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Crystal structure of Cph001-D189N in complex with ATP

Analyse Crystal structure of Cph001-D189N in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8I85
Type: protein
Length: 565 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.17
Source: Streptosporangium roseum
Molecule: Viomycin kinase
UniProt: D2B3F1
Ligands: ATP
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · resolution 2.17 · 2 distinct chains · 54% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Viomycin kinase	protein	285	54% helix, 12% strand	D2B3F1
A	Viomycin kinase	protein	280	54% helix, 15% strand	D2B3F1

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, A
ACT · Acetate ion · additive · chains A

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

Pockets

6 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	678	0.76	0.81	73	PEG
2	789	0.73	0.78	55	ATP
3	224	0.55	0.78	26	PEG
4	127	0.48	0.79	21	empty
5	205	0.46	0.74	24	empty

Interfaces

1 interface between chains.

B–A · 1458 Å² buried · 26 hydrogen bonds · protein-protein

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 D2B3F1
Elsewhere: RCSB PDB 8I85 · PDBe 8I85 · UniProt D2B3F1

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