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Ispc complex with MN2+ and fosmidomycin

Analyse Ispc complex with MN2+ and fosmidomycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ONP
Type: protein
Length: 794 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
EC: 1.1.1.267
UniProt: P45568
Ligands: FOM, MN
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267)	protein	397	46% helix, 15% strand	P45568

Ligands and binding sites

FOM · 3-[formyl(hydroxy)amino]propylphosphonic acid · ligand · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 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	221	0.78	0.92	33	empty
2	486	0.71	0.81	62	MN, FOM
3	466	0.70	0.80	54	MN, FOM
4	60	0.36	0.78	16	empty
5	59	0.34	0.77	13	empty

Interfaces

1 interface between chains.

A–B · 1588 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

1ONP · IspC complex with Mn2+ and fosmidomycin · the same entry in another collection · chain A against A, TM-score 1.00
P45568 · AlphaFold monomer V2.0 prediction for 1-deoxy-D-xylulose 5-phosphate reductoisomerase… · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P45568
Elsewhere: RCSB PDB 1ONP · PDBe 1ONP · UniProt P45568

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