Serine/threonine-protein kinase Nek7
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count | Chain A; UniProt 1–302 Chain B; UniProt 1–302 | Mutation:D161N | EDO 1,2-ETHANEDIOL × 5 | X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;294 K;0.1 M Tris pH 8.4, PEG 8000 15% | Resolution 2.40 Å R-free 0.238 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 8WS1 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2WQM Structure of apo human Nek7 Deposited 2009-08-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–302(302 aa)
|
Not recorded | SO4 SULFATE ION × 1 NI NICKEL (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
100 MM HEPES, PH 7.5, 15% PEG 5000 MME, 400 MM AMMONIUM SULFATE
|
Resolution 2.10 Å R-free 0.215 |
| 2WQN Structure of ADP-bound human Nek7 Deposited 2009-08-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–302(302 aa)
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 NI NICKEL (II) ION × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
100MM HEPES 7.5, 15% PEG 5000MME, 400MM AMMONIUM SULFATE
|
Resolution 2.30 Å R-free 0.221 |
| 5DE2 Structural mechanism of Nek7 activation by Nek9-induced dimerisation Deposited 2015-08-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
1–302(302 aa)
|
Mutation:Y97F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.5;291 K;The composition of the reservoir buffer was: 0.2M Potassium thiocyanate, 0.1M Bis-Tris propane pH 7.5, 20% (w/v) PEG 3350.
|
Resolution 2.78 Å R-free 0.254 |
| 5DE2 Structural mechanism of Nek7 activation by Nek9-induced dimerisation Deposited 2015-08-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain B
1–302(302 aa)
|
Mutation:Y97F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.5;291 K;The composition of the reservoir buffer was: 0.2M Potassium thiocyanate, 0.1M Bis-Tris propane pH 7.5, 20% (w/v) PEG 3350.
|
Resolution 2.78 Å R-free 0.254 |
| 6NPY Cryo-EM structure of NLRP3 bound to NEK7 Deposited 2019-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer;Protein × 2 PDB declaration: dimeric |
Chain B
34–302(269 aa)
|
Mutation:L54R,V58K,P59T,K87A,A99V,S100C,E103T,D104G | ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6S73 Crystal structure of Nek7 SRS mutant bound to compound 51 Deposited 2019-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–302(302 aa)
|
Mutation:L86H, Y97F, L180F | F9N 3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N}-[3-(dimethylamino)propyl]benzenesulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.5;291 K;0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane pH 6.5, 20 % w/v PEG 3350
|
Resolution 3.50 Å R-free 0.271 |
| 6S73 Crystal structure of Nek7 SRS mutant bound to compound 51 Deposited 2019-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
1–302(302 aa)
|
Mutation:L86H, Y97F, L180F | F9N 3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N}-[3-(dimethylamino)propyl]benzenesulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.5;291 K;0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane pH 6.5, 20 % w/v PEG 3350
|
Resolution 3.50 Å R-free 0.271 |
| 6S73 Crystal structure of Nek7 SRS mutant bound to compound 51 Deposited 2019-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain C
1–302(302 aa)
|
Mutation:L86H, Y97F, L180F | F9N 3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N}-[3-(dimethylamino)propyl]benzenesulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.5;291 K;0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane pH 6.5, 20 % w/v PEG 3350
|
Resolution 3.50 Å R-free 0.271 |
| 6S73 Crystal structure of Nek7 SRS mutant bound to compound 51 Deposited 2019-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain D
1–302(302 aa)
|
Mutation:L86H, Y97F, L180F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.5;291 K;0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane pH 6.5, 20 % w/v PEG 3350
|
Resolution 3.50 Å R-free 0.271 |
| 6S75 Crystal structure of Nek7 bound to compound 51 Deposited 2019-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–302(302 aa)
|
Not recorded | F9N 3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N}-[3-(dimethylamino)propyl]benzenesulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;20 % w/v Polyethylene glycol 3,350, 150 mM di-Sodium DL-malate; pH 7.0, 3% w/v 1,6-Hexanediol
|
Resolution 3.30 Å R-free 0.317 |
| 6S75 Crystal structure of Nek7 bound to compound 51 Deposited 2019-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
