data_3ZEB # _entry.id 3ZEB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3ZEB pdb_00003zeb 10.2210/pdb3zeb/pdb PDBE EBI-54990 ? ? WWPDB D_1290054990 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3ZEB _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2012-12-04 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Vinothkumar, K.R.' 1 ? 'voskya, O.' 2 ? 'Kuettler, E.V.' 3 ? 'Brouwer, A.J.' 4 ? 'Liskamp, R.M.J.' 5 ? 'Verhelst, S.H.L.' 6 ? # _citation.id primary _citation.title 'Activity-Based Probes for Rhomboid Proteases Discovered in a Mass Spectrometry-Based Assay.' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 110 _citation.page_first 2472 _citation.page_last ? _citation.year 2013 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23359682 _citation.pdbx_database_id_DOI 10.1073/PNAS.1215076110 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Vosyka, O.' 1 ? primary 'Vinothkumar, K.R.' 2 ? primary 'Wolf, E.V.' 3 ? primary 'Brouwer, A.J.' 4 ? primary 'Liskamp, R.M.J.' 5 ? primary 'Verhelst, S.H.L.' 6 ? # _cell.entry_id 3ZEB _cell.length_a 111.109 _cell.length_b 111.109 _cell.length_c 126.067 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZEB _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'RHOMBOID PROTEASE GLPG' 20214.020 1 3.4.21.105 ? 'CORE TM DOMAIN, RESIDUES 92-270' ;THE ISOCOUMARIN RING IS OPENED BY THE NUCLEOPHILIC ATTACK OF S201 FORMS ESTER BOND AND SUBSEQUENTLY A REACTION BETWEEN HISTIDINE CREATES A SECOND COVALENT BOND. ; 2 non-polymer syn '2-phenylethyl 2-(4-azanyl-2-methanoyl-phenyl)ethanoate' 283.322 1 ? ? ? ? 3 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 4 non-polymer man 'nonyl beta-D-glucopyranoside' 306.395 5 ? ? ? ? 5 water nat water 18.015 18 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'INTRAMEMBRANE SERINE PROTEASE, GLPG' # _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 ;RAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGS GKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMAN GAHIAGLAVGLAMAFVDSL ; _entity_poly.pdbx_seq_one_letter_code_can ;RAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGS GKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMAN GAHIAGLAVGLAMAFVDSL ; _entity_poly.pdbx_strand_id A _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 ALA n 1 3 GLY n 1 4 PRO n 1 5 VAL n 1 6 THR n 1 7 TRP n 1 8 VAL n 1 9 MET n 1 10 MET n 1 11 ILE n 1 12 ALA n 1 13 CYS n 1 14 VAL n 1 15 VAL n 1 16 VAL n 1 17 PHE n 1 18 ILE n 1 19 ALA n 1 20 MET n 1 21 GLN n 1 22 ILE n 1 23 LEU n 1 24 GLY n 1 25 ASP n 1 26 GLN n 1 27 GLU n 1 28 VAL n 1 29 MET n 1 30 LEU n 1 31 TRP n 1 32 LEU n 1 33 ALA n 1 34 TRP n 1 35 PRO n 1 36 PHE n 1 37 ASP n 1 38 PRO n 1 39 THR n 1 40 LEU n 1 41 LYS n 1 42 PHE n 1 43 GLU n 1 44 PHE n 1 45 TRP n 1 46 ARG n 1 47 TYR n 1 48 PHE n 1 49 THR n 1 50 HIS n 1 51 ALA n 1 52 LEU n 1 53 MET n 1 54 HIS n 1 55 PHE n 1 56 SER n 1 57 LEU n 1 58 MET n 1 59 HIS n 1 60 ILE n 1 61 LEU n 1 62 PHE n 1 63 ASN n 1 64 LEU n 1 65 LEU n 1 66 TRP n 1 67 TRP n 1 68 TRP n 1 69 TYR n 1 70 LEU n 1 71 GLY n 1 72 GLY n 1 73 ALA n 1 74 VAL n 1 75 GLU n 1 76 LYS n 1 77 ARG n 1 78 LEU n 1 79 GLY n 1 80 SER n 1 81 GLY n 1 82 LYS n 1 83 LEU n 1 84 ILE n 1 85 VAL n 1 86 ILE n 1 87 THR n 1 88 LEU n 1 89 ILE n 1 90 SER n 1 91 ALA n 1 92 LEU n 1 93 LEU n 1 94 SER n 1 95 GLY n 1 96 TYR n 1 97 VAL n 1 98 GLN n 1 99 GLN n 1 100 LYS n 1 101 PHE n 1 102 SER n 1 103 GLY n 1 104 PRO n 1 105 TRP n 1 106 PHE n 1 107 GLY n 1 108 GLY n 1 109 LEU n 1 110 SER n 1 111 GLY n 1 112 VAL n 1 113 VAL n 1 114 TYR n 1 115 ALA n 1 116 LEU n 1 117 MET n 1 118 GLY n 1 119 TYR n 1 120 VAL n 1 121 TRP n 1 122 LEU n 1 123 ARG n 1 124 GLY n 1 125 GLU n 1 126 ARG n 1 127 ASP n 1 128 PRO n 1 129 GLN n 1 130 SER n 1 131 GLY n 1 132 ILE n 1 133 TYR n 1 134 LEU n 1 135 GLN n 1 136 ARG n 1 137 GLY n 1 138 LEU n 1 139 ILE n 1 140 ILE n 1 141 PHE n 1 142 ALA n 1 143 LEU n 1 144 ILE n 1 145 TRP n 1 146 ILE n 1 147 VAL n 1 148 ALA n 1 149 GLY n 1 150 TRP n 1 151 PHE n 1 152 ASP n 1 153 LEU n 1 154 PHE n 1 155 GLY n 1 156 MET n 1 157 SER n 1 158 MET n 1 159 ALA n 1 160 ASN n 1 161 GLY n 1 162 ALA n 1 163 HIS n 1 164 ILE n 1 165 ALA n 1 166 GLY n 1 167 LEU n 1 168 ALA n 1 169 VAL n 1 170 GLY n 1 171 LEU n 1 172 ALA n 1 173 MET n 1 174 ALA n 1 175 PHE n 1 176 VAL n 1 177 ASP n 1 178 SER n 1 179 LEU 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 ? _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 'ESCHERICHIA COLI' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 469008 _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' _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 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant C41 _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 PLASMID _entity_src_gen.pdbx_host_org_vector PET _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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code GLPG_ECOLI _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession P09391 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3ZEB _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 179 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P09391 _struct_ref_seq.db_align_beg 92 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 270 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 92 _struct_ref_seq.pdbx_auth_seq_align_end 270 # 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 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 BNG D-saccharide n 'nonyl beta-D-glucopyranoside' 'Beta-NONYLGLUCOSIDE; nonyl beta-D-glucoside; nonyl D-glucoside; nonyl glucoside' 'C15 H30 O6' 306.395 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 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 HOH non-polymer . WATER ? 'H2 O' 18.015 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 SV1 non-polymer . '2-phenylethyl 2-(4-azanyl-2-methanoyl-phenyl)ethanoate' ? 'C17 H17 N O3' 283.322 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3ZEB _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.5 _exptl_crystal.density_percent_sol 64.8 _exptl_crystal.description NONE _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '2M AMMONIUM CHLORIDE, 0.1 M BIS-TRIS PH7.0, 298K' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 _diffrn.pdbx_serial_crystal_experiment ? # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2012-05-24 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9795 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I02' _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I02 _diffrn_source.pdbx_wavelength 0.9795 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 3ZEB _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 44.95 _reflns.d_resolution_high 2.20 _reflns.number_obs 15318 _reflns.number_all ? _reflns.percent_possible_obs 99.6 _reflns.pdbx_Rmerge_I_obs 0.06 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 13.50 _reflns.B_iso_Wilson_estimate 47.4 _reflns.pdbx_redundancy 4.9 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.20 _reflns_shell.d_res_low 2.32 _reflns_shell.percent_possible_all 98.1 _reflns_shell.Rmerge_I_obs 0.48 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.10 _reflns_shell.pdbx_redundancy 4.9 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3ZEB _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 14556 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 44.99 _refine.ls_d_res_high 2.20 _refine.ls_percent_reflns_obs 99.33 _refine.ls_R_factor_obs 0.21552 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.21386 _refine.ls_R_factor_R_free 0.24703 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 761 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.950 _refine.correlation_coeff_Fo_to_Fc_free 0.935 _refine.B_iso_mean 60.0 _refine.aniso_B[1][1] -1.30 _refine.aniso_B[2][2] -1.30 _refine.aniso_B[3][3] 4.21 _refine.aniso_B[1][2] -1.30 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY' _refine.pdbx_starting_model 'PDB ENTRY 2XOV' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.203 _refine.pdbx_overall_ESU_R_Free 0.179 _refine.overall_SU_ML 0.132 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 5.099 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1426 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 69 _refine_hist.number_atoms_solvent 18 _refine_hist.number_atoms_total 1513 _refine_hist.d_res_high 2.20 _refine_hist.d_res_low 44.99 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.008 0.019 ? 1554 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 1528 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.091 1.950 ? 2107 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.744 3.000 ? 3485 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 4.641 5.000 ? 182 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 24.937 21.786 ? 56 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 12.705 15.000 ? 232 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 7.983 15.000 ? 6 'X-RAY DIFFRACTION' ? r_chiral_restr 0.061 0.200 ? 226 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.004 0.020 ? 1718 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 393 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 2.897 5.672 ? 720 'X-RAY DIFFRACTION' ? r_mcbond_other 2.894 5.666 ? 718 'X-RAY DIFFRACTION' ? r_mcangle_it 4.104 8.481 ? 898 'X-RAY DIFFRACTION' ? r_mcangle_other 4.104 8.487 ? 899 'X-RAY DIFFRACTION' ? r_scbond_it 2.958 6.267 ? 834 'X-RAY DIFFRACTION' ? r_scbond_other 2.957 6.268 ? 835 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other 4.729 9.228 ? 1208 'X-RAY DIFFRACTION' ? r_long_range_B_refined 7.126 48.133 ? 