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MolNFT v2 · #197411 · protein

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC

7V3X · Circadian clock protein kinase KaiC: “Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC”. X-ray diffraction at 3.1, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.87). MolNFT v2 #197411 on GenesisL1: 3D…

PDB
7V3X
Type
protein
Length
11,050 residues
Chains
24
Method
x-ray diffraction
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
3.1
Source
Synechococcus elongatus (strain PCC 7942 / FACHB-805)
Molecule
Circadian clock protein kinase KaiC
EC
2.7.11.1
UniProt
Q79PF4
Ligands
ATP, ADP, MG
Pockets
20 · best druggability 0.87

Structure

x-ray diffraction · resolution 3.1 · 24 distinct chains · 31% helix, 26% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACircadian clock protein kinase KaiC (EC 2.7.11.1)protein46833% helix, 29% strandQ79PF4
BCircadian clock protein kinase KaiC (EC 2.7.11.1)protein46932% helix, 28% strandQ79PF4
ECircadian clock protein kinase KaiC (EC 2.7.11.1)protein47033% helix, 27% strandQ79PF4
FCircadian clock protein kinase KaiC (EC 2.7.11.1)protein46832% helix, 28% strandQ79PF4
CCircadian clock protein kinase KaiC (EC 2.7.11.1)protein47232% helix, 26% strandQ79PF4
DCircadian clock protein kinase KaiC (EC 2.7.11.1)protein47131% helix, 27% strandQ79PF4
GCircadian clock protein kinase KaiC (EC 2.7.11.1)protein46733% helix, 29% strandQ79PF4
HCircadian clock protein kinase KaiC (EC 2.7.11.1)protein46831% helix, 28% strandQ79PF4
KCircadian clock protein kinase KaiC (EC 2.7.11.1)protein47133% helix, 27% strandQ79PF4
LCircadian clock protein kinase KaiC (EC 2.7.11.1)protein47032% helix, 28% strandQ79PF4
ICircadian clock protein kinase KaiC (EC 2.7.11.1)protein47332% helix, 27% strandQ79PF4
JCircadian clock protein kinase KaiC (EC 2.7.11.1)protein46831% helix, 27% strandQ79PF4
NCircadian clock protein kinase KaiC (EC 2.7.11.1)protein45531% helix, 22% strandQ79PF4
OCircadian clock protein kinase KaiC (EC 2.7.11.1)protein46131% helix, 25% strandQ79PF4
RCircadian clock protein kinase KaiC (EC 2.7.11.1)protein46331% helix, 27% strandQ79PF4
MCircadian clock protein kinase KaiC (EC 2.7.11.1)protein46330% helix, 26% strandQ79PF4
PCircadian clock protein kinase KaiC (EC 2.7.11.1)protein45630% helix, 28% strandQ79PF4
QCircadian clock protein kinase KaiC (EC 2.7.11.1)protein46632% helix, 27% strandQ79PF4
TCircadian clock protein kinase KaiC (EC 2.7.11.1)protein41529% helix, 17% strandQ79PF4
UCircadian clock protein kinase KaiC (EC 2.7.11.1)protein43029% helix, 22% strandQ79PF4
XCircadian clock protein kinase KaiC (EC 2.7.11.1)protein46130% helix, 26% strandQ79PF4
SCircadian clock protein kinase KaiC (EC 2.7.11.1)protein44430% helix, 21% strandQ79PF4
VCircadian clock protein kinase KaiC (EC 2.7.11.1)protein43729% helix, 22% strandQ79PF4
WCircadian clock protein kinase KaiC (EC 2.7.11.1)protein46430% helix, 25% strandQ79PF4

Ligands and binding sites

  • ATP · Adenosine-5'-triphosphate · ligand · 45 copies · chains A, B, C, E, F, D, G, H, I, K, L, J, N, O, P, R, M, Q, T, U, V, X, S, W
  • ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains R, Q, U, V, X, W
  • MG · Magnesium ion · metal · 36 copies · chains A, B, C, E, F, D, G, H, I, K, L, J, N, O, P, R, M, Q, T, U, V

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
19710.870.88150empty
211670.870.88186ATP, MG
310770.860.87149empty
48330.850.88123ATP, MG
57570.850.88114ATP

Interfaces

32 interfaces between chains.

  • H–I · 3175 Ų buried · 48 hydrogen bonds · protein-protein
  • C–D · 3160 Ų buried · 40 hydrogen bonds · protein-protein
  • I–J · 3139 Ų buried · 36 hydrogen bonds · protein-protein
  • B–C · 3114 Ų buried · 42 hydrogen bonds · protein-protein
  • A–B · 3088 Ų buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 35 modified (phosphorylation).

Compared structures

  • 7V3X · Crystal structure of cyanobacterial circadian clock protein kaic · the same entry in another collection · chain A against A, TM-score 1.00

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