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Crystal structure of octameric pore form of gamma-hemolysin from staphylococcus aureus

Analyse Crystal structure of octameric pore form of gamma-hemolysin from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3B07
Type: protein
Length: 2,216 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gamma-hemolysin component B; Gamma-hemolysin component a
UniProt: Q931F3, P0A071
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 66% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Gamma-hemolysin component B	protein	284	4% helix, 63% strand	Q931F3
B, D, F, H	Gamma-hemolysin component a	protein	270	4% helix, 68% strand	P0A071

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, C, E, G

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

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	880	0.80	0.83	108	empty
2	1199	0.78	0.80	127	empty
3	879	0.77	0.80	91	empty
4	851	0.77	0.81	86	empty
5	297	0.68	0.83	43	empty

Interfaces

15 interfaces between chains.

A–H · 2463 Å² buried · 59 hydrogen bonds · protein-protein
E–D · 2420 Å² buried · 62 hydrogen bonds · protein-protein
G–F · 2409 Å² buried · 57 hydrogen bonds · protein-protein
C–B · 2399 Å² buried · 61 hydrogen bonds · protein-protein
E–F · 2079 Å² buried · 55 hydrogen bonds · protein-protein

Compared structures

3B07 · Crystal structure of octameric pore form of gamma-hemolysin from Staphylococcus aureus · the same entry in another collection · chain H against H, TM-score 1.00
P0A071 · AlphaFold monomer V2.0 prediction for gamma-hemolysin component a (P0A071) · a predicted model of the same protein · chain B against A, TM-score 0.85

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 Q931F3
Every structure of UniProt P0A071
Elsewhere: RCSB PDB 3B07 · PDBe 3B07 · UniProt Q931F3 · UniProt P0A071

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