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- PDB-6dwd: SAMHD1 Bound to Clofarabine-TP in the Catalytic Pocket and Allost... -

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Basic information

Entry
Database: PDB / ID: 6dwd
TitleSAMHD1 Bound to Clofarabine-TP in the Catalytic Pocket and Allosteric Pocket
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
Keywordshydrolase/hydrolase inhibitor / Complex / deoxynucleoside triphosphate triphosphohydrolase / dNTPase / nucleotide analogue / Clofarabine-TP / HYDROLASE / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTPase activity / dGTP catabolic process / DNA strand resection involved in replication fork processing ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTPase activity / dGTP catabolic process / DNA strand resection involved in replication fork processing / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / RNA nuclease activity / somatic hypermutation of immunoglobulin genes / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / single-stranded DNA binding / site of double-strand break / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane
Similarity search - Function
: / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
GLYCINE / GUANOSINE-5'-TRIPHOSPHATE / Chem-HDV / PHOSPHATE ION / SUCCINIC ACID / 3,3',3''-phosphanetriyltripropanoic acid / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsKnecht, K.M. / Buzovetsky, O. / Schneider, C. / Thomas, D. / Srikanth, V. / Kaderali, L. / Tofoleanu, F. / Reiss, K. / Ferreiros, N. / Geisslinger, G. ...Knecht, K.M. / Buzovetsky, O. / Schneider, C. / Thomas, D. / Srikanth, V. / Kaderali, L. / Tofoleanu, F. / Reiss, K. / Ferreiros, N. / Geisslinger, G. / Batista, V.S. / Ji, X. / Cinatl, J. / Keppler, O.T. / Xiong, Y.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: The structural basis for cancer drug interactions with the catalytic and allosteric sites of SAMHD1.
Authors: Knecht, K.M. / Buzovetsky, O. / Schneider, C. / Thomas, D. / Srikanth, V. / Kaderali, L. / Tofoleanu, F. / Reiss, K. / Ferreiros, N. / Geisslinger, G. / Batista, V.S. / Ji, X. / Cinatl Jr., ...Authors: Knecht, K.M. / Buzovetsky, O. / Schneider, C. / Thomas, D. / Srikanth, V. / Kaderali, L. / Tofoleanu, F. / Reiss, K. / Ferreiros, N. / Geisslinger, G. / Batista, V.S. / Ji, X. / Cinatl Jr., J. / Keppler, O.T. / Xiong, Y.
History
DepositionJun 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.formula_weight
Revision 1.2Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,86260
Polymers253,7064
Non-polymers8,15756
Water18,9161050
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27950 Å2
ΔGint-361 kcal/mol
Surface area66200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.477, 142.233, 98.790
Angle α, β, γ (deg.)90.00, 114.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21C
12D
22B
13D
23A
14C
24B
15C
25A
16B
26A

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNDA113 - 59937 - 523
21ASNASNCB113 - 59937 - 523
12ASNASNDA113 - 59937 - 523
22ASNASNBC113 - 59937 - 523
13ASPASPDA113 - 58337 - 507
23ASPASPAD113 - 58337 - 507
14ASNASNCB113 - 59937 - 523
24ASNASNBC113 - 59937 - 523
15ASPASPCB113 - 58337 - 507
25ASPASPAD113 - 58337 - 507
16ASPASPBC113 - 58337 - 507
26ASPASPAD113 - 58337 - 507

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules DCBA

#1: Protein
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 / dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM ...dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM domain and HD domain-containing protein 1


Mass: 63426.375 Da / Num. of mol.: 4 / Mutation: H206R, D207N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMHD1, MOP5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases

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Non-polymers , 9 types, 1106 molecules

#2: Chemical
ChemComp-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 / Clofarabine-TRIPHOSPHATE


Mass: 523.199 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H17FN5O12P3
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H5NO2
#7: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1050 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growTemperature: 298 K / Method: microbatch / Details: 100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 209481 / % possible obs: 94.1 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4 % / Num. unique obs: 10532 / CC1/2: 0.283 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.687 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20155 10589 5.1 %RANDOM
Rwork0.17623 ---
obs0.17752 198853 93.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.521 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20.05 Å2
2---0.32 Å20 Å2
3----0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15609 0 489 1050 17148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01916459
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215058
X-RAY DIFFRACTIONr_angle_refined_deg2.1331.9922301
X-RAY DIFFRACTIONr_angle_other_deg1.131335010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66751907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27323.973808
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.961152904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.08815112
X-RAY DIFFRACTIONr_chiral_restr0.1320.22344
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02117851
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023345
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8182.5677658
X-RAY DIFFRACTIONr_mcbond_other2.8172.5667657
X-RAY DIFFRACTIONr_mcangle_it4.1613.8289549
X-RAY DIFFRACTIONr_mcangle_other4.1613.8289550
X-RAY DIFFRACTIONr_scbond_it3.8032.9758801
X-RAY DIFFRACTIONr_scbond_other3.82.9738795
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8664.27212744
X-RAY DIFFRACTIONr_long_range_B_refined8.24248.21372017
X-RAY DIFFRACTIONr_long_range_B_other8.24248.21372018
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D330820.07
12C330820.07
21D330660.07
22B330660.07
31D316460.08
32A316460.08
41C328680.08
42B328680.08
51C314500.09
52A314500.09
61B316900.07
62A316900.07
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 797 -
Rwork0.308 14557 -
obs--93.32 %

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