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 109–626 Chain B； UniProt 109–626 Chain C； UniProt 109–626 Chain D； UniProt 109–626 | 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 |
| 2 | Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain E； UniProt 109–626 Chain F； UniProt 109–626 Chain G； UniProt 109–626 Chain H； UniProt 109–626 | 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 |
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 6XU1 | 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 | 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 oligomeric state 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 oligomeric state 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 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 | 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 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 × 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 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：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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 |
| 4ZWG Crystal structure of the GTP-dATP-bound catalytic core of SAMHD1 phosphomimetic T592E mutant Deposited 2015-05-19 | 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：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, T592E Mutation：H206R, D207N, T592E Mutation：H206R, D207N, T592E 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 |
| 4ZWG Crystal structure of the GTP-dATP-bound catalytic core of SAMHD1 phosphomimetic T592E mutant Deposited 2015-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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, T592E 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 |
| 4ZWG Crystal structure of the GTP-dATP-bound catalytic core of SAMHD1 phosphomimetic T592E mutant Deposited 2015-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 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, T592E 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 |
| 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 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 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 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 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 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 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 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 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 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 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 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 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 |
| 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 104 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 3–520； UniProt 109–626 Author chain B； PDBConstruct 3–520； UniProt 109–626 Author chain C； PDBConstruct 3–520； UniProt 109–626 Author chain D； PDBConstruct 3–520； UniProt 109–626 Author chain E； PDBConstruct 3–520； UniProt 109–626 Author chain F； PDBConstruct 3–520； UniProt 109–626 Author chain G； PDBConstruct 3–520； UniProt 109–626 Author chain H； PDBConstruct 3–520； UniProt 109–626 |
