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- PDB-7s2y: SAMHD1 HD domain bound to CNDAC -

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Basic information

Entry
Database: PDB / ID: 7s2y
TitleSAMHD1 HD domain bound to CNDAC
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
KeywordsHYDROLASE / SAMHD1 / inhibitor / sapacitabine
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
Chem-85T / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDigianantonio, K.M. / Xiong, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J Exp Clin Cancer Res / Year: 2021
Title: Differences between intrinsic and acquired nucleoside analogue resistance in acute myeloid leukaemia cells.
Authors: Rothenburger, T. / Thomas, D. / Schreiber, Y. / Wratil, P.R. / Pflantz, T. / Knecht, K. / Digianantonio, K. / Temple, J. / Schneider, C. / Baldauf, H.M. / McLaughlin, K.M. / Rothweiler, F. / ...Authors: Rothenburger, T. / Thomas, D. / Schreiber, Y. / Wratil, P.R. / Pflantz, T. / Knecht, K. / Digianantonio, K. / Temple, J. / Schneider, C. / Baldauf, H.M. / McLaughlin, K.M. / Rothweiler, F. / Bilen, B. / Farmand, S. / Bojkova, D. / Costa, R. / Ferreiros, N. / Geisslinger, G. / Oellerich, T. / Xiong, Y. / Keppler, O.T. / Wass, M.N. / Michaelis, M. / Cinatl Jr., J.
History
DepositionSep 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,92624
Polymers253,7064
Non-polymers6,22120
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26430 Å2
ΔGint-93 kcal/mol
Surface area68380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.840, 146.167, 99.587
Angle α, β, γ (deg.)90.000, 114.270, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

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
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMHD1, MOP5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases

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Non-polymers , 5 types, 68 molecules

#2: Chemical
ChemComp-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


Mass: 492.166 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N4O13P3 / 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.: 48 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 298 K / Method: microbatch
Details: 100 mM succinate phosphate glycine buffer pH 7.4, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→90.784 Å / Num. obs: 51457 / % possible obs: 93.4 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1 / Num. unique obs: 3706 / CC1/2: 0.53 / % possible all: 67.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bzb

4bzb


Resolution: 2.8→50.03 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 35.972 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 2482 4.8 %RANDOM
Rwork0.186 ---
obs0.1882 48975 93.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 180.14 Å2 / Biso mean: 65.182 Å2 / Biso min: 19.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å2-0 Å2-0.78 Å2
2---2.49 Å2-0 Å2
3---1.74 Å2
Refinement stepCycle: final / Resolution: 2.8→50.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15732 0 376 48 16156
Biso mean--46.39 41.92 -
Num. residues----1924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01316666
X-RAY DIFFRACTIONr_bond_other_d00.01715601
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.66122608
X-RAY DIFFRACTIONr_angle_other_deg1.5751.5935988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1751948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13422.317941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.868152946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.85115113
X-RAY DIFFRACTIONr_chiral_restr0.1560.22116
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218601
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023893
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A164820.08
12B164820.08
21A164210.09
22C164210.09
31A164250.08
32D164250.08
41B164560.08
42C164560.08
51B164660.07
52D164660.07
61C165320.07
62D165320.07
LS refinement shellResolution: 2.8→2.87 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.43 120 -
Rwork0.388 2492 -
obs--63.57 %
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)
10.10280.18960.05940.3897-0.00190.44350.1279-0.0194-0.08340.2901-0.0506-0.1655-0.01080.0665-0.07730.3011-0.0287-0.17290.02690.00130.115612.216-5.28250.789
20.13090.18220.24280.50220.44310.55880.06490.003-0.0427-0.1144-0.0410.0230.0958-0.137-0.02390.2568-0.0928-0.06870.2364-0.04170.0436-16.849-16.74711.229
30.371-0.06580.21930.34360.00170.45840.01890.2078-0.0753-0.05350.0651-0.0736-0.18550.2197-0.0840.1872-0.0796-0.00730.1783-0.06380.058216.136-2.1712.056
40.09710.24290.1450.70370.13240.7970.0245-0.10.01210.1147-0.1341-0.0114-0.1542-0.44420.10960.19380.0717-0.00340.2527-0.05940.021-22.0723.46244.288
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D113 - 599
2X-RAY DIFFRACTION1B703
3X-RAY DIFFRACTION1D703 - 704
4X-RAY DIFFRACTION2C113 - 599
5X-RAY DIFFRACTION2A702
6X-RAY DIFFRACTION2C702 - 703
7X-RAY DIFFRACTION3B113 - 599
8X-RAY DIFFRACTION3B701 - 702
9X-RAY DIFFRACTION3D702
10X-RAY DIFFRACTION4A113 - 599
11X-RAY DIFFRACTION4A701
12X-RAY DIFFRACTION4C701
13X-RAY DIFFRACTION4D701

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