Research workbench

Fructose 1,6-bisphosphate aldolase from rabbit liver

Analyse Fructose 1,6-bisphosphate aldolase from rabbit liver in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1FDJ
Type: protein
Length: 1,452 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fructose 1,6-bisphosphate aldolase
EC: 4.1.2.13
UniProt: P79226
Ligands: 13P, 2FP, G3P, SO4
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Fructose 1,6-bisphosphate aldolase (EC 4.1.2.13)	protein	363	46% helix, 15% strand	P79226

Ligands and binding sites

13P · 1,3-dihydroxyacetonephosphate · ligand · 4 copies · chains B, C, D
2FP · 1,6-fructose diphosphate (linear form) · ligand · 2 copies · chains A, B
G3P · Sn-glycerol-3-phosphate · ligand · chains B
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	874	0.77	0.80	73	13P
2	220	0.74	0.90	36	13P
3	760	0.74	0.79	85	SO4
4	70	0.71	0.96	18	empty
5	73	0.70	0.95	20	empty

Interfaces

3 interfaces between chains.

A–B · 1141 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1051 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 232 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1FDJ · Fructose 1,6-bisphosphate aldolase from rabbit liver · the same entry in another collection · chain D against D, TM-score 1.00
P79226 · AlphaFold monomer V2.0 prediction for fructose-bisphosphate aldolase B (P79226) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P79226
Elsewhere: RCSB PDB 1FDJ · PDBe 1FDJ · UniProt P79226

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