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Structure of kaia dimer in complex with C-terminal kaic peptide at 2.8 a resolution

Analyse Structure of kaia dimer in complex with C-terminal kaic peptide at 2.8 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C5E
Type: protein
Length: 604 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Circadian clock protein kaia; Kaic C-terminal peptide
UniProt: Q79PF6
Ligands: 52M
Pockets: 10 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Circadian clock protein kaia	protein	284	49% helix, 12% strand	Q79PF6
G	Kaic C-terminal peptide	protein	16	75% helix, 0% strand	—
H	Kaic C-terminal peptide	protein	20	70% helix, 0% strand	—

Ligands and binding sites

52M · 2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-5-[(sulfanylcarbonyl)amino]benzoic acid · ligand · 2 copies · chains A, G, B, H

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	354	0.69	0.82	42	empty
2	361	0.65	0.80	44	empty
3	178	0.56	0.81	27	52M
4	61	0.51	0.85	14	empty
5	94	0.47	0.81	20	empty

Interfaces

5 interfaces between chains.

A–B · 3540 Å² buried · 52 hydrogen bonds · protein-protein
A–H · 608 Å² buried · 6 hydrogen bonds · protein-protein
G–B · 572 Å² buried · 5 hydrogen bonds · protein-protein
B–H · 446 Å² buried · 2 hydrogen bonds · protein-protein
A–G · 399 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5C5E · Structure of KaiA dimer in complex with C-terminal KaiC peptide at 2.8 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
Q79PF6 · AlphaFold monomer V2.0 prediction for circadian clock protein kaia (Q79PF6) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 Q79PF6
Elsewhere: RCSB PDB 5C5E · PDBe 5C5E · UniProt Q79PF6

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