MolNFT v1 · #106651 · protein

Crystal structure of N-terminal C1 domain of kaic

4TL9 · Circadian clock protein kinase kaic: “Crystal structure of N-terminal C1 domain of kaic”. X-ray diffraction, 3 ligands (AGS, MG, CL), 19 pockets (best druggability 0.81). MolNFT v1 #106651 on GenesisL1: 3D structure, binding sites…

PDB: 4TL9
Type: protein
Length: 1,312 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Circadian clock protein kinase kaic
EC: 2.7.11.1
UniProt: Q79PF4
Ligands: AGS, MG, CL
Pockets: 19 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 34% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Circadian clock protein kinase kaic (EC 2.7.11.1)	protein	220	34% helix, 29% strand	Q79PF4
B, E	Circadian clock protein kinase kaic (EC 2.7.11.1)	protein	218	34% helix, 29% strand	Q79PF4
C	Circadian clock protein kinase kaic (EC 2.7.11.1)	protein	222	33% helix, 29% strand	Q79PF4
D	Circadian clock protein kinase kaic (EC 2.7.11.1)	protein	220	34% helix, 29% strand	Q79PF4
F	Circadian clock protein kinase kaic (EC 2.7.11.1)	protein	214	33% helix, 30% strand	Q79PF4

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 6 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F

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

Pockets

19 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	852	0.81	0.84	79	MG, AGS
2	912	0.81	0.83	78	MG, AGS
3	423	0.80	0.88	67	MG, CL, AGS
4	269	0.80	0.92	39	MG, AGS
5	277	0.78	0.91	39	MG, AGS

Interfaces

6 interfaces between chains.

A–F · 1352 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 1313 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1295 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1278 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 1179 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

4TL9 · Crystal structure of N-terminal C1 domain of KaiC · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 4TL9 · PDBe 4TL9 · UniProt Q79PF4

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