Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain A； UniProt 113–626 Chain B； UniProt 113–626 Chain C； UniProt 113–626 Chain D； UniProt 113–626 | Fragment：residues 113-626 Mutation：H206R, D207N, T592E | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 | X-RAY DIFFRACTION X-ray crystallization conditions：BATCH MODE；pH 7.4；298 K；SPG buffer, PEG 1500 | Resolution 2.30 Å R-free 0.246 |
| 2 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 113–626 Chain D； UniProt 113–626 | Fragment：residues 113-626 Mutation：H206R, D207N, T592E | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 | X-RAY DIFFRACTION X-ray crystallization conditions：BATCH MODE；pH 7.4；298 K；SPG buffer, PEG 1500 | Resolution 2.30 Å R-free 0.246 |
| 3 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain B； UniProt 113–626 Chain C； UniProt 113–626 | Fragment：residues 113-626 Mutation：H206R, D207N, T592E | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：BATCH MODE；pH 7.4；298 K；SPG buffer, PEG 1500 | Resolution 2.30 Å R-free 0.246 |
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 4ZWG | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2E8O Solution structure of the N-terminal SAM-domain of the SAM domain and HD domain containing protein 1 (Dendritic cell-derived IFNG-induced protein) (DCIP) (Monocyte protein 5) (MOP-5) Deposited 2007-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
23–118（96 aa）
Fragment：SAM domain
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure AMBIENT
NMR sample composition
1.17mM SAM DOMAIN, 20mM d-TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 3U1N Structure of the catalytic core of human SAMHD1 Deposited 2011-09-30 | Different construct 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
120–626（507 aa）
Fragment：unp residues 120-626
Chain D
120–626（507 aa）
Fragment：unp residues 120-626
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | PO4 PHOSPHATE ION × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
|
Resolution 3.10 Å R-free 0.228 |
| 3U1N Structure of the catalytic core of human SAMHD1 Deposited 2011-09-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
120–626（507 aa）
Fragment：unp residues 120-626
Chain C
120–626（507 aa）
Fragment：unp residues 120-626
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | PO4 PHOSPHATE ION × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
|
Resolution 3.10 Å R-free 0.228 |
| 4BZB Crystal structure of the tetrameric dGTP-bound SAMHD1 mutant catalytic core Deposited 2013-07-25 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：HD DOMAIN, RESIDUES 113-626
Chain B
113–626（514 aa）
Fragment：HD DOMAIN, RESIDUES 113-626
Chain C
113–626（514 aa）
Fragment：HD DOMAIN, RESIDUES 113-626
Chain D
113–626（514 aa）
Fragment：HD DOMAIN, RESIDUES 113-626
|
Mutation：YES Mutation：YES Mutation：YES Mutation：YES | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.4；100 MM SPG BUFFER, PH 7.4, 25% PEG 1500
|
Resolution 1.83 Å R-free 0.206 |
| 4BZC Crystal structure of the tetrameric dGTP-bound wild type SAMHD1 catalytic core Deposited 2013-07-25 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：HD DOMAIN, RESIDUES 113-626
Chain B
113–626（514 aa）
Fragment：HD DOMAIN, RESIDUES 113-626
Chain C
113–626（514 aa）
Fragment：HD DOMAIN, RESIDUES 113-626
Chain D
113–626（514 aa）
Fragment：HD DOMAIN, RESIDUES 113-626
|
Not recorded | T8T 2'-deoxyguanosine-5'-O-(1-thiotriphosphate) × 12 MN MANGANESE (II) ION × 4 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.7；100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500
|
Resolution 2.88 Å R-free 0.245 |
| 4CC9 Crystal structure of human SAMHD1 (amino acid residues 582-626) bound to Vpx isolated from sooty mangabey and human DCAF1 (amino acid residues 1058-1396) Deposited 2013-10-19 | 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
582–626（45 aa）
Fragment：RESIDUES 582-626
|
Not recorded | PG4 TETRAETHYLENE GLYCOL × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.2 M MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5, 15% PEG 400
|
Resolution 2.47 Å R-free 0.216 |
| 4MZ7 Structural insight into dGTP-dependent activation of tetrameric SAMHD1 deoxynucleoside triphosphate triphosphohydrolase Deposited 2013-09-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
109–626（518 aa）
Fragment：UNP residues 109-626
Chain B
109–626（518 aa）
Fragment：UNP residues 109-626
|
Mutation：C266Y Mutation：C266Y | ZN ZINC ION × 4 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 10 MG MAGNESIUM ION × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1M MES (pH 6.5), 25%(w/v) polyethylene glycol monomethyle ether 550, VAPOR DIFFUSION, SITTING DROP, temperature 289K
|
Resolution 1.80 Å R-free 0.226 |
| 4Q7H Crystal structure of SAMHD1 catalytic core with GTP Deposited 2014-04-25 | Different construct 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
109–626（518 aa）
Fragment：HD-domain, UNP residues 109-626
Chain B
109–626（518 aa）
Fragment：HD-domain, UNP residues 109-626
|
Mutation：C266Y Mutation：C266Y | ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2M Lithium citrate tribasic tetrahydrate, 24% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.59 Å R-free 0.248 |
| 4Q7H Crystal structure of SAMHD1 catalytic core with GTP Deposited 2014-04-25 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
109–626（518 aa）
Fragment：HD-domain, UNP residues 109-626
Chain D
109–626（518 aa）
Fragment：HD-domain, UNP residues 109-626
|
Mutation：C266Y Mutation：C266Y | ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2M Lithium citrate tribasic tetrahydrate, 24% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.59 Å R-free 0.248 |
| 4QFX Crystal structure of the tetrameric dGTP/dATP-bound SAMHD1 (RN206) mutant catalytic core Deposited 2014-05-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Mutation：H206R/D207N Mutation：H206R/D207N Mutation：H206R/D207N Mutation：H206R/D207N | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 8 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M SPG, pH 6.5, 25% PEG1500, 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.20 Å R-free 0.270 |
