MolNFT v1 · #183496 · protein

Structure of yeast FBP1 (fructose-1,6-bisphosphatase 1)

7NS5: “Structure of yeast FBP1 (fructose-1,6-bisphosphatase 1)”. X-ray diffraction, 2 ligands (MG, PO4), 17 pockets (best druggability 0.85). MolNFT v1 #183496 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7NS5
Type: protein
Length: 1,214 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fructose-1,6-bisphosphatase
EC: 3.1.3.11
UniProt: P09201
Ligands: MG, PO4
Pockets: 17 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fructose-1,6-bisphosphatase (EC 3.1.3.11)	protein	319	39% helix, 24% strand	P09201
D	Fructose-1,6-bisphosphatase (EC 3.1.3.11)	protein	290	38% helix, 26% strand	P09201
B	Fructose-1,6-bisphosphatase (EC 3.1.3.11)	protein	312	39% helix, 24% strand	P09201
C	Fructose-1,6-bisphosphatase (EC 3.1.3.11)	protein	293	39% helix, 28% strand	P09201

Ligands and binding sites

MG · Magnesium ion · metal · 8 copies · chains A, D, B, C
PO4 · Phosphate ion · ion · 4 copies · chains A, D, B, C

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

Pockets

17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	313	0.85	0.96	43	empty
2	91	0.76	0.97	22	empty
3	235	0.74	0.88	26	empty
4	224	0.73	0.88	26	empty
5	57	0.60	0.92	18	empty

Interfaces

6 interfaces between chains.

B–C · 2395 Å² buried · 34 hydrogen bonds · protein-protein
A–D · 2386 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1209 Å² buried · 18 hydrogen bonds · protein-protein
D–C · 975 Å² buried · 10 hydrogen bonds · protein-protein
D–B · 433 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7NS5 · Structure of yeast Fbp1 (Fructose-1,6-bisphosphatase 1) · the same entry in another collection · chain C against C, TM-score 1.00
P09201 · AlphaFold monomer V2.0 prediction for fructose-1,6-bisphosphatase (P09201) · 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 P09201
Elsewhere: RCSB PDB 7NS5 · PDBe 7NS5 · UniProt P09201

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