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- PDB-6dw4: SAMHD1 Bound to Cladribine-TP in the Catalytic Pocket and Alloste... -

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Basic information

Entry
Database: PDB / ID: 6dw4
TitleSAMHD1 Bound to Cladribine-TP in the Catalytic Pocket and Allosteric Pocket
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
Keywordshydrolase/hydrolase inhibitor / Complex / deoxynucleoside triphosphate triphosphohydrolase / dNTPase / nucleotide analogue / Cladribine-TP / 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 / dGTPase activity / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / 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 / dGTPase activity / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / 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 / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / single-stranded DNA binding / site of double-strand break / defense response to virus / protein homotetramerization / 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
GUANOSINE-5'-TRIPHOSPHATE / Chem-HF7 / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.99 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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)260,05725
Polymers253,7064
Non-polymers6,35221
Water15,637868
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23570 Å2
ΔGint-114 kcal/mol
Surface area68380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.324, 142.272, 98.438
Angle α, β, γ (deg.)90.00, 114.08, 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 / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 113 - 599 / Label seq-ID: 37 - 523

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11DA
21CB
12DA
22BC
13DA
23AD
14CB
24BC
15CB
25AD
16BC
26AD

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, 889 molecules

#2: Chemical
ChemComp-HF7 / 2'-deoxy-2-methyladenosine 5'-(tetrahydrogen triphosphate) / Cladribine-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H18N5O12P3
#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.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 868 / 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: 2.02 Å3/Da / Density % sol: 39.23 %
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: Aug 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.99→89.87 Å / Num. obs: 129994 / % possible obs: 95.1 % / Redundancy: 3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.682 / CC1/2: 0.518 / % possible all: 87.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.99→89.87 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.892 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20202 6512 5 %RANDOM
Rwork0.16933 ---
obs0.17098 123471 94.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.635 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-0.07 Å2
2--0.04 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.99→89.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15732 0 385 868 16985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01916605
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215182
X-RAY DIFFRACTIONr_angle_refined_deg2.1541.98522525
X-RAY DIFFRACTIONr_angle_other_deg1.123335316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72751940
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.29424.029819
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.869152940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.48515112
X-RAY DIFFRACTIONr_chiral_restr0.1280.22364
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02118094
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023386
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_it1.5861.7367748
X-RAY DIFFRACTIONr_mcbond_other1.5861.7357747
X-RAY DIFFRACTIONr_mcangle_it2.6882.599692
X-RAY DIFFRACTIONr_mcangle_other2.6882.5929693
X-RAY DIFFRACTIONr_scbond_it1.9951.9498857
X-RAY DIFFRACTIONr_scbond_other1.9971.9518845
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2772.83512814
X-RAY DIFFRACTIONr_long_range_B_refined6.8620.5319290
X-RAY DIFFRACTIONr_long_range_B_other6.79620.29419091
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)
11D331900.05
12C331900.05
21D331960.04
22B331960.04
31D330420.06
32A330420.06
41C331360.04
42B331360.04
51C329020.06
52A329020.06
61B329700.05
62A329700.05
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 413 -
Rwork0.266 8209 -
obs--85.39 %
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)
10.70910.09170.14360.9775-0.12560.69730.016-0.16170.01370.12440.01680.228-0.0155-0.1515-0.03290.02010.00610.03290.07390.0070.058331.10184.0922140.6535
20.57680.0130.18550.78580.19050.90760.0160.18420.0761-0.16370.007-0.1342-0.07280.172-0.0230.0587-0.02780.03270.11520.02690.040259.956713.7222100.4965
30.74460.1696-0.15240.9371-0.21470.99170.02940.1236-0.0544-0.1017-0.00650.2680.0348-0.1773-0.02290.0464-0.0245-0.04680.1139-0.01780.096726.55180.4283101.8056
40.7277-0.0975-0.24780.99610.18061.2970.0019-0.0661-0.04940.00730.0318-0.23670.05240.2732-0.03370.00960.0240.00680.0820.0130.075965.0623-6.7882134.2456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D113 - 900
2X-RAY DIFFRACTION2C113 - 900
3X-RAY DIFFRACTION3B113 - 900
4X-RAY DIFFRACTION4A113 - 900

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