MolNFT v1 · #7116 · protein

Aquifex aeolicus KDO8P synthase

1FX6 · 2-dehydro-3-deoxyphosphooctonate aldolase: “Aquifex aeolicus KDO8P synthase”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.71). MolNFT v1 #7116 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1FX6
Type: protein
Length: 500 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-dehydro-3-deoxyphosphooctonate aldolase
EC: 4.1.2.16
UniProt: O66496
Ligands: PO4
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-dehydro-3-deoxyphosphooctonate aldolase (EC 4.1.2.16)	protein	251	43% helix, 20% strand	O66496
B	2-dehydro-3-deoxyphosphooctonate aldolase (EC 4.1.2.16)	protein	249	42% helix, 20% strand	O66496

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	463	0.71	0.81	50	PO4
2	387	0.68	0.81	41	PO4
3	107	0.58	0.85	31	empty
4	100	0.41	0.77	21	empty
5	75	0.33	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 1806 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

1FX6 · Aquifex aeolicus KDO8P synthase · the same entry in another collection · chain A against A, TM-score 1.00
O66496 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxyphosphooctonate aldolase (O66496) · 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 O66496
Elsewhere: RCSB PDB 1FX6 · PDBe 1FX6 · UniProt O66496

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