| 4QFY Crystal structure of the tetrameric dGTP/dCTP-bound SAMHD1 (RN206) mutant catalytic core Deposited 2014-05-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Mutation：H206R/D207N Mutation：H206R/D207N Mutation：H206R/D207N Mutation：H206R/D207N | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 8 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M SPG, pH 6.5, 25% PEG1500, 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.10 Å R-free 0.269 |
| 4QFZ Crystal structure of the tetrameric dGTP/dTTP-bound SAMHD1 (RN206) mutant catalytic core Deposited 2014-05-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Mutation：H206R/D207N Mutation：H206R/D207N Mutation：H206R/D207N Mutation：H206R/D207N | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 4 TTP THYMIDINE-5'-TRIPHOSPHATE × 8 MG MAGNESIUM ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M SPG, pH 6.5, 25% PEG1500, 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.250 |
| 4QG0 Crystal structure of the tetrameric dGTP/dUTP-bound SAMHD1 (RN206) mutant catalytic core Deposited 2014-05-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Mutation：H206R/D207N Mutation：H206R/D207N Mutation：H206R/D207N Mutation：H206R/D207N | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 4 DUT DEOXYURIDINE-5'-TRIPHOSPHATE × 8 MG MAGNESIUM ION × 7 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M SPG, pH 6.5, 25% PEG1500, 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.250 |
| 4QG1 Crystal structure of the tetrameric GTP/dATP-bound SAMHD1 (RN206) mutant catalytic core Deposited 2014-05-22 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Mutation：H206R/D207N Mutation：H206R/D207N Mutation：H206R/D207N Mutation：H206R/D207N | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 8 MG MAGNESIUM ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M SPG, pH 6.5, 25% PEG1500, 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.20 Å R-free 0.264 |
| 4QG2 Crystal structure of the tetrameric GTP/dATP/ATP-bound SAMHD1 (RN206) mutant catalytic core Deposited 2014-05-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Mutation：H206R/D207N Mutation：H206R/D207N Mutation：H206R/D207N Mutation：H206R/D207N | GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M SPG, pH 6.5, 25% PEG1500, 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.25 Å R-free 0.271 |
| 4QG4 Crystal structure of the tetrameric GTP/dATP/ATP-bound SAMHD1 (H210A) mutant catalytic core Deposited 2014-05-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Mutation：H210A Mutation：H210A Mutation：H210A Mutation：H210A | GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M SPG, pH 6.5, 25% PEG1500, 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.10 Å R-free 0.245 |
| 4RXO The structure of GTP-bound SAMHD1 Deposited 2014-12-11 | Different construct 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
109–626（518 aa）
Chain B
109–626（518 aa）
|
Not recorded | ZN ZINC ION × 2 PO4 PHOSPHATE ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.2 M sodium chloride, 0.1M Na/K phosphate, and 25% w/v polyethylene glycol 1000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 2.60 Å R-free 0.222 |
| 4RXO The structure of GTP-bound SAMHD1 Deposited 2014-12-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
109–626（518 aa）
Chain D
109–626（518 aa）
|
Not recorded | ZN ZINC ION × 2 PO4 PHOSPHATE ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.2 M sodium chloride, 0.1M Na/K phosphate, and 25% w/v polyethylene glycol 1000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 2.60 Å R-free 0.222 |
| 4RXP The structure of GTP-dATP-bound SAMHD1 Deposited 2014-12-11 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
109–626（518 aa）
Chain B
109–626（518 aa）
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M lithium sulfate monohydrate, 0.1M sodium citrate tribasic dihydrate, and 20% w/v polyethylene glycol 1000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 2.10 Å R-free 0.208 |
| 4RXQ The structure of GTP-dUTP-bound SAMHD1 Deposited 2014-12-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
109–626（518 aa）
Chain B
109–626（518 aa）
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DUT DEOXYURIDINE-5'-TRIPHOSPHATE × 8 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M lithium sulfate monohydrate, 0.1M sodium citrate tribasic dihydrate, and 20% w/v polyethylene glycol 1000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 2.10 Å R-free 0.229 |
| 4RXR The structure of GTP-dCTP-bound SAMHD1 Deposited 2014-12-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
109–626（518 aa）
Chain B
109–626（518 aa）
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 8 MG MAGNESIUM ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M lithium sulfate monohydrate, 0.1M sodium citrate tribasic dihydrate, and 20% w/v polyethylene glycol 1000
, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 2.12 Å R-free 0.213 |
| 4RXS The structure of GTP-dTTP-bound SAMHD1 Deposited 2014-12-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
109–626（518 aa）
Chain B
109–626（518 aa）
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 4 TTP THYMIDINE-5'-TRIPHOSPHATE × 8 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M lithium sulfate monohydrate, 0.1M sodium citrate tribasic dihydrate, and 20% w/v polyethylene glycol 1000
, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 2.20 Å R-free 0.222 |
| 4TNP Structural basis of cellular dNTP regulation, SAMHD1-GTP-dCTP-cCTP complex Deposited 2014-06-04 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.4；298 K；SPG buffer, PEG 1500
|
Resolution 2.00 Å R-free 0.222 |
| 4TNQ Structural basis of cellular dNTP regulation, SAMHD1-GTP-dTTP-dTTP complex Deposited 2014-06-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Not recorded | TTP THYMIDINE-5'-TRIPHOSPHATE × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；SPG buffer, PEG 1500
|
Resolution 2.55 Å R-free 0.198 |
| 4TNR Structure basis of cellular dNTP regulation, SAMHD1-GTP-dATP-dATP complex Deposited 2014-06-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；SPG buffer, PEG 1500
|
Resolution 2.75 Å R-free 0.242 |
| 4TNX Structure basis of cellular dNTP regulation, SAMHD1-GTP-dGTP complex Deposited 2014-06-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Not recorded | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 3PO TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；SPG buffer, PEG 1500
