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- PDB-6dw3: SAMHD1 Bound to Cytarabine-TP in the Catalytic Pocket -

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Basic information

Entry
Database: PDB / ID: 6dw3
TitleSAMHD1 Bound to Cytarabine-TP in the Catalytic Pocket
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
Keywordshydrolase/hydrolase inhibitor / Complex / deoxynucleoside triphosphate triphosphohydrolase / dNTPase / nucleotide analogue / cytarabine-TP / HYDROLASE / hydrolase inhibitor / 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-HF4 / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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_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)259,89024
Polymers253,7064
Non-polymers6,18520
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26240 Å2
ΔGint-93 kcal/mol
Surface area68970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.340, 147.325, 98.537
Angle α, β, γ (deg.)90.00, 114.64, 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: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TRPTRPDA114 - 59838 - 522
21TRPTRPCB114 - 59838 - 522
12ASNASNDA114 - 59938 - 523
22ASNASNBC114 - 59938 - 523
13ASNASNDA114 - 59938 - 523
23ASNASNAD114 - 59938 - 523
14ASNASNCB114 - 59938 - 523
24ASNASNBC114 - 59938 - 523
15ASNASNCB114 - 59938 - 523
25ASNASNAD114 - 59938 - 523
16ASNASNBC114 - 59938 - 523
26ASNASNAD114 - 59938 - 523

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 , 5 types, 315 molecules

#2: Chemical
ChemComp-HF4 / 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one / Cytarabine-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
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: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 110334 / % possible obs: 98.1 % / Redundancy: 2.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.123 / Net I/σ(I): 7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 0.8 / CC1/2: 0.252 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZB

4bzb


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 21.287 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.205 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5562 5 %RANDOM
Rwork0.1901 ---
obs0.19205 104740 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.431 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20.11 Å2
2---2.39 Å20 Å2
3---0.87 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15690 0 372 295 16357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01916490
X-RAY DIFFRACTIONr_bond_other_d0.0040.0215140
X-RAY DIFFRACTIONr_angle_refined_deg2.031.98522353
X-RAY DIFFRACTIONr_angle_other_deg1.118335196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15551923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38723.968809
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41152925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.58615112
X-RAY DIFFRACTIONr_chiral_restr0.1220.22357
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02117925
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023391
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_it1.5382.2677698
X-RAY DIFFRACTIONr_mcbond_other1.5362.2677697
X-RAY DIFFRACTIONr_mcangle_it2.5313.3929619
X-RAY DIFFRACTIONr_mcangle_other2.5313.3929620
X-RAY DIFFRACTIONr_scbond_it2.1152.5018792
X-RAY DIFFRACTIONr_scbond_other2.1162.5038780
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4953.64612715
X-RAY DIFFRACTIONr_long_range_B_refined6.0342.31267607
X-RAY DIFFRACTIONr_long_range_B_other6.01942.31667448
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)
11D307200.12
12C307200.12
21D308300.11
22B308300.11
31D307780.11
32A307780.11
41C306120.12
42B306120.12
51C305260.12
52A305260.12
61B306860.12
62A306860.12
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 328 -
Rwork0.377 6197 -
obs--77.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.83830.16530.01311.19380.20361.00140.0297-0.1282-0.05320.18110.0113-0.17880.03420.1634-0.04090.02750.001-0.02740.11380.00440.028159.1004-0.4238139.7761
20.9981-0.04840.01861.0421-0.14011.2676-0.00670.2366-0.1649-0.1740.02420.13780.2266-0.2589-0.01760.0739-0.0739-0.02630.2566-0.0560.058630.3275-12.196699.8573
30.9610.17260.22641.05330.16091.4354-0.00470.2671-0.0191-0.15470.0313-0.2575-0.04140.2852-0.02650.0303-0.0360.03940.2755-0.00590.063863.35472.5915100.8076
40.8387-0.03620.29951.0289-0.0921.5575-0.0116-0.07890.0950.07790.00720.2989-0.0841-0.44970.00440.01330.04220.01830.2347-0.02530.103724.71158.0337133.0526
50.4158-0.00610.09340.1870.07690.60.00620.0110.0160.0162-0.0008-0.0198-0.0113-0.0194-0.00540.0332-0.0045-0.00050.14720.00550.027247.54052.0253122.8126
60.0660.2988-0.0912.38270.11480.40510.041-0.0032-0.0873-0.3212-0.3488-0.0803-0.1256-0.25510.30780.3429-0.1965-0.12750.68260.00590.246244.4465-0.9393118.253
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D113 - 599
2X-RAY DIFFRACTION1A701 - 702
3X-RAY DIFFRACTION1B701
4X-RAY DIFFRACTION1D701
5X-RAY DIFFRACTION2C114 - 599
6X-RAY DIFFRACTION2A703 - 704
7X-RAY DIFFRACTION2B702
8X-RAY DIFFRACTION2C701
9X-RAY DIFFRACTION3B114 - 599
10X-RAY DIFFRACTION3B703
11X-RAY DIFFRACTION3C702 - 703
12X-RAY DIFFRACTION3D702
13X-RAY DIFFRACTION4A114 - 599
14X-RAY DIFFRACTION4A705
15X-RAY DIFFRACTION4C704
16X-RAY DIFFRACTION4D703 - 704
17X-RAY DIFFRACTION5A801 - 879
18X-RAY DIFFRACTION5B801 - 870
19X-RAY DIFFRACTION5C801 - 853
20X-RAY DIFFRACTION5D801 - 893
21X-RAY DIFFRACTION6A706
22X-RAY DIFFRACTION6B704
23X-RAY DIFFRACTION6C705
24X-RAY DIFFRACTION6D705

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