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Crystal structure of ispe (4-diphosphocytidyl-2-C-methyl-D-erythritol kinase) from mycobacterium abcessus, bound to ATP

Analyse Crystal structure of ispe (4-diphosphocytidyl-2-C-methyl-D-erythritol kinase)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ED4
Type: protein
Length: 299 residues
Chains: 1
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: B1MKD5
Ligands: ATP
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 35% 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	299	35% helix, 28% strand	B1MKD5

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · 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	342	0.63	0.79	42	ATP
2	51	0.25	0.73	14	empty

Compared structures

4ED4 · Crystal structure of IspE (4-diphosphocytidyl-2-C-methyl-D-erythritol kinase) from… · the same entry in another collection · 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 B1MKD5
Elsewhere: RCSB PDB 4ED4 · PDBe 4ED4 · UniProt B1MKD5

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