MolNFT v1 · #157418 · protein

Pleurotus ostreatus ostreolysina

6MYI · Ostreolysin A6: “Pleurotus ostreatus ostreolysina”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.82). MolNFT v1 #157418 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6MYI
Type: protein
Length: 545 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ostreolysin A6
UniProt: P83467
Ligands: NA
Pockets: 3 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 3% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ostreolysin A6	protein	137	2% helix, 55% strand	P83467
B	Ostreolysin A6	protein	135	2% helix, 57% strand	P83467
C	Ostreolysin A6	protein	136	2% helix, 55% strand	P83467
D	Ostreolysin A6	protein	137	4% helix, 55% strand	P83467

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 11 copies · chains A, C, B, 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	844	0.82	0.84	110	EDO
2	214	0.51	0.76	23	empty
3	177	0.49	0.77	23	empty

Interfaces

5 interfaces between chains.

B–D · 517 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 502 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 384 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 359 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 42 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6MYI · Pleurotus ostreatus OstreolysinA · the same entry in another collection · chain D against D, TM-score 1.00
P83467 · AlphaFold monomer V2.0 prediction for ostreolysin A6 (P83467) · a predicted model of the same protein · chain C 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 6MYI · PDBe 6MYI · UniProt P83467

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