MolNFT v1 · #51287 · protein

Ispe in complex with ligand

2V2V · 4-diphosphocytidyl-2C-methyl-D-erythritol kinase: “Ispe in complex with ligand”. X-ray diffraction, 3 ligands (V12, BR, SO4), 3 pockets (best druggability 0.64). MolNFT v1 #51287 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2V2V
Type: protein
Length: 540 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: V12, BR, SO4
Pockets: 3 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	4-diphosphocytidyl-2C-methyl-D-erythritol kinase (EC 2.7.1.148)	protein	270	36% helix, 28% strand	O67060

Ligands and binding sites

V12 · 5'-[(1H-benzimidazol-2-ylacetyl)amino]-5'-deoxycytidine · ligand · 2 copies · chains A, B
BR · Bromide ion · ion · 8 copies · chains A, B
SO4 · Sulfate ion · ion · 5 copies · chains A, B
GOL · Glycerol · additive · 3 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	342	0.64	0.79	43	SO4, GOL, V12
2	372	0.63	0.78	45	SO4, GOL, V12
3	400	0.61	0.77	54	BR

Interfaces

1 interface between chains.

A–B · 390 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2V2V · 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 0.98

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 2V2V · PDBe 2V2V · UniProt O67060

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