|
Resolution 2.31 Å R-free 0.226 |
| 4TNY Structural basis of cellular dNTP regulation, SAMHD1-dGTP-dATP-dGTP complex Deposited 2014-06-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Not recorded | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 8 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；SPG buffer, PEG 1500
|
Resolution 2.60 Å R-free 0.244 |
| 4TNZ Structure basis of cellular dNTP regulation, SAMHD1-GTP-dATP-dTTP complex Deposited 2014-06-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Not recorded | TTP THYMIDINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；SPG buffer, PEG 1500
|
Resolution 2.38 Å R-free 0.243 |
| 4TO0 Structure basis of cellular dNTP regulation, SAMHD1-GTP-dATP-dCTP complex Deposited 2014-06-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；SPG buffer, PEG 1500
|
Resolution 2.30 Å R-free 0.222 |
| 4TO1 Structure basis of cellular dNTP regulation, SAMHD1-GTP-dATP/dCTP-dCTP complex Deposited 2014-06-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 6 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；SPG buffer, PEG 1500
|
Resolution 2.55 Å R-free 0.235 |
| 4TO2 Structure basis of cellular dNTP regulation, SAMHD1-dGTP-dGTP-dGTP/dTTP complex Deposited 2014-06-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Not recorded | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 11 MG MAGNESIUM ION × 8 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；SPG buffer, PEG 1500
|
Resolution 2.27 Å R-free 0.234 |
| 4TO3 Structural basis of cellular dNTP regulation, SAMHD1-dGTP-dGTP-dCTP complex Deposited 2014-06-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 8 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；SPG buffer, PEG 1500
|
Resolution 2.20 Å R-free 0.204 |
| 4TO4 Structure basis of cellular dNTP regulation, SAMHD1-GTP-dGTP-dCTP complex Deposited 2014-06-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；SPG buffer, PEG 1500
|
Resolution 2.10 Å R-free 0.225 |
| 4TO5 Structure basis of cellular dNTP regulation, SAMHD1-GTP-dTTP-dCTP complex Deposited 2014-06-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：UNP residues 113-626
Chain B
113–626（514 aa）
Fragment：UNP residues 113-626
Chain C
113–626（514 aa）
Fragment：UNP residues 113-626
Chain D
113–626（514 aa）
Fragment：UNP residues 113-626
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 TTP THYMIDINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；SPG buffer, PEG 1500
|
Resolution 2.80 Å R-free 0.285 |
| 4TO6 Structure basis of cellular dNTP regulation, SAMHD1-dGTP-dATP-dTTP/dGTP complex Deposited 2014-06-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Not recorded | TTP THYMIDINE-5'-TRIPHOSPHATE × 3 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 5 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；SPG buffer, PEG 1500
|
Resolution 2.33 Å R-free 0.244 |
| 4ZWE Crystal structure of the dGTP-bound catalytic core of SAMHD1 T592V mutant Deposited 2015-05-19 | Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Fragment：residues 113-626
Chain B
113–626（514 aa）
Fragment：residues 113-626
Chain C
113–626（514 aa）
Fragment：residues 113-626
Chain D
113–626（514 aa）
Fragment：residues 113-626
|
Mutation：H206R, D207N, T592V Mutation：H206R, D207N, T592V Mutation：H206R, D207N, T592V Mutation：H206R, D207N, T592V | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.4；298 K；SPG buffer, PEG 1500
|
Resolution 2.81 Å R-free 0.248 |
| 4ZWE Crystal structure of the dGTP-bound catalytic core of SAMHD1 T592V mutant Deposited 2015-05-19 | Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
113–626（514 aa）
Fragment：residues 113-626
Chain D
113–626（514 aa）
Fragment：residues 113-626
|
Mutation：H206R, D207N, T592V Mutation：H206R, D207N, T592V | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.4；298 K；SPG buffer, PEG 1500
|
Resolution 2.81 Å R-free 0.248 |
| 4ZWE Crystal structure of the dGTP-bound catalytic core of SAMHD1 T592V mutant Deposited 2015-05-19 | Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
113–626（514 aa）
Fragment：residues 113-626
Chain C
113–626（514 aa）
Fragment：residues 113-626
|
Mutation：H206R, D207N, T592V Mutation：H206R, D207N, T592V | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.4；298 K；SPG buffer, PEG 1500
|
Resolution 2.81 Å R-free 0.248 |
| 4ZWE Crystal structure of the dGTP-bound catalytic core of SAMHD1 T592V mutant Deposited 2015-05-19 | Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
113–626（514 aa）
Fragment：residues 113-626
Chain C
113–626（514 aa）
Fragment：residues 113-626
|
Mutation：H206R, D207N, T592V Mutation：H206R, D207N, T592V | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.4；298 K；SPG buffer, PEG 1500
|
Resolution 2.81 Å R-free 0.248 |
| 4ZWE Crystal structure of the dGTP-bound catalytic core of SAMHD1 T592V mutant Deposited 2015-05-19 | Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
113–626（514 aa）
Fragment：residues 113-626
Chain D
113–626（514 aa）
Fragment：residues 113-626
|
Mutation：H206R, D207N, T592V Mutation：H206R, D207N, T592V | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.4；298 K；SPG buffer, PEG 1500
|
Resolution 2.81 Å R-free 0.248 |
| 5AO0 Crystal structure of human SAMHD1 (amino acid residues 41-583) bound to ddGTP Deposited 2015-09-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
41–583（543 aa）
Fragment：RESIDUES 41-583
Chain B
41–583（543 aa）
Fragment：RESIDUES 41-583
|
Not recorded | FE FE (III) ION × 4 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 8 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
160 MM SUCCINIC ACID, 11% PEG 3350, PH 7
|
Resolution 3.73 Å R-free 0.268 |
| 5AO1 Crystal structure of human SAMHD1 (amino acid residues 115-583) bound to ddGTP Deposited 2015-09-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
115–583（469 aa）
Fragment：UNP RESIDUES 115-583
Chain B
115–583（469 aa）
Fragment：UNP RESIDUES 115-583
Chain C
115–583（469 aa）
Fragment：UNP RESIDUES 115-583
Chain D
115–583（469 aa）
Fragment：UNP RESIDUES 115-583
|
Not recorded | FE FE (III) ION × 4 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 8 SO4 SULFATE ION × 4 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
