.

A–B · 573 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

6NAL · Crystal Structure of Gram Negative Toxin · 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 E8RGW2
Elsewhere: RCSB PDB 6NAL · PDBe 6NAL · UniProt E8RGW2

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