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Crystal structure of human liver fbpase in complex with tricyclic inhibitor

Analyse Crystal structure of human liver fbpase in complex with tricyclic inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3A29
Type: protein
Length: 1,273 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fructose-1,6-bisphosphatase 1
EC: 3.1.3.11
UniProt: P09467
Ligands: 2T0
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11)	protein	319	38% helix, 24% strand	P09467
B, C, D	Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11)	protein	318	39% helix, 25% strand	P09467

Ligands and binding sites

2T0 · 2-amino-4,5-dihydronaphtho[1,2-d][1,3]thiazol-8-yl dihydrogen phosphate · ligand · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1164	0.83	0.84	124	empty
2	249	0.58	0.79	46	empty
3	186	0.54	0.79	34	empty
4	165	0.51	0.79	26	empty
5	54	0.49	0.86	20	empty

Interfaces

6 interfaces between chains.

C–D · 2401 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 2379 Å² buried · 36 hydrogen bonds · protein-protein
A–C · 1226 Å² buried · 24 hydrogen bonds · protein-protein
B–D · 1181 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 443 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3A29 · Crystal structure of human liver FBPase in complex with tricyclic inhibitor · the same entry in another collection · chain C against C, TM-score 1.00
P09467 · AlphaFold monomer V2.0 prediction for fructose-1,6-bisphosphatase 1 (P09467) · a predicted model of the same protein · chain C 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 P09467
Elsewhere: RCSB PDB 3A29 · PDBe 3A29 · UniProt P09467

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