100 MM BIS TRIS PROPANE-HCL, 150 MM NA2SO4, 13.5% PEG 3350 PH 6.5
|
Resolution 2.54 Å R-free 0.220 |
| 5AO2 Crystal structure of human SAMHD1 (amino acid residues 115-583) R164A variant bound to dGTP Deposited 2015-09-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
115–583（469 aa）
Fragment：UNP RESIDUES 115-583
Chain B
115–583（469 aa）
Fragment：UNP RESIDUES 115-583
Chain C
115–583（469 aa）
Fragment：UNP RESIDUES 115-583
Chain D
115–583（469 aa）
Fragment：UNP RESIDUES 115-583
|
Mutation：YES Mutation：YES Mutation：YES Mutation：YES | FE FE (III) ION × 4 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.2 M SODIUM CITRATE, 0.1 M BIS TRIS PROPANE-HCL, 20% PEG 3350, PH 8.5
|
Resolution 2.97 Å R-free 0.234 |
| 5AO3 Crystal structure of human SAMHD1 (amino acid residues 115-626) bound to GTP Deposited 2015-09-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
115–626（512 aa）
Fragment：UNP RESIDUES 115-626
Chain B
115–626（512 aa）
Fragment：UNP RESIDUES 115-626
Chain C
115–626（512 aa）
Fragment：UNP RESIDUES 115-626
Chain D
115–626（512 aa）
Fragment：UNP RESIDUES 115-626
|
Not recorded | FE FE (III) ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 SO4 SULFATE ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.2 M AMMONIUM SULPHATE, 20% PEG 3350
|
Resolution 3.00 Å R-free 0.247 |
| 5AO4 Crystal structure of in vitro phosphorylated human SAMHD1 (amino acid residues 115-626) bound to GTP Deposited 2015-09-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
115–626（512 aa）
Fragment：RESIDUES 115-626
Chain B
115–626（512 aa）
Fragment：RESIDUES 115-626
Chain C
115–626（512 aa）
Fragment：RESIDUES 115-626
Chain D
115–626（512 aa）
Fragment：RESIDUES 115-626
|
Not recorded | FE FE (III) ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.2 M SODIUM FORMATE, 20% PEG 3350
|
Resolution 3.70 Å R-free 0.308 |
| 6CM2 SAMHD1 HD domain bound to decitabine triphosphate Deposited 2018-03-02 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Mutation：H94R, D95N Mutation：H94R, D95N Mutation：H94R, D95N Mutation：H94R, D95N | F6G 6-amino-3-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,4-dihydro-1,3,5-triazin-2(1H)-one × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；298 K；SPG buffer, PEG 1500
|
Resolution 2.14 Å R-free 0.225 |
| 6DW3 SAMHD1 Bound to Cytarabine-TP in the Catalytic Pocket Deposited 2018-06-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N | HF4 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；298 K；100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500
|
Resolution 2.20 Å R-free 0.228 |
| 6DW4 SAMHD1 Bound to Cladribine-TP in the Catalytic Pocket and Allosteric Pocket Deposited 2018-06-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N | HF7 2'-deoxy-2-methyladenosine 5'-(tetrahydrogen triphosphate) × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 8 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；298 K；100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500
|
Resolution 1.99 Å R-free 0.202 |
| 6DW5 SAMHD1 Bound to Gemcitabine-TP in the Catalytic Pocket Deposited 2018-06-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N | GTF 2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate) × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 10 NA SODIUM ION × 4 NI NICKEL (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；298 K；100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500
|
Resolution 1.93 Å R-free 0.205 |
| 6DW7 SAMHD1 without Catalytic Nucleotides Deposited 2018-06-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 GLY GLYCINE × 2 NA SODIUM ION × 3 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；298 K；100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500
|
Resolution 2.50 Å R-free 0.250 |
| 6DWD SAMHD1 Bound to Clofarabine-TP in the Catalytic Pocket and Allosteric Pocket Deposited 2018-06-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N | HDV 9-{2-deoxy-2-fluoro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-2-me thyl-9H-purin-6-amine × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 10 NA SODIUM ION × 23 GLY GLYCINE × 7 SIN SUCCINIC ACID × 2 PO4 PHOSPHATE ION × 1 TCE 3,3',3''-phosphanetriyltripropanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；298 K；100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500
|
Resolution 1.70 Å R-free 0.202 |
| 6DWJ SAMHD1 Bound to Vidarabine-TP in the Catalytic Pocket Deposited 2018-06-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N | HEJ 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 10 NA SODIUM ION × 17 GLY GLYCINE × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；298 K；100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500
|
Resolution 2.50 Å R-free 0.208 |
| 6DWK SAMHD1 Bound to Fludarabine-TP in the Catalytic Pocket Deposited 2018-06-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N Mutation：H206R, D207N | HFD 2-fluoro-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-a mine × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 9 NA SODIUM ION × 23 GLY GLYCINE × 12 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；298 K；100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500
|
Resolution 2.30 Å R-free 0.212 |
| 6TX0 Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dAMPNPP and Mg Deposited 2020-01-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
109–626（518 aa）
Chain B
109–626（518 aa）
|
Mutation：D137N Mutation：D137N | FE FE (III) ION × 4 MG MAGNESIUM ION × 12 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 8 CZF [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 16% (w/v) PEG 3350
|
Resolution 2.01 Å R-free 0.228 |
| 6TXA Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dGMPNPP and Mg Deposited 2020-01-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
109–626（518 aa）
Chain B
109–626（518 aa）
Chain C
109–626（518 aa）
Chain D
109–626（518 aa）
|
Mutation：D137N Mutation：D137N Mutation：D137N Mutation：D137N | FE FE (III) ION × 4 MG MAGNESIUM ION × 12 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 8 CZF [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 4 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.15 M Li2SO4.
