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Ispe in complex with ligand

Analyse 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: 2V2Q
Type: protein
Length: 539 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
EC: 2.7.1.148
UniProt: O67060
Ligands: NVG, BR, SO4
Pockets: 3 · best druggability 0.64

Structure

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

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

Ligands and binding sites

NVG · 4-amino-1-(5-{[3-(1H-benzimidazol-2-yl)propanoyl]amino}-5-deoxy-alpha-L-lyxofuranosyl)pyrimidin-2(1H)-one · ligand · 2 copies · chains A, B
BR · Bromide ion · ion · 7 copies · chains A, B
SO4 · Sulfate ion · ion · 5 copies · chains A, B
GOL · Glycerol · additive · 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	332	0.64	0.80	43	GOL, NVG, SO4
2	351	0.63	0.78	43	GOL, NVG, SO4
3	425	0.62	0.77	56	BR

Interfaces

1 interface between chains.

A–B · 394 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2V2Q · 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 2V2Q · PDBe 2V2Q · UniProt O67060

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