MolNFT v1 · #113740 · protein

Crystal structure of pneumolysin D168A mutant.

5AOE: “Crystal structure of pneumolysin D168A mutant.”. X-ray diffraction, 11 pockets (best druggability 0.61). MolNFT v1 #113740 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5AOE
Type: protein
Length: 976 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pneumolysin
UniProt: Q04IN8
Pockets: 11 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pneumolysin	protein	488	18% helix, 40% strand	Q04IN8

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	195	0.61	0.82	34	empty
2	211	0.60	0.81	38	empty
3	85	0.54	0.85	22	empty
4	92	0.53	0.84	20	empty
5	125	0.51	0.80	24	empty

Interfaces

1 interface between chains.

A–B · 305 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5AOE · Crystal structure of pneumolysin D168A mutant. · the same entry in another collection · chain A against A, TM-score 1.00
Q04IN8 · AlphaFold monomer V2.0 prediction for pneumolysin (Q04IN8) · a predicted model of the same protein · chain A against A, TM-score 0.80

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 Q04IN8
Elsewhere: RCSB PDB 5AOE · PDBe 5AOE · UniProt Q04IN8

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