data_2J5D # _entry.id 2J5D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.321 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2J5D PDBE EBI-29911 WWPDB D_1290029911 BMRB 7288 # _pdbx_database_related.db_id 7288 _pdbx_database_related.details . _pdbx_database_related.db_name BMRB _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2J5D _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2006-09-14 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_cs REL # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Bocharov, E.V.' 1 ? 'Pustovalova, Y.E.' 2 ? 'Volynsky, P.E.' 3 ? 'Maslennikov, I.V.' 4 ? 'Goncharuk, M.V.' 5 ? 'Ermolyuk, Y.S.' 6 ? 'Arseniev, A.S.' 7 ? # _citation.id primary _citation.title 'Unique dimeric structure of BNip3 transmembrane domain suggests membrane permeabilization as a cell death trigger.' _citation.journal_abbrev 'J. Biol. Chem.' _citation.journal_volume 282 _citation.page_first 16256 _citation.page_last 16266 _citation.year 2007 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17412696 _citation.pdbx_database_id_DOI 10.1074/jbc.M701745200 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Bocharov, E.V.' 1 ? primary 'Pustovalova, Y.E.' 2 ? primary 'Pavlov, K.V.' 3 ? primary 'Volynsky, P.E.' 4 ? primary 'Goncharuk, M.V.' 5 ? primary 'Ermolyuk, Y.S.' 6 ? primary 'Karpunin, D.V.' 7 ? primary 'Schulga, A.A.' 8 ? primary 'Kirpichnikov, M.P.' 9 ? primary 'Efremov, R.G.' 10 ? primary 'Maslennikov, I.V.' 11 ? primary 'Arseniev, A.S.' 12 ? # _cell.entry_id 2J5D _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2J5D _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'BCL2/ADENOVIRUS E1B 19 KDA PROTEIN-INTERACTING PROTEIN 3' _entity.formula_weight 4926.933 _entity.pdbx_number_of_molecules 2 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'HOMODIMERIC TRANSMEMBRANE DOMAIN, RESIDUES 146-190' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'BNIP3 TM' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code RNTSVMKKGGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLTTS _entity_poly.pdbx_seq_one_letter_code_can RNTSVMKKGGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLTTS _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ARG n 1 2 ASN n 1 3 THR n 1 4 SER n 1 5 VAL n 1 6 MET n 1 7 LYS n 1 8 LYS n 1 9 GLY n 1 10 GLY n 1 11 ILE n 1 12 PHE n 1 13 SER n 1 14 ALA n 1 15 GLU n 1 16 PHE n 1 17 LEU n 1 18 LYS n 1 19 VAL n 1 20 PHE n 1 21 LEU n 1 22 PRO n 1 23 SER n 1 24 LEU n 1 25 LEU n 1 26 LEU n 1 27 SER n 1 28 HIS n 1 29 LEU n 1 30 LEU n 1 31 ALA n 1 32 ILE n 1 33 GLY n 1 34 LEU n 1 35 GLY n 1 36 ILE n 1 37 TYR n 1 38 ILE n 1 39 GLY n 1 40 ARG n 1 41 ARG n 1 42 LEU n 1 43 THR n 1 44 THR n 1 45 SER n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name