MolNFT v1 · #177303 · protein

Crystal structure of pltc toxin

7EE6 · Subtilase cytotoxin subunit B-like protein: “Crystal structure of pltc toxin”. X-ray diffraction, 1 ligand (ACN), 9 pockets (best druggability 0.76). MolNFT v1 #177303 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7EE6
Type: protein
Length: 1,060 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Subtilase cytotoxin subunit B-like protein; Cytolethal distending toxin subunit B family…
UniProt: A0A716TY65, A0A718C6E5, A0A716AET8
Ligands: ACN
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 20% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Subtilase cytotoxin subunit B-like protein	protein	118	17% helix, 42% strand	A0A716TY65
B, C	Subtilase cytotoxin subunit B-like protein	protein	120	17% helix, 42% strand	A0A716TY65
E	Subtilase cytotoxin subunit B-like protein	protein	119	17% helix, 42% strand	A0A716TY65
F	Cytolethal distending toxin subunit B family protein	protein	248	18% helix, 35% strand	A0A718C6E5
G	Pertussis-like toxin subunit arta	protein	217	28% helix, 25% strand	A0A716AET8

Ligands and binding sites

ACN · Acetone · ligand · 16 copies · chains A, B, C, D, E, G, F
PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, B, D, C, E, G, F
GOL · Glycerol · additive · 9 copies · chains A, B, E, C, D, F, G
FLC · Citrate anion · additive · 2 copies · chains F, G, D

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

Pockets

9 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	659	0.76	0.82	73	ACN
2	967	0.75	0.78	99	PEG, FLC, ACN
3	317	0.72	0.85	50	empty
4	250	0.62	0.81	41	ACN
5	74	0.54	0.86	18	empty

Interfaces

11 interfaces between chains.

A–B · 1075 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1062 Å² buried · 20 hydrogen bonds · protein-protein
C–E · 1050 Å² buried · 25 hydrogen bonds · protein-protein
B–E · 1025 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1021 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

7EE6 · Crystal structure of PltC 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 A0A716TY65
Every structure of UniProt A0A718C6E5
Every structure of UniProt A0A716AET8
Elsewhere: RCSB PDB 7EE6 · PDBe 7EE6 · UniProt A0A716TY65 · UniProt A0A718C6E5 · UniProt A0A716AET8

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