MolNFT v1 · #122368 · protein

Trapped toxin

5IMY · Vaginolysin: “Trapped toxin”. X-ray diffraction, 10 pockets (best druggability 0.88). MolNFT v1 #122368 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IMY
Type: protein
Length: 1,102 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vaginolysin; CD59 glycoprotein
UniProt: B2YGA4, P13987
Pockets: 10 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vaginolysin	protein	474	18% helix, 39% strand	B2YGA4
C, D	CD59 glycoprotein	protein	78	18% helix, 32% strand	P13987
B	Vaginolysin	protein	472	15% helix, 38% strand	B2YGA4

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1011	0.88	0.89	113	empty
2	447	0.84	0.91	63	empty
3	119	0.72	0.93	26	empty
4	104	0.64	0.90	25	empty
5	182	0.49	0.76	27	empty

Interfaces

5 interfaces between chains.

A–B · 1349 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 722 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 721 Å² buried · 4 hydrogen bonds · protein-protein
D–B · 714 Å² buried · 9 hydrogen bonds · protein-protein
C–B · 705 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

5IMY · Trapped Toxin · the same entry in another collection · chain A against A, TM-score 1.00
P13987 · AlphaFold monomer V2.0 prediction for CD59 glycoprotein (P13987) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 B2YGA4
Every structure of UniProt P13987
Elsewhere: RCSB PDB 5IMY · PDBe 5IMY · UniProt B2YGA4 · UniProt P13987

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