Research workbench

Pleurotus ostreatus ostreolysina mutant E69A with bis-tris

Analyse Pleurotus ostreatus ostreolysina mutant E69A with bis-tris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MYK
Type: protein
Length: 542 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ostreolysin A6
UniProt: P83467
Ligands: NA, SO4
Pockets: 3 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 2% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Ostreolysin A6	protein	135	2% helix, 59% strand	P83467
B	Ostreolysin A6	protein	137	2% helix, 55% strand	P83467

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 8 copies · chains A, C, D
BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1198	0.84	0.85	139	EDO
2	144	0.40	0.74	22	empty
3	60	0.33	0.77	17	empty

Interfaces

5 interfaces between chains.

A–C · 579 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 547 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 542 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 260 Å² buried · 1 hydrogen bond · protein-protein
A–D · 256 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6MYK · Pleurotus ostreatus OstreolysinA mutant E69A with Bis-Tris · the same entry in another collection · chain A against A, 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 0.98

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 6MYK · PDBe 6MYK · UniProt P83467

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