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Crystal structure of KDO8P synthase in its binary complex with substrate pep

Analyse Crystal structure of KDO8P synthase in its binary complex with substrate pep in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Q3N
Type: protein
Length: 272 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-dehydro-3-deoxyphosphooctonate aldolase
EC: 2.5.1.55
UniProt: P0A715
Ligands: PEP
Pockets: 2 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55)	protein	272	39% helix, 15% strand	P0A715

Ligands and binding sites

PEP · Phosphoenolpyruvate · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	431	0.71	0.82	52	PEP
2	107	0.34	0.73	15	empty

Compared structures

1Q3N · Crystal structure of KDO8P synthase in its binary complex with substrate PEP · the same entry in another collection · chain A against A, TM-score 1.00
P0A715 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxyphosphooctonate aldolase (P0A715) · a predicted model of the same protein · chain A 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 P0A715
Elsewhere: RCSB PDB 1Q3N · PDBe 1Q3N · UniProt P0A715

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