|
Resolution 2.85 Å R-free 0.212 |
| 6TXA Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dGMPNPP and Mg Deposited 2020-01-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain E
109–626（518 aa）
Chain F
109–626（518 aa）
Chain G
109–626（518 aa）
Chain H
109–626（518 aa）
|
Mutation：D137N Mutation：D137N Mutation：D137N Mutation：D137N | FE FE (III) ION × 4 MG MAGNESIUM ION × 12 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 8 CZF [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 4 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.15 M Li2SO4.
|
Resolution 2.85 Å R-free 0.212 |
| 6TXA Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dGMPNPP and Mg Deposited 2020-01-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain I
109–626（518 aa）
Chain J
109–626（518 aa）
Chain K
109–626（518 aa）
Chain L
109–626（518 aa）
|
Mutation：D137N Mutation：D137N Mutation：D137N Mutation：D137N | FE FE (III) ION × 4 MG MAGNESIUM ION × 12 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 8 CZF [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 4 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.15 M Li2SO4.
|
Resolution 2.85 Å R-free 0.212 |
| 6TXA Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dGMPNPP and Mg Deposited 2020-01-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain M
109–626（518 aa）
Chain N
109–626（518 aa）
Chain O
109–626（518 aa）
Chain P
109–626（518 aa）
|
Mutation：D137N Mutation：D137N Mutation：D137N Mutation：D137N | FE FE (III) ION × 4 MG MAGNESIUM ION × 12 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 8 CZF [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 4 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.15 M Li2SO4.
|
Resolution 2.85 Å R-free 0.212 |
| 6TXC Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP, dCMPNPP and Mg Deposited 2020-01-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
109–626（518 aa）
Chain B
109–626（518 aa）
Chain C
109–626（518 aa）
Chain D
109–626（518 aa）
|
Not recorded | FE FE (III) ION × 4 MG MAGNESIUM ION × 12 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 SO4 SULFATE ION × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCL pH 6, 17% (w/v) PEG 3350, 0.15 M Li2SO4.
|
Resolution 2.84 Å R-free 0.249 |
| 6TXC Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP, dCMPNPP and Mg Deposited 2020-01-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain E
109–626（518 aa）
Chain F
109–626（518 aa）
Chain G
109–626（518 aa）
Chain H
109–626（518 aa）
|
Not recorded | FE FE (III) ION × 4 MG MAGNESIUM ION × 9 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 SO4 SULFATE ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCL pH 6, 17% (w/v) PEG 3350, 0.15 M Li2SO4.
|
Resolution 2.84 Å R-free 0.249 |
| 6TXC Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP, dCMPNPP and Mg Deposited 2020-01-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain I
109–626（518 aa）
Chain J
109–626（518 aa）
Chain K
109–626（518 aa）
Chain L
109–626（518 aa）
|
Not recorded | FE FE (III) ION × 4 MG MAGNESIUM ION × 11 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 SO4 SULFATE ION × 3 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCL pH 6, 17% (w/v) PEG 3350, 0.15 M Li2SO4.
|
Resolution 2.84 Å R-free 0.249 |
| 6TXC Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP, dCMPNPP and Mg Deposited 2020-01-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain M
109–626（518 aa）
Chain N
109–626（518 aa）
Chain O
109–626（518 aa）
Chain P
109–626（518 aa）
|
Not recorded | FE FE (III) ION × 4 MG MAGNESIUM ION × 10 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 SO4 SULFATE ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCL pH 6, 17% (w/v) PEG 3350, 0.15 M Li2SO4.