1836 'X-RAY DIFFRACTION' ? r_long_range_B_other 7.069 48.113 ? 1832 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.199 _refine_ls_shell.d_res_low 2.256 _refine_ls_shell.number_reflns_R_work 1020 _refine_ls_shell.R_factor_R_work 0.299 _refine_ls_shell.percent_reflns_obs 95.93 _refine_ls_shell.R_factor_R_free 0.302 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 65 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 3ZEB _struct.title 'A complex of GlpG with isocoumarin inhibitor covalently bonded to serine 201 and histidine 150' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3ZEB _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text 'HYDROLASE, INTRA-MEMBRANE PROTEASE, SERINE PROTEASE, ACYL ENZYME' # 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 2 ? C N N 3 ? D N N 4 ? E N N 4 ? F N N 4 ? G N N 4 ? H N N 4 ? I N N 5 ? # 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 GLY A 3 ? GLY A 24 ? GLY A 94 GLY A 115 1 ? 22 HELX_P HELX_P2 2 GLY A 24 ? ALA A 33 ? GLY A 115 ALA A 124 1 ? 10 HELX_P HELX_P3 3 ASP A 37 ? LYS A 41 ? ASP A 128 LYS A 132 5 ? 5 HELX_P HELX_P4 4 GLU A 43 ? PHE A 48 ? GLU A 134 PHE A 139 5 ? 6 HELX_P HELX_P5 5 PHE A 48 ? MET A 53 ? PHE A 139 MET A 144 5 ? 6 HELX_P HELX_P6 6 SER A 56 ? GLY A 79 ? SER A 147 GLY A 170 1 ? 24 HELX_P HELX_P7 7 GLY A 79 ? GLY A 103 ? GLY A 170 GLY A 194 1 ? 25 HELX_P HELX_P8 8 LEU A 109 ? ASP A 127 ? LEU A 200 ASP A 218 1 ? 19 HELX_P HELX_P9 9 PRO A 128 ? GLY A 131 ? PRO A 219 GLY A 222 5 ? 4 HELX_P HELX_P10 10 GLN A 135 ? PHE A 151 ? GLN A 226 PHE A 242 1 ? 17 HELX_P HELX_P11 11 ALA A 159 ? SER A 178 ? ALA A 250 SER A 269 1 ? 20 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale one ? A HIS 59 ND1 ? ? ? 1_555 B SV1 . C7 ? ? A HIS 150 A SV1 401 1_555 ? ? ? ? ? ? ? 1.502 ? ? covale2 covale one ? A SER 110 OG ? ? ? 1_555 B SV1 . C ? ? A SER 201 A SV1 401 1_555 ? ? ? ? ? ? ? 1.479 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 3ZEB _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 3ZEB _atom_sites.fract_transf_matrix[1][1] 0.009000 _atom_sites.fract_transf_matrix[1][2] 0.005196 _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] 0.010393 _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] 0.007932 _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 CL 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 92 92 ARG ARG A . n A 1 2 ALA 2 93 93 ALA ALA A . n A 1 3 GLY 3 94 94 GLY GLY A . n A 1 4 PRO 4 95 95 PRO PRO A . n A 1 5 VAL 5 96 96 VAL VAL A . n A 1 6 THR 6 97 97 THR THR A . n A 1 7 TRP 7 98 98 TRP TRP A . n A 1 8 VAL 8 99 99 VAL VAL A . n A 1 9 MET 9 100 100 MET MET A . n A 1 10 MET 10 101 101 MET MET A . n A 1 11 ILE 11 102 102 ILE ILE A . n A 1 12 ALA 12 103 103 ALA ALA A . n A 1 13 CYS 13 104 104 CYS CYS A . n A 1 14 VAL 14 105 105 VAL VAL A . n A 1 15 VAL 15 106 106 VAL VAL A . n A 1 16 VAL 16 107 107 VAL VAL A . n A 1 17 PHE 17 108 108 PHE PHE A . n A 1 18 ILE 18 109 109 ILE ILE A . n A 1 19 ALA 19 110 110 ALA ALA A . n A 1 20 MET 20 111 111 MET MET A . n A 1 21 GLN 21 112 112 GLN GLN A . n A 1 22 ILE 22 113 113 ILE ILE A . n A 1 23 LEU 23 114 114 LEU LEU A . n A 1 24 GLY 24 115 115 GLY GLY A . n A 1 25 ASP 25 116 116 ASP ASP A . n A 1 26 GLN 26 117 117 GLN GLN A . n A 1 27 GLU 27 118 118 GLU GLU A . n A 1 28 VAL 28 119 119 VAL VAL A . n A 1 29 MET 29 120 120 MET MET A . n A 1 30 LEU 30 121 121 LEU LEU A . n A 1 31 TRP 31 122 122 TRP TRP A . n A 1 32 LEU 32 123 123 LEU LEU A . n A 1 33 ALA 33 124 124 ALA ALA A . n A 1 34 TRP 34 125 125 TRP TRP A . n A 1 35 PRO 35 126 126 PRO PRO A . n A 1 36 PHE 36 127 127 PHE PHE A . n A 1 37 ASP 37 128 128 ASP ASP A . n A 1 38 PRO 38 129 129 PRO PRO A . n A 1 39 THR 39 130 130 THR THR A . n A 1 40 LEU 40 131 131 LEU LEU A . n A 1 41 LYS 41 132 132 LYS LYS A . n A 1 42 PHE 42 133 133 PHE PHE A . n A 1 43 GLU 43 134 134 GLU GLU A . n A 1 44 PHE 44 135 135 PHE PHE A . n A 1 45 TRP 45 136 136 TRP TRP A . n A 1 46 ARG 46 137 137 ARG ARG A . n A 1 47 TYR 47 138 138 TYR TYR A . n A 1 48 PHE 48 139 139 PHE PHE A . n A 1 49 THR 49 140 140 THR THR A . n A 1 50 HIS 50 141 141 HIS HIS A . n A 1 51 ALA 51 142 142 ALA ALA A . n A 1 52 LEU 52 143 143 LEU LEU A . n A 1 53 MET 53 144 144 MET MET A . n A 1 54 HIS 54 145 145 HIS HIS A . n A 1 55 PHE 55 146 146 PHE PHE A . n A 1 56 SER 56 147 147 SER SER A . n A 1 57 LEU 57 148 148 LEU LEU A . n A 1 58 MET 58 149 149 MET MET A . n A 1 59 HIS 59 150 150 HIS HIS A . n A 1 60 ILE 60 151 151 ILE ILE A . n A 1 61 LEU 61 152 152 LEU LEU A . n A 1 62 PHE 62 153 153 PHE PHE A . n A 1 63 ASN 63 154 154 ASN ASN A . n A 1 64 LEU 64 155 155 LEU LEU A . n A 1 65 LEU 65 156 156 LEU LEU A . n A 1 66 TRP 66 157 157 TRP TRP A . n A 1 67 TRP 67 158 158 TRP TRP A . n A 1 68 TRP 68 159 159 TRP TRP A . n A 1 69 TYR 69 160 160 TYR