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Crystal structure of foldswitch-stabilized kaib in complex with the N- terminal ci domain of kaic and a dimer of kaia C-terminal domains from thermosynechococcus elongatus

Analyse Crystal structure of foldswitch-stabilized kaib in complex with the N- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JWR
Type: protein
Length: 1,160 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Circadian clock protein kinase kaic; Circadian clock protein kaib; Circadian clock…
EC: 2.7.11.1
UniProt: Q79V60, Q79V61, Q79V62
Ligands: PO4
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 8 distinct chains · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Circadian clock protein kinase kaic (EC 2.7.11.1)	protein	231	32% helix, 27% strand	Q79V60
B	Circadian clock protein kaib	protein	89	33% helix, 30% strand	Q79V61
C	Circadian clock protein kinase kaic (EC 2.7.11.1)	protein	221	30% helix, 29% strand	Q79V60
D	Circadian clock protein kaib	protein	87	33% helix, 29% strand	Q79V61
E	Circadian clock protein kaia	protein	132	70% helix, 5% strand	Q79V62
F	Circadian clock protein kaia	protein	134	72% helix, 0% strand	Q79V62
G	Circadian clock protein kaia	protein	133	70% helix, 5% strand	Q79V62
H	Circadian clock protein kaia	protein	133	70% helix, 0% strand	Q79V62

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A, C

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

Pockets

20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1195	0.76	0.78	130	empty
2	296	0.65	0.81	39	empty
3	554	0.63	0.75	37	empty
4	441	0.61	0.76	40	empty
5	138	0.57	0.83	23	empty

Interfaces

12 interfaces between chains.

E–F · 1726 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 1710 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1189 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1152 Å² buried · 20 hydrogen bonds · protein-protein
D–G · 985 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5JWR · Crystal structure of foldswitch-stabilized KaiB in complex with the N-terminal CI domain… · the same entry in another collection · chain H against H, TM-score 1.00
Q79V62 · AlphaFold monomer V2.0 prediction for circadian clock protein kaia (Q79V62) · a predicted model of the same protein · chain G against A, TM-score 0.96
Q79V60 · AlphaFold monomer V2.0 prediction for circadian clock protein kinase kaic (Q79V60) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q79V60
Every structure of UniProt Q79V61
Every structure of UniProt Q79V62
Elsewhere: RCSB PDB 5JWR · PDBe 5JWR · UniProt Q79V60 · UniProt Q79V61 · UniProt Q79V62

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