|
Resolution 2.84 Å R-free 0.249 |
| 6TXE Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP, dTMPNPP and Mg Deposited 2020-01-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
109–626（518 aa）
Chain B
109–626（518 aa）
Chain C
109–626（518 aa）
Chain D
109–626（518 aa）
|
Not recorded | FE FE (III) ION × 4 MG MAGNESIUM ION × 8 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 19% (w/v) PEG 3350, 0.15 M Li2SO4
|
Resolution 3.19 Å R-free 0.252 |
| 6TXE Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP, dTMPNPP and Mg Deposited 2020-01-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain E
109–626（518 aa）
Chain F
109–626（518 aa）
Chain G
109–626（518 aa）
Chain H
109–626（518 aa）
|
Not recorded | FE FE (III) ION × 4 MG MAGNESIUM ION × 8 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 19% (w/v) PEG 3350, 0.15 M Li2SO4
|
Resolution 3.19 Å R-free 0.252 |
| 6TXE Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP, dTMPNPP and Mg Deposited 2020-01-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain I
109–626（518 aa）
Chain J
109–626（518 aa）
Chain K
109–626（518 aa）
Chain L
109–626（518 aa）
|
Not recorded | FE FE (III) ION × 4 MG MAGNESIUM ION × 8 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 19% (w/v) PEG 3350, 0.15 M Li2SO4
|
Resolution 3.19 Å R-free 0.252 |
| 6TXE Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP, dTMPNPP and Mg Deposited 2020-01-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain M
109–626（518 aa）
Chain N
109–626（518 aa）
Chain O
109–626（518 aa）
Chain P
109–626（518 aa）
|
Not recorded | FE FE (III) ION × 4 MG MAGNESIUM ION × 8 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 19% (w/v) PEG 3350, 0.15 M Li2SO4
|
Resolution 3.19 Å R-free 0.252 |
| 6TXF Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dAMPNPP and Mn Deposited 2020-01-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
109–626（518 aa）
Chain B
109–626（518 aa）
|
Mutation：D137N Mutation：D137N | FE FE (III) ION × 4 MN MANGANESE (II) ION × 12 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 8 CZF [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 14% (w/v) PEG 3350
|
Resolution 2.25 Å R-free 0.239 |
| 6U6X Human SAMHD1 bound to deoxyribo(C*G*C*C*T)-oligonucleotide Deposited 2019-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
114–626（513 aa）
Chain D
114–626（513 aa）
|
Mutation：D311A Mutation：D311A | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M sodium tartrate dibasic, 20% polyethylene glycol 3350
|
Resolution 2.58 Å R-free 0.236 |
| 6U6X Human SAMHD1 bound to deoxyribo(C*G*C*C*T)-oligonucleotide Deposited 2019-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain B
114–626（513 aa）
Chain C
114–626（513 aa）
|
Mutation：D311A Mutation：D311A | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M sodium tartrate dibasic, 20% polyethylene glycol 3350
|
Resolution 2.58 Å R-free 0.236 |
| 6U6Y Human SAMHD1 bound to ribo(CGCCU)-oligonucleotide Deposited 2019-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
114–626（513 aa）
Chain D
114–626（513 aa）
|
Mutation：D311A Mutation：D311A | ZN ZINC ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；20% PEG 4000, 0.6 M NaCl, 0.1 M MES:NaOH pH 6.5
|
Resolution 2.47 Å R-free 0.235 |
| 6U6Y Human SAMHD1 bound to ribo(CGCCU)-oligonucleotide Deposited 2019-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain B
114–626（513 aa）
Chain C
114–626（513 aa）
|
Mutation：D311A Mutation：D311A | ZN ZINC ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；20% PEG 4000, 0.6 M NaCl, 0.1 M MES:NaOH pH 6.5
|
Resolution 2.47 Å R-free 0.235 |
| 6U6Z Human SAMHD1 bound to deoxyribo(TG*TTCA)-oligonucleotide Deposited 2019-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
116–626（511 aa）
Chain D
116–626（511 aa）
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.26 M sodium malonate, 20% polyethylene glycol 3350, 0.1 M bis-Tris propane pH 8.5
|
Resolution 2.10 Å R-free 0.206 |
| 6U6Z Human SAMHD1 bound to deoxyribo(TG*TTCA)-oligonucleotide Deposited 2019-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain B
116–626（511 aa）
Chain C
116–626（511 aa）
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.26 M sodium malonate, 20% polyethylene glycol 3350, 0.1 M bis-Tris propane pH 8.5
|
Resolution 2.10 Å R-free 0.206 |
| 6XU1 Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with GTP, dAMPNPP and Mg Deposited 2020-01-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
109–626（518 aa）
Chain B
109–626（518 aa）
Chain C
109–626（518 aa）
Chain D
109–626（518 aa）
|
Mutation：H215A Mutation：H215A Mutation：H215A Mutation：H215A | FE FE (III) ION × 4 MG MAGNESIUM ION × 13 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.1 M MgCl2
|
Resolution 2.20 Å R-free 0.202 |
| 6XU1 Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with GTP, dAMPNPP and Mg Deposited 2020-01-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain E
109–626（518 aa）
Chain F
109–626（518 aa）
Chain G
109–626（518 aa）
Chain H
109–626（518 aa）
|
Mutation：H215A Mutation：H215A Mutation：H215A Mutation：H215A | FE FE (III) ION × 4 MG MAGNESIUM ION × 12 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.1 M MgCl2
|
Resolution 2.20 Å R-free 0.202 |
| 6YOM Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dATP, dCMPNPP, Mn and Mg Deposited 2020-04-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
109–626（518 aa）
Chain B
109–626（518 aa）
|
Mutation：D137N Mutation：D137N | FE FE (III) ION × 4 MN MANGANESE (II) ION × 4 MG MAGNESIUM ION × 8 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 4 CZF [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.05 M MgCl2
|
Resolution 3.25 Å R-free 0.236 |
| 7A5Y Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with Rp-dGTP-alphaS (T8T) and Mg Deposited 2020-08-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
109–626（518 aa）
Chain B
109–626（518 aa）
Chain C
109–626（518 aa）
Chain D
109–626（518 aa）
|
Mutation：H215A Mutation：H215A Mutation：H215A Mutation：H215A | FE FE (III) ION × 4 MG MAGNESIUM ION × 12 T8T 2'-deoxyguanosine-5'-O-(1-thiotriphosphate) × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.15 M Li2SO4
|
Resolution 2.29 Å R-free 0.240 |
| 7A5Y Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with Rp-dGTP-alphaS (T8T) and Mg Deposited 2020-08-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain E