HUMAN _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'HOMO SAPIENS' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant pLysS _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector PGEMEX1 _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description 'MITOCHONDIONAL PROTEIN FROM BCL-2 FAMILY' # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code BNIP3_HUMAN _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession Q12983 _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2J5D A 1 ? 45 ? Q12983 146 ? 190 ? 146 190 2 1 2J5D B 1 ? 45 ? Q12983 146 ? 190 ? 146 190 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 15N-HSQC 1 2 1 '3D-15N-EDITED- NOESY' 1 3 1 3D-15N-EDITED-TOCSY 1 4 1 13C-HSQC 1 5 1 '3D-13C-EDITED- NOESY' 1 6 1 '3D HCCH-TOCSY' 1 7 1 '2D- NOESY' 1 8 1 2D-TOCSY 1 9 1 2D-ROESY 1 10 1 HNCA 1 11 1 HNCOCA 1 12 1 HNCACB 1 13 1 CBCACONH 1 14 1 HBHACONH 1 15 1 '2D-15N- 13C-F1-FILT.-F3-SEPAR.- NOESY-HSQC' 1 16 1 '3D-13C-F1-FILT. -F3-SEPAR.-NOESY-HSQC' 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 313.0 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1.0 _pdbx_nmr_exptl_sample_conditions.pH 5.1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 20 _pdbx_nmr_exptl_sample_conditions.ionic_strength_units mM _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.temperature_units K _pdbx_nmr_exptl_sample_conditions.label ? # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '95% H2O/ 5% D2O' _pdbx_nmr_sample_details.solvent_system ? _pdbx_nmr_sample_details.label ? _pdbx_nmr_sample_details.type ? _pdbx_nmr_sample_details.details ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.type ? # _pdbx_nmr_refine.entry_id 2J5D _pdbx_nmr_refine.method TAD _pdbx_nmr_refine.details ;NMR-DERIVED STRUCTURES OF BNIP3 TM DIMERIC WERE RELAXATED BY MOLECULAR DYNAMICS IN EXPLICIT LIPID DMPC BILAYER USING NMR CONSTRAINTS THERE ARE SLOW CONFORMATIONAL EXCHANGE IN HYDROGEN BOND NET OF (SER172, HIS173)2 CLUSTER ON THE DIMERIZATION INTERFACE. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 2J5D _pdbx_nmr_details.text 'THE FIRST 12 AND THE LAST 4 STRUCTERES DIFFER IN HIS173 TAUTOMERIC FORM WITH PROTONATED NE OR ND, RESPECTIVELY.' # _pdbx_nmr_ensemble.entry_id 2J5D _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 16 _pdbx_nmr_ensemble.conformer_selection_criteria 'THE BEST TARGET FUNCTION' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement GROMACS ? LINDAHL 1 'structure solution' CYANA ? ? 