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- PDB-6ob7: Human equilibrative nucleoside transporter-1, dilazep bound -

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Basic information

Entry
Database: PDB / ID: 6ob7
TitleHuman equilibrative nucleoside transporter-1, dilazep bound
ComponentsEquilibrative nucleoside transporter 1
KeywordsTRANSPORT PROTEIN / nucleoside transport / adenosine transport / nucleoside-drug transport / adenosine reuptake inhibitor / SLC29 / hENT1 / ENT / dilazep
Function / homology
Function and homology information


adenine transmembrane transporter activity / guanine transmembrane transporter activity / purine nucleoside transmembrane transporter activity / cytidine transport / inosine transport / hypoxanthine transport / thymine transport / guanine transmembrane transport / uracil transmembrane transport / pyrimidine nucleobase transmembrane transport ...adenine transmembrane transporter activity / guanine transmembrane transporter activity / purine nucleoside transmembrane transporter activity / cytidine transport / inosine transport / hypoxanthine transport / thymine transport / guanine transmembrane transport / uracil transmembrane transport / pyrimidine nucleobase transmembrane transport / uracil transmembrane transporter activity / cytidine transmembrane transporter activity / pyrimidine-containing compound transmembrane transport / purine nucleobase transmembrane transport / nucleoside transport / uridine transmembrane transport / adenosine transport / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / nucleobase transport / nucleoside transmembrane transport / adenine transport / nucleoside transmembrane transporter activity / neurotransmitter uptake / pyrimidine- and adenosine-specific:sodium symporter activity / uridine transmembrane transporter activity / purine nucleoside transmembrane transport / Ribavirin ADME / neurotransmitter transmembrane transporter activity / xenobiotic transmembrane transport / Azathioprine ADME / nucleobase-containing compound metabolic process / neurotransmitter transport / transport across blood-brain barrier / lactation / xenobiotic metabolic process / excitatory postsynaptic potential / cellular response to glucose stimulus / presynapse / cellular response to hypoxia / basolateral plasma membrane / postsynapse / apical plasma membrane / membrane / plasma membrane
Similarity search - Function
Nucleoside transporter ENT1/ENT2 / Nucleoside transporter / Equilibrative nucleoside transporter / MFS transporter superfamily
Similarity search - Domain/homology
Chem-8DZ / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Equilibrative nucleoside transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å
AuthorsWright, N.J. / Lee, S.-Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35NS097241 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Structures of human ENT1 in complex with adenosine reuptake inhibitors.
Authors: Wright, N.J. / Lee, S.Y.
History
DepositionMar 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Sep 18, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_related / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_site_gen.label_seq_id
Revision 2.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Equilibrative nucleoside transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,88620
Polymers48,8641
Non-polymers7,02219
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.040, 72.040, 173.371
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Equilibrative nucleoside transporter 1 / Equilibrative nitrobenzylmercaptopurine riboside-sensitive nucleoside transporter / Equilibrative ...Equilibrative nitrobenzylmercaptopurine riboside-sensitive nucleoside transporter / Equilibrative NBMPR-sensitive nucleoside transporter / Nucleoside transporter / es-type / Solute carrier family 29 member 1


Mass: 48863.707 Da / Num. of mol.: 1 / Mutation: L168F, P175A, N288K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC29A1, ENT1 / Plasmid: pEG-BacMam / Cell line (production host): HEK293S GnTI -/- / Production host: Homo sapiens (human) / References: UniProt: Q99808
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-8DZ / (1,4-diazepane-1,4-diyl)di(propane-3,1-diyl) bis(3,4,5-trimethoxybenzoate)


Mass: 604.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H44N2O10 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 9 / Details: 50% PEG 400, 0.5 M NaCl, 0.1 M glycine pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→62.39 Å / Num. obs: 22877 / % possible obs: 91.8 % / Redundancy: 4.6 % / CC1/2: 0.99 / Rpim(I) all: 0.11 / Net I/σ(I): 6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2236 / CC1/2: 0.39 / Rpim(I) all: 0.56 / % possible all: 82.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→62.388 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1
RfactorNum. reflection% reflection
Rfree0.2427 1098 5 %
Rwork0.2034 --
obs0.2054 21963 91.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→62.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 275 63 3286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063288
X-RAY DIFFRACTIONf_angle_d0.8684405
X-RAY DIFFRACTIONf_dihedral_angle_d18.521128
X-RAY DIFFRACTIONf_chiral_restr0.038504
X-RAY DIFFRACTIONf_plane_restr0.011518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.40480.33411210.26622312X-RAY DIFFRACTION83
2.4048-2.53150.29171290.24522385X-RAY DIFFRACTION86
2.5315-2.69020.27331360.22962612X-RAY DIFFRACTION93
2.6902-2.89790.26031410.20782659X-RAY DIFFRACTION95
2.8979-3.18950.23131410.20332725X-RAY DIFFRACTION97
3.1895-3.6510.22681410.18592679X-RAY DIFFRACTION95
3.651-4.59960.23231430.17862731X-RAY DIFFRACTION95
4.5996-62.41110.20781460.19512762X-RAY DIFFRACTION91

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