MolNFT v1 · #57841 · protein

Crystal structure of cmp kinase in complex with cdp from thermus thermophilus HB8

3AKD · Cytidylate kinase: “Crystal structure of cmp kinase in complex with cdp from thermus thermophilus HB8”. X-ray diffraction, 1 ligand (CDP), 1 pocket (best druggability 0.67). MolNFT v1 #57841 on GenesisL1: 3D structure, binding sites…

PDB: 3AKD
Type: protein
Length: 202 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytidylate kinase
EC: 2.7.4.14
UniProt: Q5SL35
Ligands: CDP
Pockets: 1 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytidylate kinase (EC 2.7.4.14)	protein	202	51% helix, 16% strand	Q5SL35

Ligands and binding sites

CDP · Cytidine-5'-diphosphate · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	451	0.67	0.79	44	CDP

Compared structures

3AKD · Crystal structure of CMP kinase in complex with CDP from Thermus thermophilus HB8 · the same entry in another collection · chain A against A, TM-score 1.00
Q5SL35 · AlphaFold monomer V2.0 prediction for cytidylate kinase (Q5SL35) · 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 Q5SL35
Elsewhere: RCSB PDB 3AKD · PDBe 3AKD · UniProt Q5SL35

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