Research workbench

Aquifex aeolicus ispe in complex with ligand

Analyse Aquifex aeolicus ispe in complex with ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VF3
Type: protein
Length: 539 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4-diphosphocytidyl-2C-methyl-D-erythritol kinase
EC: 2.7.1.148
UniProt: O67060
Ligands: GVS, POP, CL, BR
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	4-diphosphocytidyl-2C-methyl-D-erythritol kinase (EC 2.7.1.148)	protein	269	38% helix, 28% strand	O67060
B	4-diphosphocytidyl-2C-methyl-D-erythritol kinase (EC 2.7.1.148)	protein	270	38% helix, 28% strand	O67060

Ligands and binding sites

GVS · ethyl {3-[4-amino-5-{3-[(cyclopropylsulfonyl)amino]prop-1-yn-1-yl}-2-oxopyrimidin-1(2H)-yl]oxetan-3-yl}acetate · ligand · 2 copies · chains A, B
POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · 6 copies · chains A, B
BR · Bromide ion · ion · 2 copies · chains A, B

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

Pockets

3 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	372	0.65	0.79	41	GVS, POP
2	358	0.64	0.79	40	GVS, POP, CL
3	437	0.63	0.77	54	CL, BR

Interfaces

1 interface between chains.

A–B · 395 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2VF3 · Aquifex aeolicus IspE in complex with ligand · the same entry in another collection · chain A against A, TM-score 1.00
O67060 · AlphaFold monomer V2.0 prediction for 4-diphosphocytidyl-2-C-methyl- D-erythritol kinase… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O67060
Elsewhere: RCSB PDB 2VF3 · PDBe 2VF3 · UniProt O67060

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