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Crystal structure of kaic S431E in complex with foldswitch-stabilized kaib from thermosynechococcus elongatus

Analyse Crystal structure of kaic S431E in complex with foldswitch-stabilized kaib from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JWQ
Type: protein
Length: 998 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Circadian clock protein kinase kaic; Circadian clock protein kaib
EC: 2.7.11.1
UniProt: Q79V60, Q79V61
Ligands: ADP
Pockets: 15 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Circadian clock protein kinase kaic (EC 2.7.11.1)	protein	413	31% helix, 20% strand	Q79V60
B	Circadian clock protein kaib	protein	88	26% helix, 18% strand	Q79V61
C	Circadian clock protein kinase kaic (EC 2.7.11.1)	protein	408	28% helix, 20% strand	Q79V60
D	Circadian clock protein kaib	protein	89	27% helix, 15% strand	Q79V61

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C

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

Pockets

15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	308	0.82	0.93	57	ADP
2	327	0.82	0.92	48	empty
3	978	0.81	0.82	99	empty
4	561	0.81	0.87	72	empty
5	190	0.78	0.93	42	empty

Interfaces

4 interfaces between chains.

A–C · 2015 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1136 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 927 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 217 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5JWQ · Crystal structure of KaiC S431E in complex with foldswitch-stabilized KaiB from… · the same entry in another collection · chain D against D, TM-score 1.00
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 0.96
Q79V61 · AlphaFold monomer V2.0 prediction for circadian clock protein kaib (Q79V61) · a predicted model of the same protein · chain B against A, TM-score 0.83

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
Elsewhere: RCSB PDB 5JWQ · PDBe 5JWQ · UniProt Q79V60 · UniProt Q79V61

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