TYR A . n A 1 70 LEU 70 161 161 LEU LEU A . n A 1 71 GLY 71 162 162 GLY GLY A . n A 1 72 GLY 72 163 163 GLY GLY A . n A 1 73 ALA 73 164 164 ALA ALA A . n A 1 74 VAL 74 165 165 VAL VAL A . n A 1 75 GLU 75 166 166 GLU GLU A . n A 1 76 LYS 76 167 167 LYS LYS A . n A 1 77 ARG 77 168 168 ARG ARG A . n A 1 78 LEU 78 169 169 LEU LEU A . n A 1 79 GLY 79 170 170 GLY GLY A . n A 1 80 SER 80 171 171 SER SER A . n A 1 81 GLY 81 172 172 GLY GLY A . n A 1 82 LYS 82 173 173 LYS LYS A . n A 1 83 LEU 83 174 174 LEU LEU A . n A 1 84 ILE 84 175 175 ILE ILE A . n A 1 85 VAL 85 176 176 VAL VAL A . n A 1 86 ILE 86 177 177 ILE ILE A . n A 1 87 THR 87 178 178 THR THR A . n A 1 88 LEU 88 179 179 LEU LEU A . n A 1 89 ILE 89 180 180 ILE ILE A . n A 1 90 SER 90 181 181 SER SER A . n A 1 91 ALA 91 182 182 ALA ALA A . n A 1 92 LEU 92 183 183 LEU LEU A . n A 1 93 LEU 93 184 184 LEU LEU A . n A 1 94 SER 94 185 185 SER SER A . n A 1 95 GLY 95 186 186 GLY GLY A . n A 1 96 TYR 96 187 187 TYR TYR A . n A 1 97 VAL 97 188 188 VAL VAL A . n A 1 98 GLN 98 189 189 GLN GLN A . n A 1 99 GLN 99 190 190 GLN GLN A . n A 1 100 LYS 100 191 191 LYS LYS A . n A 1 101 PHE 101 192 192 PHE PHE A . n A 1 102 SER 102 193 193 SER SER A . n A 1 103 GLY 103 194 194 GLY GLY A . n A 1 104 PRO 104 195 195 PRO PRO A . n A 1 105 TRP 105 196 196 TRP TRP A . n A 1 106 PHE 106 197 197 PHE PHE A . n A 1 107 GLY 107 198 198 GLY GLY A . n A 1 108 GLY 108 199 199 GLY GLY A . n A 1 109 LEU 109 200 200 LEU LEU A . n A 1 110 SER 110 201 201 SER SER A . n A 1 111 GLY 111 202 202 GLY GLY A . n A 1 112 VAL 112 203 203 VAL VAL A . n A 1 113 VAL 113 204 204 VAL VAL A . n A 1 114 TYR 114 205 205 TYR TYR A . n A 1 115 ALA 115 206 206 ALA ALA A . n A 1 116 LEU 116 207 207 LEU LEU A . n A 1 117 MET 117 208 208 MET MET A . n A 1 118 GLY 118 209 209 GLY GLY A . n A 1 119 TYR 119 210 210 TYR TYR A . n A 1 120 VAL 120 211 211 VAL VAL A . n A 1 121 TRP 121 212 212 TRP TRP A . n A 1 122 LEU 122 213 213 LEU LEU A . n A 1 123 ARG 123 214 214 ARG ARG A . n A 1 124 GLY 124 215 215 GLY GLY A . n A 1 125 GLU 125 216 216 GLU GLU A . n A 1 126 ARG 126 217 217 ARG ARG A . n A 1 127 ASP 127 218 218 ASP ASP A . n A 1 128 PRO 128 219 219 PRO PRO A . n A 1 129 GLN 129 220 220 GLN GLN A . n A 1 130 SER 130 221 221 SER SER A . n A 1 131 GLY 131 222 222 GLY GLY A . n A 1 132 ILE 132 223 223 ILE ILE A . n A 1 133 TYR 133 224 224 TYR TYR A . n A 1 134 LEU 134 225 225 LEU LEU A . n A 1 135 GLN 135 226 226 GLN GLN A . n A 1 136 ARG 136 227 227 ARG ARG A . n A 1 137 GLY 137 228 228 GLY GLY A . n A 1 138 LEU 138 229 229 LEU LEU A . n A 1 139 ILE 139 230 230 ILE ILE A . n A 1 140 ILE 140 231 231 ILE ILE A . n A 1 141 PHE 141 232 232 PHE PHE A . n A 1 142 ALA 142 233 233 ALA ALA A . n A 1 143 LEU 143 234 234 LEU LEU A . n A 1 144 ILE 144 235 235 ILE ILE A . n A 1 145 TRP 145 236 236 TRP TRP A . n A 1 146 ILE 146 237 237 ILE ILE A . n A 1 147 VAL 147 238 238 VAL VAL A . n A 1 148 ALA 148 239 239 ALA ALA A . n A 1 149 GLY 149 240 240 GLY GLY A . n A 1 150 TRP 150 241 241 TRP TRP A . n A 1 151 PHE 151 242 242 PHE PHE A . n A 1 152 ASP 152 243 243 ASP ASP A . n A 1 153 LEU 153 244 244 LEU LEU A . n A 1 154 PHE 154 245 245 PHE PHE A . n A 1 155 GLY 155 246 246 GLY GLY A . n A 1 156 MET 156 247 247 MET MET A . n A 1 157 SER 157 248 248 SER SER A . n A 1 158 MET 158 249 249 MET MET A . n A 1 159 ALA 159 250 250 ALA ALA A . n A 1 160 ASN 160 251 251 ASN ASN A . n A 1 161 GLY 161 252 252 GLY GLY A . n A 1 162 ALA 162 253 253 ALA ALA A . n A 1 163 HIS 163 254 254 HIS HIS A . n A 1 164 ILE 164 255 255 ILE ILE A . n A 1 165 ALA 165 256 256 ALA ALA A . n A 1 166 GLY 166 257 257 GLY GLY A . n A 1 167 LEU 167 258 258 LEU LEU A . n A 1 168 ALA 168 259 259 ALA ALA A . n A 1 169 VAL 169 260 260 VAL VAL A . n A 1 170 GLY 170 261 261 GLY GLY A . n A 1 171 LEU 171 262 262 LEU LEU A . n A 1 172 ALA 172 263 263 ALA ALA A . n A 1 173 MET 173 264 264 MET MET A . n A 1 174 ALA 174 265 265 ALA ALA A . n A 1 175 PHE 175 266 266 PHE PHE A . n A 1 176 VAL 176 267 267 VAL VAL A . n A 1 177 ASP 177 268 268 ASP ASP A . n A 1 178 SER 178 269 269 SER SER A . n A 1 179 LEU 179 270 270 LEU LEU A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 SV1 1 401 401 SV1 SV1 A . C 3 CL 1 402 402 CL CL A . D 4 BNG 1 403 403 BNG BNG A . E 4 BNG 1 404 404 BNG BNG A . F 4 BNG 1 405 405 BNG BNG A . G 4 BNG 1 406 406 BNG BNG A . H 4 BNG 1 407 407 BNG BNG A . I 5 HOH 1 2001 2001 HOH HOH A . I 5 HOH 2 2002 2002 HOH HOH A . I 5 HOH 3 2003 2003 HOH HOH A . I 5 HOH 4 2004 2004 HOH HOH A . I 5 HOH 5 2005 2005 HOH HOH A . I 5 HOH 6 2006 2006 HOH HOH A . I 5 HOH 7 2007 2007 HOH HOH A . I 5 HOH 8 2008 2008 HOH HOH A . I 5 HOH 9 2009 2009 HOH HOH A . I 5 HOH 10 2010 2010 HOH HOH A . I 5 HOH 11 2011 2011 HOH HOH A . I 5 HOH 12 2012 2012 HOH HOH A . I 5 HOH 13 2013 2013 HOH HOH A . I 