MolNFT v1 · #102963 · protein

Crystal structure of staphylococcal gamma-hemolysin prepore

4P1Y · Gamma-hemolysin component B: “Crystal structure of staphylococcal gamma-hemolysin prepore”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #102963 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4P1Y
Type: protein
Length: 2,120 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 0.79

Structure

x-ray diffraction · 5 distinct chains · 4% helix, 63% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gamma-hemolysin component B	protein	267	4% helix, 63% strand	Q931F3
B, D, F, H	Gamma-hemolysin component a	protein	264	4% helix, 65% strand	P0A071
C	Gamma-hemolysin component B	protein	266	4% helix, 63% strand	Q931F3
E	Gamma-hemolysin component B	protein	265	4% helix, 63% strand	Q931F3
G	Gamma-hemolysin component B	protein	266	4% helix, 63% strand	Q931F3

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1102	0.79	0.81	109	empty
2	837	0.76	0.80	81	empty
3	897	0.76	0.79	90	empty
4	794	0.75	0.80	68	empty
5	409	0.71	0.82	59	empty

Interfaces

14 interfaces between chains.

A–H · 2188 Å² buried · 46 hydrogen bonds · protein-protein
B–C · 2185 Å² buried · 48 hydrogen bonds · protein-protein
D–E · 2184 Å² buried · 48 hydrogen bonds · protein-protein
F–G · 2160 Å² buried · 46 hydrogen bonds · protein-protein
G–H · 2024 Å² buried · 42 hydrogen bonds · protein-protein

Compared structures

4P1Y · Crystal structure of staphylococcal gamma-hemolysin prepore · 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 0.87

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 4P1Y · PDBe 4P1Y · UniProt Q931F3 · UniProt P0A071

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