MolNFT v1 · #102962 · protein

Crystal structure of staphylococcal luk prepore

4P1X · Gamma-hemolysin component C: “Crystal structure of staphylococcal luk prepore”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #102962 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4P1X
Type: protein
Length: 2,092 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gamma-hemolysin component C; Gamma-hemolysin component B
UniProt: Q99RL1, Q931F3
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 4% helix, 64% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D	Gamma-hemolysin component C	protein	257	4% helix, 67% strand	Q99RL1
A	Gamma-hemolysin component B	protein	265	4% helix, 62% strand	Q931F3
C, E	Gamma-hemolysin component B	protein	267	3% helix, 62% strand	Q931F3
F	Gamma-hemolysin component C	protein	255	4% helix, 67% strand	Q99RL1
G	Gamma-hemolysin component B	protein	266	3% helix, 62% strand	Q931F3
H	Gamma-hemolysin component C	protein	258	4% helix, 67% strand	Q99RL1

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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1173	0.79	0.81	117	empty
2	1200	0.79	0.81	117	empty
3	828	0.76	0.80	72	empty
4	830	0.75	0.79	73	empty
5	427	0.73	0.83	68	empty

Interfaces

16 interfaces between chains.

A–H · 2245 Å² buried · 48 hydrogen bonds · protein-protein
B–C · 2177 Å² buried · 42 hydrogen bonds · protein-protein
F–G · 2153 Å² buried · 49 hydrogen bonds · protein-protein
D–E · 2149 Å² buried · 48 hydrogen bonds · protein-protein
C–D · 1799 Å² buried · 42 hydrogen bonds · protein-protein

Compared structures

4P1X · Crystal structure of staphylococcal LUK prepore · the same entry in another collection · chain H against H, TM-score 1.00
Q99RL1 · AlphaFold monomer V2.0 prediction for gamma-hemolysin component C (Q99RL1) · a predicted model of the same protein · chain B against A, TM-score 0.88

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 Q99RL1
Every structure of UniProt Q931F3
Elsewhere: RCSB PDB 4P1X · PDBe 4P1X · UniProt Q99RL1 · UniProt Q931F3

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