5 HOH 14 2014 2014 HOH HOH A . I 5 HOH 15 2015 2015 HOH HOH A . I 5 HOH 16 2016 2016 HOH HOH A . I 5 HOH 17 2017 2017 HOH HOH A . I 5 HOH 18 2018 2018 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I # _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 2013-02-13 2 'Structure model' 1 1 2013-03-06 3 'Structure model' 1 2 2019-02-27 4 'Structure model' 1 3 2020-07-29 5 'Structure model' 1 4 2023-12-20 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 4 'Structure model' repository Remediation 'Carbohydrate remediation' ? # 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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Derived calculations' 4 3 'Structure model' 'Experimental preparation' 5 3 'Structure model' Other 6 4 'Structure model' 'Data collection' 7 4 'Structure model' 'Derived calculations' 8 4 'Structure model' Other 9 4 'Structure model' 'Structure summary' 10 5 'Structure model' 'Data collection' 11 5 'Structure model' 'Database references' 12 5 'Structure model' 'Refinement description' 13 5 'Structure model' 'Structure summary' # 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 3 'Structure model' exptl_crystal_grow 2 3 'Structure model' pdbx_database_proc 3 3 'Structure model' pdbx_database_status 4 3 'Structure model' struct_biol 5 3 'Structure model' struct_conn 6 4 'Structure model' chem_comp 7 4 'Structure model' entity 8 4 'Structure model' pdbx_chem_comp_identifier 9 4 'Structure model' pdbx_database_status 10 4 'Structure model' pdbx_entity_nonpoly 11 4 'Structure model' struct_conn 12 4 'Structure model' struct_site 13 4 'Structure model' struct_site_gen 14 5 'Structure model' chem_comp 15 5 'Structure model' chem_comp_atom 16 5 'Structure model' chem_comp_bond 17 5 'Structure model' database_2 18 5 'Structure model' pdbx_initial_refinement_model # 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 3 'Structure model' '_exptl_crystal_grow.method' 2 3 'Structure model' '_exptl_crystal_grow.temp' 3 3 'Structure model' '_pdbx_database_status.recvd_author_approval' 4 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_chem_comp.mon_nstd_flag' 6 4 'Structure model' '_chem_comp.name' 7 4 'Structure model' '_chem_comp.type' 8 4 'Structure model' '_entity.pdbx_description' 9 4 'Structure model' '_pdbx_database_status.status_code_sf' 10 4 'Structure model' '_pdbx_entity_nonpoly.name' 11 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 12 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 13 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 14 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 15 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 16 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 17 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 18 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 19 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 20 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 21 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 22 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 23 5 'Structure model' '_chem_comp.pdbx_synonyms' 24 5 'Structure model' '_database_2.pdbx_DOI' 25 5 'Structure model' '_database_2.pdbx_database_accession' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language REFMAC refinement 5.7.0032 ? 1 ? ? ? ? XDS 'data reduction' . ? 2 ? ? ? ? SCALA 'data scaling' . ? 3 ? ? ? ? PHASER phasing . ? 4 ? ? ? ? # _pdbx_entry_details.entry_id 3ZEB _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ;2-PHENYLETHYL 2-(4-AZANYL-2-METHANOYL-PHENYL)ETHANOATE (SV1): THE NUCLEOPHILIC ATTACK OF SER 201 ON ISOCOUMARIN OPENS THE RING AND FORMS AN ESTER BOND. A SUBSEQUENT REACTION WITH HIS 150 RESULTS IN TWIN COVALENTLY BONDED MOLECULE. ; _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id SER _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 269 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -102.39 _pdbx_validate_torsion.psi 61.60 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A GLN 220 ? CG ? A GLN 129 CG 2 1 Y 1 A GLN 220 ? CD ? A GLN 129 CD 3 1 Y 1 A GLN 220 ? OE1 ? A GLN 129 OE1 4 1 Y 1 A GLN 220 ? NE2 ? A GLN 129 NE2 5 1 N 1 A BNG 403 ? C1 ? D BNG 1 C1 6 1 N 1 A BNG 403 ? C2 ? D BNG 1 C2 7 1 N 1 A BNG 403 ? C3 ? D BNG 1 C3 8 1 N 1 A BNG 403 ? C4 ? D BNG 1 C4 9 1 N 1 A BNG 403 ? C5 ? D BNG 1 C5 10 1 N 1 A BNG 403 ? C6 ? D BNG 1 C6 11 1 N 1 A BNG 403 ? O1 ? D BNG 1 O1 12 1 N 1 A BNG 403 ? O2 ? D BNG 1 O2 13 1 N 1 A BNG 403 ? O3 ? D BNG 1 O3 14 1 N 1 A BNG 403 ? O4 ? D BNG 1 O4 15 1 N 1 A BNG 403 ? O5 ? D BNG 1 O5 16 1 N 1 A BNG 403 ? O6 ? D BNG 1 O6 17 1 N 1 A BNG 404 ? C1 ? E BNG 1 C1 18 1 N 1 A BNG 404 ? C2 ? E BNG 1 C2 19 1 N 1 A BNG 404 ? C3 ? E BNG 1 C3 20 1 N 1 A BNG 404 ? C4 ? E BNG 1 C4 21 1 N 1 A BNG 404 ? C5 ? E BNG 1 C5 22 1 N 1 A BNG 404 ? C6 ? E