Research workbench

Disulfide-locked early prepore intermedilysin-CD59

Analyse Disulfide-locked early prepore intermedilysin-CD59 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZD0
Type: protein
Length: 1,611 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thiol-activated cytolysin; CD59 glycoprotein
UniProt: Q9LCB8, P13987
Pockets: 20 · best druggability 0.76

Structure

electron microscopy · 2 distinct chains · 20% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Thiol-activated cytolysin	protein	460	22% helix, 37% strand	Q9LCB8
B, D, F	CD59 glycoprotein	protein	77	9% helix, 34% strand	P13987

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	438	0.76	0.85	67	empty
2	253	0.75	0.89	57	empty
3	219	0.72	0.88	54	empty
4	201	0.72	0.89	38	empty
5	550	0.69	0.79	83	empty

Interfaces

7 interfaces between chains.

A–E · 1026 Å² buried · 1 hydrogen bond · protein-protein
A–C · 961 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 241 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 233 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 191 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6ZD0 · Disulfide-locked early prepore intermedilysin-CD59 · the same entry in another collection · chain F against F, TM-score 1.00
P13987 · AlphaFold monomer V2.0 prediction for CD59 glycoprotein (P13987) · a predicted model of the same protein · chain B against A, TM-score 0.89

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 Q9LCB8
Every structure of UniProt P13987
Elsewhere: RCSB PDB 6ZD0 · PDBe 6ZD0 · UniProt Q9LCB8 · UniProt P13987

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