2 # _exptl.entry_id 2J5D _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 2J5D _struct.title 'NMR structure of BNIP3 transmembrane domain in lipid bicelles' _struct.pdbx_descriptor 'BCL2/ADENOVIRUS E1B 19 KDA PROTEIN-INTERACTING PROTEIN 3' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2J5D _struct_keywords.pdbx_keywords 'MEMBRANE PROTEIN' _struct_keywords.text 'MEMBRANE PROTEIN, MITOCHONDRION, TRANSMEMBRANE, TRANSMEMBRANE DOMAIN, BCL-2, BNIP3, MEMBRANE, HOMODIMER, APOPTOSIS' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 SER A 13 ? THR A 44 ? SER A 158 THR A 189 1 ? 32 HELX_P HELX_P2 2 GLU B 15 ? PHE B 20 ? GLU B 160 PHE B 165 1 ? 6 HELX_P HELX_P3 3 PHE B 20 ? LEU B 42 ? PHE B 165 LEU B 187 1 ? 23 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _database_PDB_matrix.entry_id 2J5D _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2J5D _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 ARG 1 146 146 ARG ARG A . n A 1 2 ASN 2 147 147 ASN ASN A . n A 1 3 THR 3 148 148 THR THR A . n A 1 4 SER 4 149 149 SER SER A . n A 1 5 VAL 5 150 150 VAL VAL A . n A 1 6 MET 6 151 151 MET MET A . n A 1 7 LYS 7 152 152 LYS LYS A . n A 1 8 LYS 8 153 153 LYS LYS A . n A 1 9 GLY 9 154 154 GLY GLY A . n A 1 10 GLY 10 155 155 GLY GLY A . n A 1 11 ILE 11 156 156 ILE ILE A . n A 1 12 PHE 12 157 157 PHE PHE A . n A 1 13 SER 13 158 158 SER SER A . n A 1 14 ALA 14 159 159 ALA ALA A . n A 1 15 GLU 15 160 160 GLU GLU A . n A 1 16 PHE 16 161 161 PHE PHE A . n A 1 17 LEU 17 162 162 LEU LEU A . n A 1 18 LYS 18 163 163 LYS LYS A . n A 1 19 VAL 19 164 164 VAL VAL A . n A 1 20 PHE 20 165 165 PHE PHE A . n A 1 21 LEU 21 166 166 LEU LEU A . n A 1 22 PRO 22 167 167 PRO PRO A . n A 1 23 SER 23 168 168 SER SER A . n A 1 24 LEU 24 169 169 LEU LEU A . n A 1 25 LEU 25 170 170 LEU LEU A . n A 1 26 LEU 26 171 171 LEU LEU A . n A 1 27 SER 27 172 172 SER SER A . n A 1 28 HIS 28 173 173 HIS HIS A . n A 1 29 LEU 29 174 174 LEU LEU A . n A 1 30 LEU 30 175 175 LEU LEU A . n A 1 31 ALA 31 176 176 ALA ALA A . n A 1 32 ILE 32 177 177 ILE ILE A . n A 1 33 GLY 33 178 178 GLY GLY A . n A 1 34 LEU 34 179 179 LEU LEU A . n A 1 35 GLY 35 180 180 GLY GLY A . n A 1 36 ILE 36 181 181 ILE ILE A . n A 1 37 TYR 37 182 182 TYR TYR A . n A 1 38 ILE 38 183 183 ILE ILE A . n A 1 39 GLY 39 184 184 GLY GLY A . n A 1 40 ARG 40 185 185 ARG ARG A . n A 1 41 ARG 41 186 186 ARG ARG A . n A 1 42 LEU 42 187 187 LEU LEU A . n A 1 43 THR 43 188 188 THR THR A . n A 1 44 THR 44 189 189 THR THR A . n A 1 45 SER 45 190 190 SER SER A . n B 1 1 ARG 1 146 146 ARG ARG B . n B 1 2 ASN 2 147 147 ASN ASN B . n B 1 3 THR 3 148 148 THR THR B . n B 1 4 SER 4 149 149 SER SER B . n B 1 5 VAL 5 150 150 VAL VAL B . n B 1 6 MET 6 151 151 MET MET B . n B 1 7 LYS 7 152 152 LYS LYS B . n B 1 8 LYS 8 153 153 LYS LYS B . n B 1 9 GLY 9 154 154 GLY GLY B . n B 1 10 GLY 10 155 155 GLY GLY B . n B 1 11 ILE 11 156 156 ILE ILE B . n B 1 12 PHE 12 157 157 PHE PHE B . n B 1 13 SER 13 158 158 SER SER B . n B 1 14 ALA 14 159 159 ALA ALA B . n B 1 15 GLU 15 160 160 GLU GLU B . n B 1 16 