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Structure of the cak complex form chaetomium thermophilum bound to ATP-gamma-S

Analyse Structure of the cak complex form chaetomium thermophilum bound to ATP-gamma-S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z4X
Type: protein
Length: 1,404 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclin domain-containing protein; Protein kinase domain-containing protein; Ring-type…
UniProt: G0SH78, G0SFC6, G0SF48
Ligands: AGS, MG, CL
Pockets: 19 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 54% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin domain-containing protein	protein	312	72% helix, 0% strand	G0SH78
B	Protein kinase domain-containing protein	protein	322	38% helix, 15% strand	G0SFC6
C	Ring-type domain-containing protein	protein	66	47% helix, 0% strand	G0SF48
D	Cyclin domain-containing protein	protein	314	72% helix, 0% strand	G0SH78
E	Protein kinase domain-containing protein	protein	323	38% helix, 15% strand	G0SFC6
F	Ring-type domain-containing protein	protein	67	46% helix, 0% strand	G0SF48

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains B, E
MG · Magnesium ion · metal · 2 copies · chains B, E
CL · Chloride ion · ion · chains B, E

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

Pockets

19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	505	0.77	0.84	73	empty
2	408	0.76	0.86	61	empty
3	283	0.73	0.86	32	empty
4	317	0.69	0.83	31	empty
5	487	0.65	0.77	60	empty

Interfaces

7 interfaces between chains.

A–C · 1819 Å² buried · 32 hydrogen bonds · protein-protein
D–F · 1794 Å² buried · 33 hydrogen bonds · protein-protein
D–E · 1592 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1496 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 1201 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6Z4X · Structure of the CAK complex form Chaetomium thermophilum bound to ATP-gamma-S · the same entry in another collection · chain A against A, TM-score 1.00

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 G0SH78
Every structure of UniProt G0SFC6
Every structure of UniProt G0SF48
Elsewhere: RCSB PDB 6Z4X · PDBe 6Z4X · UniProt G0SH78 · UniProt G0SFC6 · UniProt G0SF48

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