MolNFT v1 · #57827 · protein

Crystal structure of 3-hexulose-6-phosphate synthase

3AJX: “Crystal structure of 3-hexulose-6-phosphate synthase”. X-ray diffraction, 3 ligands (MG, SO4, CL), 6 pockets (best druggability 0.79). MolNFT v1 #57827 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3AJX
Type: protein
Length: 828 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-hexulose-6-phosphate synthase
EC: 4.1.2.43
UniProt: Q9LBW4
Ligands: MG, SO4, CL
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	3-hexulose-6-phosphate synthase (EC 4.1.2.43)	protein	207	49% helix, 20% strand	Q9LBW4

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 3 copies · chains A, C, D

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

Pockets

6 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	955	0.79	0.81	99	MG, SO4
2	384	0.74	0.84	48	empty
3	116	0.66	0.90	36	MG, SO4
4	125	0.63	0.87	31	MG, SO4
5	101	0.37	0.75	27	empty

Interfaces

5 interfaces between chains.

C–D · 1251 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 1250 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 286 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 184 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 162 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3AJX · Crystal Structure of 3-Hexulose-6-Phosphate Synthase · the same entry in another collection · chain A against A, TM-score 1.00
Q9LBW4 · AlphaFold monomer V2.0 prediction for 3-hexulose-6-phosphate synthase (Q9LBW4) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q9LBW4
Elsewhere: RCSB PDB 3AJX · PDBe 3AJX · UniProt Q9LBW4

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