PHE 16 161 161 PHE PHE B . n B 1 17 LEU 17 162 162 LEU LEU B . n B 1 18 LYS 18 163 163 LYS LYS B . n B 1 19 VAL 19 164 164 VAL VAL B . n B 1 20 PHE 20 165 165 PHE PHE B . n B 1 21 LEU 21 166 166 LEU LEU B . n B 1 22 PRO 22 167 167 PRO PRO B . n B 1 23 SER 23 168 168 SER SER B . n B 1 24 LEU 24 169 169 LEU LEU B . n B 1 25 LEU 25 170 170 LEU LEU B . n B 1 26 LEU 26 171 171 LEU LEU B . n B 1 27 SER 27 172 172 SER SER B . n B 1 28 HIS 28 173 173 HIS HIS B . n B 1 29 LEU 29 174 174 LEU LEU B . n B 1 30 LEU 30 175 175 LEU LEU B . n B 1 31 ALA 31 176 176 ALA ALA B . n B 1 32 ILE 32 177 177 ILE ILE B . n B 1 33 GLY 33 178 178 GLY GLY B . n B 1 34 LEU 34 179 179 LEU LEU B . n B 1 35 GLY 35 180 180 GLY GLY B . n B 1 36 ILE 36 181 181 ILE ILE B . n B 1 37 TYR 37 182 182 TYR TYR B . n B 1 38 ILE 38 183 183 ILE ILE B . n B 1 39 GLY 39 184 184 GLY GLY B . n B 1 40 ARG 40 185 185 ARG ARG B . n B 1 41 ARG 41 186 186 ARG ARG B . n B 1 42 LEU 42 187 187 LEU LEU B . n B 1 43 THR 43 188 188 THR THR B . n B 1 44 THR 44 189 189 THR THR B . n B 1 45 SER 45 190 190 SER SER B . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2007-04-17 2 'Structure model' 1 1 2011-05-08 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-02-28 5 'Structure model' 1 4 2020-01-15 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Source and taxonomy' 5 5 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' citation 2 4 'Structure model' entity_src_gen 3 5 'Structure model' pdbx_database_status # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_citation.journal_abbrev' 2 4 'Structure model' '_citation.page_last' 3 4 'Structure model' '_citation.pdbx_database_id_DOI' 4 4 'Structure model' '_citation.title' 5 4 'Structure model' '_entity_src_gen.pdbx_host_org_cell_line' 6 4 'Structure model' '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id' 7 4 'Structure model' '_entity_src_gen.pdbx_host_org_scientific_name' 8 4 'Structure model' '_entity_src_gen.pdbx_host_org_variant' 9 5 'Structure model' '_pdbx_database_status.status_code_cs' 10 5 'Structure model' '_pdbx_database_status.status_code_mr' # _pdbx_entry_details.entry_id 2J5D _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;WE STUDIED BNIP3 FRAGMENT ARG146-SER190 WHICH CONTAINS THE TRANSMEMBRANE SEGMENT WITH ADJACENT REGION ; # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 HG B SER 158 ? ? OE2 B GLU 160 ? ? 1.54 2 2 O A LEU 169 ? ? HG A SER 172 ? ? 1.57 3 3 O B LEU 169 ? ? HG B SER 172 ? ? 1.56 4 4 HG B SER 158 ? ? OE2 B GLU 160 ? ? 1.59 5 4 HG A SER 158 ? ? OE1 A GLU 160 ? ? 1.59 6 5 HG B SER 149 ? ? O B LYS 152 ? ? 1.57 7 11 O A ARG 186 ? ? HG A SER 190 ? ? 1.58 8 12 HG A SER 158 ? ? OE1 A GLU 160 ? ? 1.59 9 13 HG A SER 158 ? ? OE2 A GLU 160 ? ? 