Research workbench

Phosphopyruvate hydratase from campylobacter jejuni.

Analyse Phosphopyruvate hydratase from campylobacter jejuni. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QN3
Type: protein
Length: 1,660 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Enolase
EC: 4.2.1.11
UniProt: P42448
Ligands: MG, SO4
Pockets: 16 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Enolase (EC 4.2.1.11)	protein	415	41% helix, 20% strand	P42448

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 3 copies · chains B, C, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 3 copies · chains A, B, C, D

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

Pockets

16 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	1077	0.77	0.80	88	SO4
2	1105	0.77	0.79	81	MPD, GOL
3	961	0.76	0.79	55	MPD, GOL
4	919	0.73	0.77	132	empty
5	181	0.58	0.81	29	empty

Interfaces

3 interfaces between chains.

A–B · 1584 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1581 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1468 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

3QN3 · Phosphopyruvate hydratase from Campylobacter jejuni. · the same entry in another collection · chain B against B, TM-score 1.00
P42448 · AlphaFold monomer V2.0 prediction for enolase (P42448) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 P42448
Elsewhere: RCSB PDB 3QN3 · PDBe 3QN3 · UniProt P42448

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.