109–626（518 aa）
Chain F
109–626（518 aa）
Chain G
109–626（518 aa）
Chain H
109–626（518 aa）
|
Mutation：H215A Mutation：H215A Mutation：H215A Mutation：H215A | FE FE (III) ION × 4 MG MAGNESIUM ION × 12 T8T 2'-deoxyguanosine-5'-O-(1-thiotriphosphate) × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Bistris methane-HCl pH 6, 15% (w/v) PEG 3350, 0.15 M Li2SO4
|
Resolution 2.29 Å R-free 0.240 |
| 7LTT SAMHD1(113-626) H206R D207N R366C Deposited 2021-02-20 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Mutation：H206R, D207N, R366C Mutation：H206R, D207N, R366C Mutation：H206R, D207N, R366C Mutation：H206R, D207N, R366C | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 8 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 8.2；293 K；PEG 1500, dGTP, SPG buffer, sodium chloride, magnesium chloride, TCEP
|
Resolution 1.90 Å R-free 0.212 |
| 7LU5 SAMHD1(113-626) H206R D207N R366H Deposited 2021-02-20 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Mutation：H206R, D207N, R366H Mutation：H206R, D207N, R366H Mutation：H206R, D207N, R366H Mutation：H206R, D207N, R366H | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 9；293 K；PEG 1500, dGTP, SPG buffer, sodium chloride, magnesium chloride
|
Resolution 3.57 Å R-free 0.274 |
| 7LU5 SAMHD1(113-626) H206R D207N R366H Deposited 2021-02-20 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain E
113–626（514 aa）
Chain F
113–626（514 aa）
Chain G
113–626（514 aa）
Chain H
113–626（514 aa）
|
Mutation：H206R, D207N, R366H Mutation：H206R, D207N, R366H Mutation：H206R, D207N, R366H Mutation：H206R, D207N, R366H | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 9；293 K；PEG 1500, dGTP, SPG buffer, sodium chloride, magnesium chloride
|
Resolution 3.57 Å R-free 0.274 |
| 7LU5 SAMHD1(113-626) H206R D207N R366H Deposited 2021-02-20 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain I
113–626（514 aa）
Chain J
113–626（514 aa）
Chain K
113–626（514 aa）
Chain L
113–626（514 aa）
|
Mutation：H206R, D207N, R366H Mutation：H206R, D207N, R366H Mutation：H206R, D207N, R366H Mutation：H206R, D207N, R366H | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 9；293 K；PEG 1500, dGTP, SPG buffer, sodium chloride, magnesium chloride
|
Resolution 3.57 Å R-free 0.274 |
| 7LU5 SAMHD1(113-626) H206R D207N R366H Deposited 2021-02-20 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain M
113–626（514 aa）
Chain N
113–626（514 aa）
Chain O
113–626（514 aa）
Chain P
113–626（514 aa）
|
Mutation：H206R, D207N, R366H Mutation：H206R, D207N, R366H Mutation：H206R, D207N, R366H Mutation：H206R, D207N, R366H | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 9；293 K；PEG 1500, dGTP, SPG buffer, sodium chloride, magnesium chloride
|
Resolution 3.57 Å R-free 0.274 |
| 7S2Y SAMHD1 HD domain bound to CNDAC Deposited 2021-09-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Not recorded | 85T 4-amino-1-{2-cyano-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；298 K；100 mM
succinate phosphate glycine buffer pH 7.4, 25% PEG 1500
|
Resolution 2.80 Å R-free 0.232 |
| 7UJN Structure of Human SAMHD1 with Non-Hydrolysable dGTP Analog Deposited 2022-03-31 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–626（626 aa）
Chain B
1–626（626 aa）
Chain C
1–626（626 aa）
Chain D
1–626（626 aa）
|
Not recorded | T8T 2'-deoxyguanosine-5'-O-(1-thiotriphosphate) × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.89 Å |
| 8D94 SAMHD1-DNA complex Deposited 2022-06-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
1–626（626 aa）
Chain D
1–626（626 aa）
|
Not recorded | FE FE (III) ION × 2 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris-HCl pH 7.5, 150 mM CaCl2, 20% PEG 3350, and 4% 2-methyl-2,4-pentanediol (MPD)
|
Resolution 2.44 Å R-free 0.243 |
| 8D94 SAMHD1-DNA complex Deposited 2022-06-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain B
1–626（626 aa）
Chain C
1–626（626 aa）
|
Not recorded | FE FE (III) ION × 2 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris-HCl pH 7.5, 150 mM CaCl2, 20% PEG 3350, and 4% 2-methyl-2,4-pentanediol (MPD)
|
Resolution 2.44 Å R-free 0.243 |
| 8D9J SAMHD1-DNA complex Deposited 2022-06-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
1–626（626 aa）
Chain D
1–626（626 aa）
|
Not recorded | FE FE (III) ION × 2 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris-HCl pH 7.5, 150 mM CaCl2, 20% PEG 3350, and 4% 2-methyl-2,4-pentanediol (MPD)
|
Resolution 2.82 Å R-free 0.242 |
| 8D9J SAMHD1-DNA complex Deposited 2022-06-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain B
1–626（626 aa）
Chain C
1–626（626 aa）
|
Not recorded | FE FE (III) ION × 2 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris-HCl pH 7.5, 150 mM CaCl2, 20% PEG 3350, and 4% 2-methyl-2,4-pentanediol (MPD)
|
Resolution 2.82 Å R-free 0.242 |
| 8GB1 Crystal structure of SAMHD1 dimer bound to deoxyguanosine linked inhibitor Deposited 2023-02-24 | Different construct 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
113–626（514 aa）
Chain B
113–626（514 aa）
|
Not recorded | YWI 5'-O-[(R)-(3-{[(1M)-3'-bromo[1,1'-biphenyl]-3-carbonyl]amino}propoxy)(hydroxy)phosphoryl]-2'-deoxyguanosine × 2 FE FE (III) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；17% PEG3350, 0.15 M Ammonium citrate pH 7.3, 293 K, 5 mg/mL, 1 uL protein + 2 uL ML. Soak 1 uL of 1 mM compound
|
Resolution 2.46 Å R-free 0.236 |
| 8GB1 Crystal structure of SAMHD1 dimer bound to deoxyguanosine linked inhibitor Deposited 2023-02-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Not recorded | YWI 5'-O-[(R)-(3-{[(1M)-3'-bromo[1,1'-biphenyl]-3-carbonyl]amino}propoxy)(hydroxy)phosphoryl]-2'-deoxyguanosine × 2 FE FE (III) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；17% PEG3350, 0.15 M Ammonium citrate pH 7.3, 293 K, 5 mg/mL, 1 uL protein + 2 uL ML. Soak 1 uL of 1 mM compound
|
Resolution 2.46 Å R-free 0.236 |
| 8GB2 Crystal structure of Apo-SAMHD1 Deposited 2023-02-24 | Different construct 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
113–626（514 aa）
Chain D
113–626（514 aa）
|
Not recorded | FE FE (III) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；17% PEG3350, 0.15 M Ammonium citrate pH 7.3, 293 K, 5 mg/mL, 1 uL protein + 2 uL ML.