1–302(302 aa)
|
Not recorded | F9N 3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N}-[3-(dimethylamino)propyl]benzenesulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;20 % w/v Polyethylene glycol 3,350, 150 mM di-Sodium DL-malate; pH 7.0, 3% w/v 1,6-Hexanediol
|
Resolution 3.30 Å R-free 0.317 |
| 6S75 Crystal structure of Nek7 bound to compound 51 Deposited 2019-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain C
1–302(302 aa)
|
Not recorded | F9N 3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N}-[3-(dimethylamino)propyl]benzenesulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;20 % w/v Polyethylene glycol 3,350, 150 mM di-Sodium DL-malate; pH 7.0, 3% w/v 1,6-Hexanediol
|
Resolution 3.30 Å R-free 0.317 |
| 6S75 Crystal structure of Nek7 bound to compound 51 Deposited 2019-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain D
1–302(302 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;20 % w/v Polyethylene glycol 3,350, 150 mM di-Sodium DL-malate; pH 7.0, 3% w/v 1,6-Hexanediol
|
Resolution 3.30 Å R-free 0.317 |
| 6S76 Crystal structure of human Nek7 Deposited 2019-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–302(302 aa)
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;20 % w/v Polyethylene glycol 3,350, 150 mM di-Sodium DL-malate; pH 7.0
|
Resolution 3.38 Å R-free 0.286 |
| 6S76 Crystal structure of human Nek7 Deposited 2019-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
1–302(302 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;20 % w/v Polyethylene glycol 3,350, 150 mM di-Sodium DL-malate; pH 7.0
|
Resolution 3.38 Å R-free 0.286 |
| 6S76 Crystal structure of human Nek7 Deposited 2019-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain C
1–302(302 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;20 % w/v Polyethylene glycol 3,350, 150 mM di-Sodium DL-malate; pH 7.0
|
Resolution 3.38 Å R-free 0.286 |
| 6S76 Crystal structure of human Nek7 Deposited 2019-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain D
1–302(302 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;20 % w/v Polyethylene glycol 3,350, 150 mM di-Sodium DL-malate; pH 7.0
|
Resolution 3.38 Å R-free 0.286 |
| 8EJ4 Cryo-EM structure of the active NLRP3 inflammasome disk Deposited 2022-09-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 20 PDB declaration: eicosameric |
Chain K
20–297(278 aa)
Chain L
20–297(278 aa)
Chain M
20–297(278 aa)
Chain N
20–297(278 aa)
Chain O
20–297(278 aa)
Chain P
20–297(278 aa)
Chain Q
20–297(278 aa)
Chain R
20–297(278 aa)
Chain S
20–297(278 aa)
Chain T
20–297(278 aa)
|
Not recorded | AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 10 MG MAGNESIUM ION × 10 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8SXN Structure of NLRP3 and NEK7 complex Deposited 2023-05-22 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric |
Chain A
1–302(302 aa)
Chain B
1–302(302 aa)
|
Not recorded | 7YN 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.04 Å |
| 8WS0 Crystal structure of human NEK7 S195D mutant Deposited 2023-10-16 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer;Protein × 2 PDB declaration: dimeric |
Chain A
1–302(302 aa)
Chain B
1–302(302 aa)
|
Mutation:S195D Mutation:S195D | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;294 K;0.1 M Tris pH 8.5, 20% PEG 3350
|
Resolution 2.12 Å R-free 0.242 |
| 9H59 Cryo-EM structure of DDB1-CRBN in complex with NK7-902 and NEK7 Deposited 2024-10-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric |
Chain C
1–302(302 aa)
|
Not recorded | A1ISP 2-[(3S)-2,6-bis(oxidanylidene)piperidin-3-yl]-5-[(1S,2R,5S)-2-(ethylamino)-8-azabicyclo[3.2.1]octan-8-yl]isoindole-1,3-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9NFQ Crystal structure of CRBN-DDB1 and MRT-3486 in complex with NEK7 Deposited 2025-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric |
Chain C
1–302(302 aa)
|
Not recorded | A1BX6 (3S)-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-2-(phenylmethanesulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;293 K;0.029 M HEPES salt, 0.071 M MOPS acid, 0.06 M NaNO3, 0.06 M Na2HPO4, 0.06 M (NH4)2SO4, 11 % (w/v) PEG 8,000 and 25 % (v/v) ethylene glycol.
|
Resolution 3.25 Å R-free 0.261 |
12 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | NEK7_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A; PDBConstruct 1–302; UniProt 1–302 Author chain B; PDBConstruct 1–302; UniProt 1–302 |