1.57 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 2 NE A ARG 146 ? ? CZ A ARG 146 ? ? NH1 A ARG 146 ? ? 123.45 120.30 3.15 0.50 N 2 2 NE A ARG 185 ? ? CZ A ARG 185 ? ? NH1 A ARG 185 ? ? 123.77 120.30 3.47 0.50 N 3 3 CB B TYR 182 ? ? CG B TYR 182 ? ? CD2 B TYR 182 ? ? 116.36 121.00 -4.64 0.60 N 4 3 NE B ARG 186 ? ? CZ B ARG 186 ? ? NH1 B ARG 186 ? ? 124.58 120.30 4.28 0.50 N 5 3 NE B ARG 186 ? ? CZ B ARG 186 ? ? NH2 B ARG 186 ? ? 116.58 120.30 -3.72 0.50 N 6 4 CB B PHE 165 ? ? CG B PHE 165 ? ? CD2 B PHE 165 ? ? 116.32 120.80 -4.48 0.70 N 7 4 NE B ARG 186 ? ? CZ B ARG 186 ? ? NH1 B ARG 186 ? ? 123.77 120.30 3.47 0.50 N 8 5 NE A ARG 146 ? ? CZ A ARG 146 ? ? NH1 A ARG 146 ? ? 123.97 120.30 3.67 0.50 N 9 5 CB A PHE 165 ? ? CG A PHE 165 ? ? CD2 A PHE 165 ? ? 116.53 120.80 -4.27 0.70 N 10 5 NE B ARG 146 ? ? CZ B ARG 146 ? ? NH1 B ARG 146 ? ? 123.78 120.30 3.48 0.50 N 11 5 CB B TYR 182 ? ? CG B TYR 182 ? ? CD2 B TYR 182 ? ? 117.13 121.00 -3.87 0.60 N 12 6 NE B ARG 186 ? ? CZ B ARG 186 ? ? NH1 B ARG 186 ? ? 123.81 120.30 3.51 0.50 N 13 7 CB B PHE 161 ? ? CG B PHE 161 ? ? CD2 B PHE 161 ? ? 115.07 120.80 -5.73 0.70 N 14 8 NE A ARG 185 ? ? CZ A ARG 185 ? ? NH1 A ARG 185 ? ? 124.66 120.30 4.36 0.50 N 15 9 CB A PHE 161 ? ? CG A PHE 161 ? ? CD2 A PHE 161 ? ? 116.45 120.80 -4.35 0.70 N 16 9 CB B PHE 157 ? ? CG B PHE 157 ? ? CD2 B PHE 157 ? ? 116.39 120.80 -4.41 0.70 N 17 10 NE B ARG 186 ? ? CZ B ARG 186 ? ? NH1 B ARG 186 ? ? 123.47 120.30 3.17 0.50 N 18 11 NE B ARG 185 ? ? CZ B ARG 185 ? ? NH1 B ARG 185 ? ? 123.30 120.30 3.00 0.50 N 19 12 NE B ARG 186 ? ? CZ B ARG 186 ? ? NH1 B ARG 186 ? ? 123.63 120.30 3.33 0.50 N 20 12 NE B ARG 186 ? ? CZ B ARG 186 ? ? NH2 B ARG 186 ? ? 117.28 120.30 -3.02 0.50 N 21 13 CB A PHE 157 ? ? CG A PHE 157 ? ? CD2 A PHE 157 ? ? 116.15 120.80 -4.65 0.70 N 22 13 CB A PHE 161 ? ? CG A PHE 161 ? ? CD2 A PHE 161 ? ? 116.53 120.80 -4.27 0.70 N 23 13 CB B TYR 182 ? ? CG B TYR 182 ? ? CD2 B TYR 182 ? ? 116.55 121.00 -4.45 0.60 N 24 14 NE A ARG 146 ? ? CZ A ARG 146 ? ? NH1 A ARG 146 ? ? 124.28 120.30 3.98 0.50 N 25 14 NE A ARG 146 ? ? CZ A ARG 146 ? ? NH2 A ARG 146 ? ? 117.04 120.30 -3.26 0.50 N 26 14 CB A PHE 157 ? ? CG A PHE 157 ? ? CD2 A PHE 157 ? ? 115.88 120.80 -4.92 0.70 N 27 14 CB A PHE 161 ? ? CG A PHE 161 ? ? CD2 A PHE 161 ? ? 116.58 120.80 -4.22 0.70 N 28 14 NE A ARG 186 ? ? CZ A ARG 186 ? ? NH2 A ARG 186 ? ? 117.26 120.30 -3.04 0.50 N 29 14 NE B ARG 185 ? ? CZ B ARG 185 ? ? NH1 B ARG 185 ? ? 124.57 120.30 4.27 0.50 N 30 15 NE A ARG 186 ? ? CZ A ARG 186 ? ? NH2 A ARG 186 ? ? 117.25 120.30 -3.05 0.50 N 31 15 NE B ARG 186 ? ? CZ B ARG 186 ? ? NH1 B ARG 186 ? ? 124.52 120.30 4.22 0.50 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 MET A 151 ? ? -64.08 96.23 2 1 LYS A 153 ? ? -104.17 -69.63 3 1 SER B 149 ? ? 