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

Analyse Crystal structure of cmp kinase in complex with cdp from thermus thermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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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