MolNFT v1 · #12335 · protein

Cytidine monophosphate kinase from E. COLI in complex with cytidine monophosphate

1KDO · Cytidylate kinase: “Cytidine monophosphate kinase from E. COLI in complex with cytidine monophosphate”. X-ray diffraction, 2 ligands (C, SO4), 2 pockets (best druggability 0.70). MolNFT v1 #12335 on GenesisL1: 3D structure, binding…

PDB: 1KDO
Type: protein
Length: 446 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytidylate kinase
EC: 2.7.4.14
UniProt: P0A6I0
Ligands: C, SO4
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cytidylate kinase (EC 2.7.4.14)	protein	223	49% helix, 15% strand	P0A6I0

Ligands and binding sites

C · Cytidine-5'-monophosphate · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 5 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	446	0.70	0.81	50	SO4, C
2	489	0.69	0.79	62	SO4, C

Compared structures

1KDO · Cytidine monophosphate kinase from E. COLI in complex with cytidine monophosphate · the same entry in another collection · chain A against A, TM-score 1.00
P0A6I0 · AlphaFold monomer V2.0 prediction for cytidylate kinase (P0A6I0) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P0A6I0
Elsewhere: RCSB PDB 1KDO · PDBe 1KDO · UniProt P0A6I0

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