177.08 149.18 4 1 LEU B 162 ? ? -80.70 31.73 5 1 LYS B 163 ? ? -127.09 -72.58 6 1 THR B 188 ? ? -117.05 -79.98 7 2 SER B 149 ? ? -56.83 109.70 8 2 ILE B 156 ? ? -36.84 139.57 9 3 MET B 151 ? ? 65.01 -64.65 10 3 LYS B 153 ? ? 46.84 27.38 11 3 SER B 158 ? ? -60.39 93.40 12 3 THR B 188 ? ? -84.35 -73.00 13 4 LYS A 153 ? ? 44.57 85.64 14 4 PHE A 157 ? ? -64.17 -71.44 15 4 SER B 149 ? ? 63.43 116.98 16 4 VAL B 150 ? ? 70.93 135.69 17 4 SER B 158 ? ? 172.28 141.53 18 5 SER A 149 ? ? -114.76 54.98 19 5 THR A 189 ? ? -109.33 53.88 20 5 SER B 149 ? ? 175.59 140.94 21 5 MET B 151 ? ? 59.83 -47.79 22 5 PHE B 161 ? ? -95.77 48.70 23 5 LYS B 163 ? ? -148.22 -39.97 24 5 PHE B 165 ? ? -51.43 -70.18 25 5 THR B 189 ? ? -106.04 70.21 26 6 VAL A 150 ? ? 36.95 50.24 27 6 SER A 158 ? ? -16.20 125.07 28 6 ASN B 147 ? ? -130.52 -49.80 29 6 LEU B 187 ? ? 6.47 -73.09 30 6 THR B 189 ? ? -90.52 58.40 31 7 ASN A 147 ? ? 21.40 78.41 32 7 MET A 151 ? ? -15.37 99.11 33 7 ILE A 156 ? ? -134.88 -148.95 34 7 THR A 189 ? ? -96.84 52.96 35 7 PHE B 165 ? ? -36.40 -71.79 36 7 ARG B 185 ? ? -96.55 -81.29 37 7 THR B 189 ? ? -79.01 26.71 38 8 PRO A 167 ? ? -51.96 -71.31 39 8 LYS B 152 ? ? -101.10 68.17 40 9 THR A 188 ? ? -95.98 -66.15 41 9 THR A 189 ? ? -106.23 67.46 42 9 ASN B 147 ? ? -135.37 -69.22 43 9 LYS B 152 ? ? -39.96 134.62 44 9 LEU B 169 ? ? -53.95 -71.08 45 10 THR A 148 ? ? -127.35 -66.05 46 10 LYS A 152 ? ? 64.25 97.30 47 10 THR A 189 ? ? -104.07 -74.58 48 10 SER B 158 ? ? 64.66 129.64 49 10 THR B 188 ? ? -101.47 -60.63 50 11 PHE A 157 ? ? -98.29 -72.07 51 11 ALA A 159 ? ? 35.99 50.35 52 11 GLU A 160 ? ? 66.75 -55.66 53 11 VAL A 164 ? ? -97.13 43.10 54 11 PHE A 165 ? ? -151.47 -68.20 55 11 ASN B 147 ? ? 74.76 -64.97 56 11 LYS B 152 ? ? 67.14 -64.56 57 11 LYS B 153 ? ? -65.97 94.37 58 12 ILE A 156 ? ? -110.93 -167.43 59 12 THR A 189 ? ? -67.11 68.76 60 12 MET B 151 ? ? -19.77 -64.43 61 13 THR A 148 ? ? -52.00 105.75 62 13 VAL A 150 ? ? -108.88 -77.80 63 13 PHE A 157 ? ? -66.96 -77.33 64 13 ILE B 156 ? ? -21.24 98.28 65 13 PHE B 157 ? ? 71.94 -46.28 66 13 SER B 158 ? ? -161.74 113.23 67 14 SER A 149 ? ? -93.42 -70.28 68 14 VAL A 150 ? ? 36.58 103.84 69 14 SER A 158 ? ? -174.85 119.34 70 14 ALA A 159 ? ? -124.89 -77.99 71 14 THR A 189 ? ? 20.40 89.94 72 14 ASN B 147 ? ? 7.91 75.73 73 14 LYS B 152 ? ? 34.60 86.35 74 14 THR B 188 ? ? -97.22 -75.17 75 15 THR A 188 ? ? -87.77 40.45 76 15 ASN B 147 ? ? 41.83 87.11 77 15 SER B 158 ? ? -173.53 119.95 78 16 SER A 158 ? ? 18.77 109.59 79 16 SER B 149 ? ? 65.25 117.38 80 16 THR B 188 ? ? -96.54 -75.22 # loop_ _pdbx_validate_main_chain_plane.id _pdbx_validate_main_chain_plane.PDB_model_num _pdbx_validate_main_chain_plane.auth_comp_id _pdbx_validate_main_chain_plane.auth_asym_id _pdbx_validate_main_chain_plane.auth_seq_id _pdbx_validate_main_chain_plane.PDB_ins_code _pdbx_validate_main_chain_plane.label_alt_id _pdbx_validate_main_chain_plane.improper_torsion_angle 1 1 THR B 148 ? ? 