MolNFT v1 · #112275 · protein

Structure of sugar binding protein pneumolysin

4ZGH: “Structure of sugar binding protein pneumolysin”. X-ray diffraction, 1 ligand (AUC), 7 pockets (best druggability 0.67). MolNFT v1 #112275 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4ZGH
Type: protein
Length: 473 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pneumolysin
UniProt: Q04IN8
Ligands: AUC
Pockets: 7 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pneumolysin	protein	473	14% helix, 35% strand	Q04IN8

Ligands and binding sites

AUC · Gold (I) cyanide ion · ligand · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 5 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.67	0.96	19	empty
2	264	0.65	0.82	42	empty
3	160	0.61	0.84	35	empty
4	110	0.58	0.85	21	empty
5	92	0.49	0.82	23	empty

Compared structures

4ZGH · Structure of Sugar Binding Protein Pneumolysin · 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 0.84

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 4ZGH · PDBe 4ZGH · UniProt Q04IN8

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