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Pleurotus ostreatus ostreolysina plus sphingomyelin

Analyse Pleurotus ostreatus ostreolysina plus sphingomyelin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MYJ
Type: protein
Length: 541 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ostreolysin A6
UniProt: P83467
Ligands: K6V, NA
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 3% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ostreolysin A6	protein	135	4% helix, 56% strand	P83467
B	Ostreolysin A6	protein	134	4% helix, 56% strand	P83467
C	Ostreolysin A6	protein	135	2% helix, 57% strand	P83467
D	Ostreolysin A6	protein	137	2% helix, 55% strand	P83467

Ligands and binding sites

K6V · N-[(2S)-1-hydroxypropan-2-yl]butanamide · ligand · chains D
NA · Sodium ion · metal · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 20 copies · chains A, D, B, C

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	887	0.76	0.80	97	EDO
2	667	0.74	0.81	50	EDO
3	247	0.52	0.76	37	empty

Interfaces

5 interfaces between chains.

B–D · 514 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 396 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 339 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 107 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 50 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6MYJ · Pleurotus ostreatus OstreolysinA plus sphingomyelin · the same entry in another collection · chain C against C, TM-score 1.00
P83467 · AlphaFold monomer V2.0 prediction for ostreolysin A6 (P83467) · 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 P83467
Elsewhere: RCSB PDB 6MYJ · PDBe 6MYJ · UniProt P83467

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