11.00 2 1 LEU B 169 ? ? -10.32 3 3 LEU A 169 ? ? -10.04 4 4 PHE A 161 ? ? -10.07 5 5 LEU B 169 ? ? -10.45 6 6 PHE A 157 ? ? 11.12 7 7 VAL A 150 ? ? 10.29 8 7 LEU B 169 ? ? -10.76 9 7 THR B 188 ? ? -10.40 10 8 LEU B 169 ? ? -11.91 11 10 LEU B 169 ? ? -10.16 12 13 THR A 148 ? ? 10.81 13 15 LEU A 187 ? ? -11.22 # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 TYR A 182 ? ? 0.075 'SIDE CHAIN' 2 1 ARG A 185 ? ? 0.075 'SIDE CHAIN' 3 1 TYR B 182 ? ? 0.068 'SIDE CHAIN' 4 2 TYR A 182 ? ? 0.088 'SIDE CHAIN' 5 3 PHE A 161 ? ? 0.104 'SIDE CHAIN' 6 3 PHE B 161 ? ? 0.083 'SIDE CHAIN' 7 3 TYR B 182 ? ? 0.172 'SIDE CHAIN' 8 4 PHE A 157 ? ? 0.126 'SIDE CHAIN' 9 4 PHE A 165 ? ? 0.111 'SIDE CHAIN' 10 4 TYR A 182 ? ? 0.094 'SIDE CHAIN' 11 4 ARG A 185 ? ? 0.110 'SIDE CHAIN' 12 4 TYR B 182 ? ? 0.071 'SIDE CHAIN' 13 4 ARG B 186 ? ? 0.090 'SIDE CHAIN' 14 5 PHE A 165 ? ? 0.100 'SIDE CHAIN' 15 5 TYR A 182 ? ? 0.093 'SIDE CHAIN' 16 5 ARG A 185 ? ? 0.083 'SIDE CHAIN' 17 5 PHE B 161 ? ? 0.078 'SIDE CHAIN' 18 5 TYR B 182 ? ? 0.067 'SIDE CHAIN' 19 5 ARG B 185 ? ? 0.089 'SIDE CHAIN' 20 6 PHE B 161 ? ? 0.075 'SIDE CHAIN' 21 6 TYR B 182 ? ? 0.085 'SIDE CHAIN' 22 7 PHE A 161 ? ? 0.136 'SIDE CHAIN' 23 7 TYR A 182 ? ? 0.071 'SIDE CHAIN' 24 7 PHE B 161 ? ? 0.093 'SIDE CHAIN' 25 7 TYR B 182 ? ? 0.068 'SIDE CHAIN' 26 8 TYR A 182 ? ? 0.167 'SIDE CHAIN' 27 8 ARG B 146 ? ? 0.074 'SIDE CHAIN' 28 9 PHE A 157 ? ? 0.086 'SIDE CHAIN' 29 9 PHE A 161 ? ? 0.085 'SIDE CHAIN' 30 9 TYR A 182 ? ? 0.078 'SIDE CHAIN' 31 9 TYR B 182 ? ? 0.091 'SIDE CHAIN' 32 10 ARG A 146 ? ? 0.084 'SIDE CHAIN' 33 10 TYR A 182 ? ? 0.121 'SIDE CHAIN' 34 10 PHE B 165 ? ? 0.101 'SIDE CHAIN' 35 10 TYR B 182 ? ? 0.087 'SIDE CHAIN' 36 11 PHE B 161 ? ? 0.113 'SIDE CHAIN' 37 11 TYR B 182 ? ? 0.153 'SIDE CHAIN' 38 12 PHE A 165 ? ? 0.105 'SIDE CHAIN' 39 12 PHE B 157 ? ? 0.087 'SIDE CHAIN' 40 12 PHE B 165 ? ? 0.128 'SIDE CHAIN' 41 12 TYR B 182 ? ? 0.107 'SIDE CHAIN' 42 13 PHE A 157 ? ? 0.133 'SIDE CHAIN' 43 13 PHE A 161 ? ? 0.098 'SIDE CHAIN' 44 13 TYR A 182 ? ? 0.066 'SIDE CHAIN' 45 13 ARG A 185 ? ? 0.071 'SIDE CHAIN' 46 13 TYR B 182 ? ? 0.210 'SIDE CHAIN' 47 13 ARG B 185 ? ? 0.082 'SIDE CHAIN' 48 14 PHE A 157 ? ? 0.114 'SIDE CHAIN' 49 14 ARG A 185 ? ? 0.119 'SIDE CHAIN' 50 14 TYR B 182 ? ? 0.076 'SIDE CHAIN' 51 15 PHE A 161 ? ? 0.075 'SIDE CHAIN' 52 15 PHE B 165 ? ? 0.117 'SIDE CHAIN' 53 15 TYR B 182 ? ? 0.165 'SIDE CHAIN' 54 15 ARG B 185 ? ? 0.072 'SIDE CHAIN' 55 16 PHE A 161 ? ? 0.088 'SIDE CHAIN' 56 16 TYR A 182 ? ? 0.141 'SIDE CHAIN' 57 16 TYR B 182 ? ? 0.171 'SIDE CHAIN' 58 16 ARG B 186 ? ? 0.096 'SIDE CHAIN' #