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Wild type crystal structure of full length circadian clock protein kaib from thermosynechococcus elongatus bp-1

Analyse Wild type crystal structure of full length circadian clock protein kaib from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QKE
Type: protein
Length: 615 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Circadian clock protein kaib
UniProt: Q79V61
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · 6 distinct chains · 31% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Circadian clock protein kaib	protein	98	31% helix, 29% strand	Q79V61
B	Circadian clock protein kaib	protein	108	30% helix, 26% strand	Q79V61
C	Circadian clock protein kaib	protein	98	36% helix, 23% strand	Q79V61
D	Circadian clock protein kaib	protein	107	29% helix, 22% strand	Q79V61
E	Circadian clock protein kaib	protein	104	29% helix, 24% strand	Q79V61
F	Circadian clock protein kaib	protein	100	33% helix, 26% strand	Q79V61

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1034	0.73	0.76	109	empty
2	356	0.53	0.73	39	empty
3	226	0.49	0.74	29	empty
4	125	0.39	0.74	14	empty
5	84	0.36	0.76	21	empty

Interfaces

9 interfaces between chains.

C–D · 829 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 773 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 771 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 425 Å² buried · 2 hydrogen bonds · protein-protein
B–F · 312 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2QKE · Wild Type Crystal Structure of Full Length Circadian Clock Protein KaiB from… · the same entry in another collection · chain F against F, TM-score 1.00
Q79V61 · AlphaFold monomer V2.0 prediction for circadian clock protein kaib (Q79V61) · a predicted model of the same protein · chain A against A, TM-score 0.48

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 Q79V61
Elsewhere: RCSB PDB 2QKE · PDBe 2QKE · UniProt Q79V61

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