BNG 1 C6 23 1 N 1 A BNG 404 ? "C8'" ? E BNG 1 "C8'" 24 1 N 1 A BNG 404 ? "C9'" ? E BNG 1 "C9'" 25 1 N 1 A BNG 404 ? O1 ? E BNG 1 O1 26 1 N 1 A BNG 404 ? O2 ? E BNG 1 O2 27 1 N 1 A BNG 404 ? O3 ? E BNG 1 O3 28 1 N 1 A BNG 404 ? O4 ? E BNG 1 O4 29 1 N 1 A BNG 404 ? O5 ? E BNG 1 O5 30 1 N 1 A BNG 404 ? O6 ? E BNG 1 O6 31 1 N 1 A BNG 405 ? C1 ? F BNG 1 C1 32 1 N 1 A BNG 405 ? C2 ? F BNG 1 C2 33 1 N 1 A BNG 405 ? C3 ? F BNG 1 C3 34 1 N 1 A BNG 405 ? C4 ? F BNG 1 C4 35 1 N 1 A BNG 405 ? C5 ? F BNG 1 C5 36 1 N 1 A BNG 405 ? C6 ? F BNG 1 C6 37 1 N 1 A BNG 405 ? "C6'" ? F BNG 1 "C6'" 38 1 N 1 A BNG 405 ? "C7'" ? F BNG 1 "C7'" 39 1 N 1 A BNG 405 ? "C8'" ? F BNG 1 "C8'" 40 1 N 1 A BNG 405 ? "C9'" ? F BNG 1 "C9'" 41 1 N 1 A BNG 405 ? O1 ? F BNG 1 O1 42 1 N 1 A BNG 405 ? O2 ? F BNG 1 O2 43 1 N 1 A BNG 405 ? O3 ? F BNG 1 O3 44 1 N 1 A BNG 405 ? O4 ? F BNG 1 O4 45 1 N 1 A BNG 405 ? O5 ? F BNG 1 O5 46 1 N 1 A BNG 405 ? O6 ? F BNG 1 O6 47 1 N 1 A BNG 407 ? C1 ? H BNG 1 C1 48 1 N 1 A BNG 407 ? C2 ? H BNG 1 C2 49 1 N 1 A BNG 407 ? C3 ? H BNG 1 C3 50 1 N 1 A BNG 407 ? C4 ? H BNG 1 C4 51 1 N 1 A BNG 407 ? C5 ? H BNG 1 C5 52 1 N 1 A BNG 407 ? C6 ? H BNG 1 C6 53 1 N 1 A BNG 407 ? "C6'" ? H BNG 1 "C6'" 54 1 N 1 A BNG 407 ? "C7'" ? H BNG 1 "C7'" 55 1 N 1 A BNG 407 ? "C8'" ? H BNG 1 "C8'" 56 1 N 1 A BNG 407 ? "C9'" ? H BNG 1 "C9'" 57 1 N 1 A BNG 407 ? O1 ? H BNG 1 O1 58 1 N 1 A BNG 407 ? O2 ? H BNG 1 O2 59 1 N 1 A BNG 407 ? O3 ? H BNG 1 O3 60 1 N 1 A BNG 407 ? O4 ? H BNG 1 O4 61 1 N 1 A BNG 407 ? O5 ? H BNG 1 O5 62 1 N 1 A BNG 407 ? O6 ? H BNG 1 O6 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASN N N N N 41 ASN CA C N S 42 ASN C C N N 43 ASN O O N N 44 ASN CB C N N 45 ASN CG C N N 46 ASN OD1 O N N 47 ASN ND2 N N N 48 ASN OXT O N N 49 ASN H H N N 50 ASN H2 H N N 51 ASN HA H N N 52 ASN HB2 H N N 53 ASN HB3 H N N 54 ASN HD21 H N N 55 ASN HD22 H N N 56 ASN HXT H N N 57 ASP N N N N 58 ASP CA C N S 59 ASP C C N N 60 ASP O O N N 61 ASP CB C N N 62 ASP CG C N N 63 ASP OD1 O N N 64 ASP OD2 O N N 65 ASP OXT O N N 66 ASP H H N N 67 ASP H2 H N N 68 ASP HA H N N 69 ASP HB2 H N N 70 ASP HB3 H N N 71 ASP HD2 H N N 72 ASP HXT H N N 73 BNG C1 C N R 74 BNG C2 C N R 75 BNG C3 C N S 76 BNG C4 C N S 77 BNG C5 C N R 78 BNG C6 C N N 79 BNG "C1'" C N N 80 BNG "C2'" C N N 81 BNG "C3'" C N N 82 BNG "C4'" C N N 83 BNG "C5'" C N N 84 BNG "C6'" C N N 85 BNG "C7'" C N N 86 BNG "C8'" C N N 87 BNG "C9'" C N N 88 BNG O1 O N N 89 BNG O2 O N N 90 BNG O3 O N N 91 BNG O4 O N N 92 BNG O5 O N N 93 BNG O6 O N N 94 BNG H1 H N N 95 BNG H2 H N N 96 BNG H3 H N N 97 BNG H4 H N N 98 BNG H5 H N N 99 BNG H61 H N N 100 BNG H62 H N N 101 BNG "H1'1" H N N 102 BNG "H1'2" H N N 103 BNG "H2'1" H N N 104 BNG "H2'2" H N N 105 BNG "H3'1" H N N 106 BNG "H3'2" H N N 107 BNG "H4'1" H N N 108 BNG "H4'2" H N N 109 BNG "H5'1" H N N 110 BNG "H5'2" H N N 111 BNG "H6'1" H N N 112 BNG "H6'2" H N N 113 BNG "H7'1" H N N 114 BNG "H7'2" H N N 115 BNG "H8'1" H N N 116 BNG "H8'2" H N N 117 BNG "H9'1" H N N 118 BNG "H9'2" H N N 119 BNG "H9'3" H N N 120 BNG HO2 H N N 121 BNG HO3 H N N 122 BNG HO4 H N N 123 BNG HO6 H N N 124 CL CL CL N N 125 CYS N N N N 126 CYS CA C N R 127 CYS C C N N 128 CYS O O N N 129 CYS CB C N N 130 CYS SG S N N 131 CYS OXT O N N 132 CYS H H N N 133 CYS H2 H N N 134 CYS HA H N N 135 CYS HB2 H N N 136 CYS HB3 H N N 137 CYS HG H N N 138 CYS HXT H N N 139 GLN N N N N 140 GLN CA C N S 141 GLN C C N N 142 GLN O O N N 143 GLN CB C N N 144 GLN CG C N N 145 GLN CD C N N 146 GLN OE1 O N N 147 GLN NE2 N N N 148 GLN OXT O N N 149 GLN H H N N 150 GLN H2 H N N 151 GLN HA H N N 152 GLN HB2 H N N 153 GLN HB3 H N N 154 GLN HG2 H N N 155 GLN HG3 H N N 156 GLN HE21 H N N 157 GLN HE22 H N N 158 GLN HXT H N N 159 GLU N N N N 160 GLU CA C N S 161 GLU C C N N 162 GLU O O N N 163 GLU CB C N N 164 GLU CG C N N 165 GLU CD C N N 166 GLU OE1 O N N 167 GLU OE2 O N N 168 GLU OXT O N N 169 GLU H H N N 170 GLU H2 H N N 171 GLU HA H N N 172 GLU HB2 H N N 173 GLU HB3 H N N 174 GLU HG2 H N N 175 GLU HG3 H N N 176 GLU HE2 H N N 177 GLU HXT H N N 178 GLY N N N N 179 GLY CA C N N 180 GLY C C N N 181 GLY O O N N 182 GLY OXT O N N 183 GLY H H N N 184 GLY H2 H N N 185 GLY HA2 H N N 186 GLY HA3 H N N 187 GLY HXT H N N 188 HIS N N N N 189 HIS CA C N S 190 HIS C C N N 191 HIS O O N N 192 HIS CB C N N 193 HIS CG C Y N 194 HIS ND1 N Y N 195 HIS CD2 C Y N 196 HIS CE1 C Y N 197 HIS NE2 N Y N 198 HIS OXT O N N 199 HIS H H N N 200 HIS H2 H N N 201 HIS HA H N N 202 HIS HB2 H N N 203 HIS HB3 H N N 204 HIS HD1 H N N 205 HIS HD2 H N N 206 HIS HE1 H N N 207 HIS HE2 H N N 208 HIS HXT H N N 209 HOH O O N N 210 HOH H1 H N N 211 HOH H2 H N N 212 ILE N N N N 213 ILE CA C N S 214 ILE C C N N 215 ILE O O N N 216 ILE CB C N S 217 ILE CG1 C N N 218 ILE CG2 C N N 219 ILE CD1 C N N 220 ILE OXT O N N 221 ILE H H N N 222 ILE H2 H N N 223 ILE HA H N N 