MolNFT v1 · #127851 · protein

Kaicba circadian clock backbone model based on a cryo-EM density

5N8Y · Circadian clock protein kinase kaic: “Kaicba circadian clock backbone model based on a cryo-EM density”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #127851 on GenesisL1: 3D structure, binding sites and…

PDB: 5N8Y
Type: protein
Length: 4,752 residues
Chains: 24
Method: electron microscopy
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: Q79PF4, Q79PF5, Q79PF6
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 4 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Circadian clock protein kinase kaic (EC 2.7.11.1)	protein	483	32% helix, 24% strand	Q79PF4
G, H, K, J, I, L	Circadian clock protein kaib	protein	93	42% helix, 24% strand	Q79PF5
M, O, Q, S, U, X	Circadian clock protein kaia	protein	109	72% helix, 0% strand	Q79PF6
N, P, R, T, V, W	Circadian clock protein kaia	protein	107	81% helix, 0% strand	Q79PF6

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	927	0.83	0.85	121	empty
2	1159	0.82	0.83	137	empty
3	1194	0.82	0.83	146	empty
4	1148	0.82	0.83	134	empty
5	941	0.81	0.83	131	empty

Interfaces

24 interfaces between chains.

B–C · 832 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 831 Å² buried · 4 hydrogen bonds · protein-protein
D–E · 819 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 809 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 808 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5N8Y · KaiCBA circadian clock backbone model based on a Cryo-EM density · the same entry in another collection · chain J against J, 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 Q79PF4
Every structure of UniProt Q79PF5
Every structure of UniProt Q79PF6
Elsewhere: RCSB PDB 5N8Y · PDBe 5N8Y · UniProt Q79PF4 · UniProt Q79PF5 · UniProt Q79PF6

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