|
Resolution 3.07 Å R-free 0.250 |
| 8GB2 Crystal structure of Apo-SAMHD1 Deposited 2023-02-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
|
Not recorded | FE FE (III) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；17% PEG3350, 0.15 M Ammonium citrate pH 7.3, 293 K, 5 mg/mL, 1 uL protein + 2 uL ML.
|
Resolution 3.07 Å R-free 0.250 |
| 8QXJ Cryo-EM structure of tetrameric human SAMHD1 with dApNHpp Deposited 2023-10-24 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–626（626 aa）
Chain B
1–626（626 aa）
Chain C
1–626（626 aa）
Chain D
1–626（626 aa）
|
Not recorded | DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 8 FE FE (III) ION × 4 MG MAGNESIUM ION × 12 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.65 Å |
| 8QXK Cryo-EM structure of tetrameric human SAMHD1 State I - Tense Deposited 2023-10-24 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–626（626 aa）
Chain B
1–626（626 aa）
Chain C
1–626（626 aa）
Chain D
1–626（626 aa）
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 4 FE FE (III) ION × 4 MG MAGNESIUM ION × 12 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 4 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.66 Å |
| 8QXL Cryo-EM structure of tetrameric human SAMHD1 State II - Hemi-relaxed Deposited 2023-10-24 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–626（626 aa）
Chain B
1–626（626 aa）
Chain C
1–626（626 aa）
Chain D
1–626（626 aa）
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 4 FE FE (III) ION × 4 MG MAGNESIUM ION × 10 DCZ 2'-DEOXYCYTIDINE × 2 3PO TRIPHOSPHATE × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.82 Å |
| 8QXM Cryo-EM structure of tetrameric human SAMHD1 State III - Relaxed Deposited 2023-10-24 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–626（626 aa）
Chain B
1–626（626 aa）
Chain C
1–626（626 aa）
Chain D
1–626（626 aa）
|
Not recorded | FE FE (III) ION × 4 MG MAGNESIUM ION × 10 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 8QXN Cryo-EM structure of tetrameric human SAMHD1 State IV - Depleted relaxed Deposited 2023-10-24 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–626（626 aa）
Chain B
1–626（626 aa）
Chain C
1–626（626 aa）
Chain D
1–626（626 aa）
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 4 FE FE (III) ION × 4 MG MAGNESIUM ION × 8 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 4 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 8QXO Cryo-EM structure of tetrameric human SAMHD1 State V - Depleted relaxed Deposited 2023-10-24 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–626（626 aa）
Chain B
1–626（626 aa）
Chain C
1–626（626 aa）
Chain D
1–626（626 aa）
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 4 FE FE (III) ION × 4 MG MAGNESIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.43 Å |
| 8TDV ssRNA bound SAMHD1 T closed Deposited 2023-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–626（626 aa）
Chain B
1–626（626 aa）
Chain E
1–626（626 aa）
Chain F
1–626（626 aa）
|
Not recorded | FE FE (III) ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.44 Å |
| 8TDW ssRNA bound SAMHD1 T open Deposited 2023-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 4 PDB declaration: hexameric |
Chain A
1–626（626 aa）
Chain B
1–626（626 aa）
Chain E
1–626（626 aa）
Chain F
1–626（626 aa）
|
Not recorded | FE FE (III) ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 9EC2 Crystal structure of SAMHD1 dimer bound to an inhibitor obtained from high-throughput chemical tethering to the guanine antiviral acyclovir Deposited 2024-11-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
113–626（514 aa）
Chain B
113–626（514 aa）
Chain C
113–626（514 aa）
Chain D
113–626（514 aa）
|
Not recorded | A1BHL N-[5-({2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methoxy]ethyl}amino)-5-oxopentyl]-4,7-dibromo-3-hydroxynaphthalene-2-carboxamide × 4 FE FE (III) ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；Apo DELTA 112- SAMHD1 crystals were obtained by the hanging drop method using 1 micro L of 5 mg/mL Delta 112-SAMHD1 (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 4 mM MgCl2, 0.5 mM TCEP) and 2 L 17% PEG3350, 0.15 M Ammonium citrate pH 7.3. Drops were placed in 20 degrees C for over a week, and large crystal rods and plates were observed
|
Resolution 2.72 Å R-free 0.234 |
| 9HIW Cryo-EM structure of CDK2-cyclin A bound to a SAMHD1 peptide Deposited 2024-11-27 | 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
614–626（13 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
75 other PDB entries and 103 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | SAMH1_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–514； UniProt 113–626 Author chain B； PDBConstruct 1–514； UniProt 113–626 Author chain C； PDBConstruct 1–514； UniProt 113–626 Author chain D； PDBConstruct 1–514； UniProt 113–626 |