224 ILE HB H N N 225 ILE HG12 H N N 226 ILE HG13 H N N 227 ILE HG21 H N N 228 ILE HG22 H N N 229 ILE HG23 H N N 230 ILE HD11 H N N 231 ILE HD12 H N N 232 ILE HD13 H N N 233 ILE HXT H N N 234 LEU N N N N 235 LEU CA C N S 236 LEU C C N N 237 LEU O O N N 238 LEU CB C N N 239 LEU CG C N N 240 LEU CD1 C N N 241 LEU CD2 C N N 242 LEU OXT O N N 243 LEU H H N N 244 LEU H2 H N N 245 LEU HA H N N 246 LEU HB2 H N N 247 LEU HB3 H N N 248 LEU HG H N N 249 LEU HD11 H N N 250 LEU HD12 H N N 251 LEU HD13 H N N 252 LEU HD21 H N N 253 LEU HD22 H N N 254 LEU HD23 H N N 255 LEU HXT H N N 256 LYS N N N N 257 LYS CA C N S 258 LYS C C N N 259 LYS O O N N 260 LYS CB C N N 261 LYS CG C N N 262 LYS CD C N N 263 LYS CE C N N 264 LYS NZ N N N 265 LYS OXT O N N 266 LYS H H N N 267 LYS H2 H N N 268 LYS HA H N N 269 LYS HB2 H N N 270 LYS HB3 H N N 271 LYS HG2 H N N 272 LYS HG3 H N N 273 LYS HD2 H N N 274 LYS HD3 H N N 275 LYS HE2 H N N 276 LYS HE3 H N N 277 LYS HZ1 H N N 278 LYS HZ2 H N N 279 LYS HZ3 H N N 280 LYS HXT H N N 281 MET N N N N 282 MET CA C N S 283 MET C C N N 284 MET O O N N 285 MET CB C N N 286 MET CG C N N 287 MET SD S N N 288 MET CE C N N 289 MET OXT O N N 290 MET H H N N 291 MET H2 H N N 292 MET HA H N N 293 MET HB2 H N N 294 MET HB3 H N N 295 MET HG2 H N N 296 MET HG3 H N N 297 MET HE1 H N N 298 MET HE2 H N N 299 MET HE3 H N N 300 MET HXT H N N 301 PHE N N N N 302 PHE CA C N S 303 PHE C C N N 304 PHE O O N N 305 PHE CB C N N 306 PHE CG C Y N 307 PHE CD1 C Y N 308 PHE CD2 C Y N 309 PHE CE1 C Y N 310 PHE CE2 C Y N 311 PHE CZ C Y N 312 PHE OXT O N N 313 PHE H H N N 314 PHE H2 H N N 315 PHE HA H N N 316 PHE HB2 H N N 317 PHE HB3 H N N 318 PHE HD1 H N N 319 PHE HD2 H N N 320 PHE HE1 H N N 321 PHE HE2 H N N 322 PHE HZ H N N 323 PHE HXT H N N 324 PRO N N N N 325 PRO CA C N S 326 PRO C C N N 327 PRO O O N N 328 PRO CB C N N 329 PRO CG C N N 330 PRO CD C N N 331 PRO OXT O N N 332 PRO H H N N 333 PRO HA H N N 334 PRO HB2 H N N 335 PRO HB3 H N N 336 PRO HG2 H N N 337 PRO HG3 H N N 338 PRO HD2 H N N 339 PRO HD3 H N N 340 PRO HXT H N N 341 SER N N N N 342 SER CA C N S 343 SER C C N N 344 SER O O N N 345 SER CB C N N 346 SER OG O N N 347 SER OXT O N N 348 SER H H N N 349 SER H2 H N N 350 SER HA H N N 351 SER HB2 H N N 352 SER HB3 H N N 353 SER HG H N N 354 SER HXT H N N 355 SV1 O1 O N N 356 SV1 C8 C N N 357 SV1 C7 C N N 358 SV1 C6 C Y N 359 SV1 C5 C Y N 360 SV1 C4 C Y N 361 SV1 C3 C Y N 362 SV1 N N N N 363 SV1 C2 C Y N 364 SV1 C1 C Y N 365 SV1 C C N N 366 SV1 O O N N 367 SV1 O2 O N N 368 SV1 C9 C N N 369 SV1 C10 C N N 370 SV1 C11 C Y N 371 SV1 C16 C Y N 372 SV1 C15 C Y N 373 SV1 C14 C Y N 374 SV1 C13 C Y N 375 SV1 C12 C Y N 376 SV1 H H N N 377 SV1 H72 H N N 378 SV1 H71 H N N 379 SV1 H5 H N N 380 SV1 H4 H N N 381 SV1 HN1 H N N 382 SV1 HN2 H N N 383 SV1 H2 H N N 384 SV1 H91C H N N 385 SV1 H92C H N N 386 SV1 H101 H N N 387 SV1 H102 H N N 388 SV1 H16 H N N 389 SV1 H12 H N N 390 SV1 H15 H N N 391 SV1 H14 H N N 392 SV1 H13 H N N 393 THR N N N N 394 THR CA C N S 395 THR C C N N 396 THR O O N N 397 THR CB C N R 398 THR OG1 O N N 399 THR CG2 C N N 400 THR OXT O N N 401 THR H H N N 402 THR H2 H N N 403 THR HA H N N 404 THR HB H N N 405 THR HG1 H N N 406 THR HG21 H N N 407 THR HG22 H N N 408 THR HG23 H N N 409 THR HXT H N N 410 TRP N N N N 411 TRP CA C N S 412 TRP C C N N 413 TRP O O N N 414 TRP CB C N N 415 TRP CG C Y N 416 TRP CD1 C Y N 417 TRP CD2 C Y N 418 TRP NE1 N Y N 419 TRP CE2 C Y N 420 TRP CE3 C Y N 421 TRP CZ2 C Y N 422 TRP CZ3 C Y N 423 TRP CH2 C Y N 424 TRP OXT O N N 425 TRP H H N N 426 TRP H2 H N N 427 TRP HA H N N 428 TRP HB2 H N N 429 TRP HB3 H N N 430 TRP HD1 H N N 431 TRP HE1 H N N 432 TRP HE3 H N N 433 TRP HZ2 H N N 434 TRP HZ3 H N N 435 TRP HH2 H N N 436 TRP HXT H N N 437 TYR N N N N 438 TYR CA C N S 439 TYR C C N N 440 TYR O O N N 441 TYR CB C N N 442 TYR CG C Y N 443 TYR CD1 C Y N 444 TYR CD2 C Y N 445 TYR CE1 C Y N 446 TYR CE2 C Y N 447 TYR CZ C Y N 448 TYR OH O N N 449 TYR OXT O N N 450 TYR H H N N 451 TYR H2 H N N 452 TYR HA H N N 453 TYR HB2 H N N 454 TYR HB3 H N N 455 TYR HD1 H N N 456 TYR HD2 H N N 457 TYR HE1 H N N 458 TYR HE2 H N N 459 TYR HH H N N 460 TYR HXT H N N 461 VAL N N N N 462 VAL CA C N S 463 VAL C C N N 464 VAL O O N N 465 VAL CB C N N 466 VAL CG1 C N N 467 VAL CG2 C N N 468 VAL OXT O N N 469 VAL H H N N 470 VAL H2 H N N 471 VAL HA H N N 472 VAL HB H N N 473 VAL HG11 H N N 474 VAL HG12 H N N 475 VAL HG13 H N N 476 VAL HG21 H N N 477 VAL HG22 H N N 478 VAL HG23 H N N 479 VAL HXT H N N 480 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASN N CA sing N N 39 ASN N H sing N N 40 ASN N H2 sing N N 41 ASN CA C sing N N 42 ASN CA CB sing N N 43 ASN CA HA sing N N 44 ASN C O doub N N 45 ASN C OXT sing N N 46 ASN CB CG sing N N 47 ASN CB HB2 sing N N 48 ASN CB HB3 sing N N 49 ASN CG OD1 doub N N 50 ASN CG ND2 sing