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Fructose-1,6-BISPHOSPHATASE(D-fructose-1,6-bisphosphate-1- phosphohydrolase) (E.C.3.1.3.11) complexed with an AMP site inhibitor

Analyse Fructose-1,6-BISPHOSPHATASE(D-fructose-1,6-bisphosphate-1- phosphohydrolase)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WBB
Type: protein
Length: 2,540 residues
Chains: 8
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: RO3
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11)	protein	319	38% helix, 25% strand	P09467
B, C, D, F, G, H	Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11)	protein	317	39% helix, 26% strand	P09467

Ligands and binding sites

RO3 · N-{[(2Z)-5-bromo-1,3-thiazol-2(3H)-ylidene]carbamoyl}-4-methylbenzenesulfonamide · ligand · 8 copies · chains A, C, B, D, E, G, F, H

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	825	0.84	0.87	107	empty
2	806	0.82	0.85	88	empty
3	451	0.72	0.82	44	empty
4	645	0.68	0.77	68	empty
5	412	0.67	0.80	48	RO3

Interfaces

14 interfaces between chains.

C–D · 2410 Å² buried · 35 hydrogen bonds · protein-protein
E–F · 2407 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 2407 Å² buried · 29 hydrogen bonds · protein-protein
G–H · 2375 Å² buried · 34 hydrogen bonds · protein-protein
B–D · 1315 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

2WBB · Fructose-1,6-BISPHOSPHATASE(D-fructose-1,6-bisphosphate-1- phosphohydrolase)… · the same entry in another collection · chain H against H, 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 H 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 2WBB · PDBe 2WBB · UniProt P09467

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