N N 51 ASN ND2 HD21 sing N N 52 ASN ND2 HD22 sing N N 53 ASN OXT HXT sing N N 54 ASP N CA sing N N 55 ASP N H sing N N 56 ASP N H2 sing N N 57 ASP CA C sing N N 58 ASP CA CB sing N N 59 ASP CA HA sing N N 60 ASP C O doub N N 61 ASP C OXT sing N N 62 ASP CB CG sing N N 63 ASP CB HB2 sing N N 64 ASP CB HB3 sing N N 65 ASP CG OD1 doub N N 66 ASP CG OD2 sing N N 67 ASP OD2 HD2 sing N N 68 ASP OXT HXT sing N N 69 BNG C1 C2 sing N N 70 BNG C1 O1 sing N N 71 BNG C1 O5 sing N N 72 BNG C1 H1 sing N N 73 BNG C2 C3 sing N N 74 BNG C2 O2 sing N N 75 BNG C2 H2 sing N N 76 BNG C3 C4 sing N N 77 BNG C3 O3 sing N N 78 BNG C3 H3 sing N N 79 BNG C4 C5 sing N N 80 BNG C4 O4 sing N N 81 BNG C4 H4 sing N N 82 BNG C5 C6 sing N N 83 BNG C5 O5 sing N N 84 BNG C5 H5 sing N N 85 BNG C6 O6 sing N N 86 BNG C6 H61 sing N N 87 BNG C6 H62 sing N N 88 BNG "C1'" "C2'" sing N N 89 BNG "C1'" O1 sing N N 90 BNG "C1'" "H1'1" sing N N 91 BNG "C1'" "H1'2" sing N N 92 BNG "C2'" "C3'" sing N N 93 BNG "C2'" "H2'1" sing N N 94 BNG "C2'" "H2'2" sing N N 95 BNG "C3'" "C4'" sing N N 96 BNG "C3'" "H3'1" sing N N 97 BNG "C3'" "H3'2" sing N N 98 BNG "C4'" "C5'" sing N N 99 BNG "C4'" "H4'1" sing N N 100 BNG "C4'" "H4'2" sing N N 101 BNG "C5'" "C6'" sing N N 102 BNG "C5'" "H5'1" sing N N 103 BNG "C5'" "H5'2" sing N N 104 BNG "C6'" "C7'" sing N N 105 BNG "C6'" "H6'1" sing N N 106 BNG "C6'" "H6'2" sing N N 107 BNG "C7'" "C8'" sing N N 108 BNG "C7'" "H7'1" sing N N 109 BNG "C7'" "H7'2" sing N N 110 BNG "C8'" "C9'" sing N N 111 BNG "C8'" "H8'1" sing N N 112 BNG "C8'" "H8'2" sing N N 113 BNG "C9'" "H9'1" sing N N 114 BNG "C9'" "H9'2" sing N N 115 BNG "C9'" "H9'3" sing N N 116 BNG O2 HO2 sing N N 117 BNG O3 HO3 sing N N 118 BNG O4 HO4 sing N N 119 BNG O6 HO6 sing N N 120 CYS N CA sing N N 121 CYS N H sing N N 122 CYS N H2 sing N N 123 CYS CA C sing N N 124 CYS CA CB sing N N 125 CYS CA HA sing N N 126 CYS C O doub N N 127 CYS C OXT sing N N 128 CYS CB SG sing N N 129 CYS CB HB2 sing N N 130 CYS CB HB3 sing N N 131 CYS SG HG sing N N 132 CYS OXT HXT sing N N 133 GLN N CA sing N N 134 GLN N H sing N N 135 GLN N H2 sing N N 136 GLN CA C sing N N 137 GLN CA CB sing N N 138 GLN CA HA sing N N 139 GLN C O doub N N 140 GLN C OXT sing N N 141 GLN CB CG sing N N 142 GLN CB HB2 sing N N 143 GLN CB HB3 sing N N 144 GLN CG CD sing N N 145 GLN CG HG2 sing N N 146 GLN CG HG3 sing N N 147 GLN CD OE1 doub N N 148 GLN CD NE2 sing N N 149 GLN NE2 HE21 sing N N 150 GLN NE2 HE22 sing N N 151 GLN OXT HXT sing N N 152 GLU N CA sing N N 153 GLU N H sing N N 154 GLU N H2 sing N N 155 GLU CA C sing N N 156 GLU CA CB sing N N 157 GLU CA HA sing N N 158 GLU C O doub N N 159 GLU C OXT sing N N 160 GLU CB CG sing N N 161 GLU CB HB2 sing N N 162 GLU CB HB3 sing N N 163 GLU CG CD sing N N 164 GLU CG HG2 sing N N 165 GLU CG HG3 sing N N 166 GLU CD OE1 doub N N 167 GLU CD OE2 sing N N 168 GLU OE2 HE2 sing N N 169 GLU OXT HXT sing N N 170 GLY N CA sing N N 171 GLY N H sing N N 172 GLY N H2 sing N N 173 GLY CA C sing N N 174 GLY CA HA2 sing N N 175 GLY CA HA3 sing N N 176 GLY C O doub N N 177 GLY C OXT sing N N 178 GLY OXT HXT sing N N 179 HIS N CA sing N N 180 HIS N H sing N N 181 HIS N H2 sing N N 182 HIS CA C sing N N 183 HIS CA CB sing N N 184 HIS CA HA sing N N 185 HIS C O doub N N 186 HIS C OXT sing N N 187 HIS CB CG sing N N 188 HIS CB HB2 sing N N 189 HIS CB HB3 sing N N 190 HIS CG ND1 sing Y N 191 HIS CG CD2 doub Y N 192 HIS ND1 CE1 doub Y N 193 HIS ND1 HD1 sing N N 194 HIS CD2 NE2 sing Y N 195 HIS CD2 HD2 sing N N 196 HIS CE1 NE2 sing Y N 197 HIS CE1 HE1 sing N N 198 HIS NE2 HE2 sing N N 199 HIS OXT HXT sing N N 200 HOH O H1 sing N N 201 HOH O H2 sing N N 202 ILE N CA sing N N 203 ILE N H sing N N 204 ILE N H2 sing N N 205 ILE CA C sing N N 206 ILE CA CB sing N N 207 ILE CA HA sing N N 208 ILE C O doub N N 209 ILE C OXT sing N N 210 ILE CB CG1 sing N N 211 ILE CB CG2 sing N N 212 ILE CB HB sing N N 213 ILE CG1 CD1 sing N N 214 ILE CG1 HG12 sing N N 215 ILE CG1 HG13 sing N N 216 ILE CG2 HG21 sing N N 217 ILE CG2 HG22 sing N N 218 ILE CG2 HG23 sing N N 219 ILE CD1 HD11 sing N N 220 ILE CD1 HD12 sing N N 221 ILE CD1 HD13 sing N N 222 ILE OXT HXT sing N N 223 LEU N CA sing N N 224 LEU N H sing N N 225 LEU N H2 sing N N 226 LEU CA C sing N N 227 LEU CA CB sing N N 228 LEU CA HA sing N N 229 LEU C O doub N N 230 LEU C OXT sing N N 231 LEU CB CG sing N N 232 LEU CB HB2 sing N N 233 LEU CB HB3 sing N N 234 LEU CG CD1 sing N N 235 LEU CG CD2 sing N N 236 LEU CG HG sing N N 237 LEU CD1 HD11 sing N N 238 LEU CD1 HD12 sing N N 239 LEU CD1 HD13 sing N N 240 LEU CD2 HD21 sing N N 241 LEU CD2 HD22 sing N N 242 LEU CD2 HD23 sing N N 243 LEU OXT HXT sing N N 244 LYS N CA sing N N 245 LYS N H sing N N 246 LYS N H2 sing N N 247 LYS CA C sing N N 248 LYS CA CB sing N N 249 LYS CA HA sing N N 250 LYS C O doub N N 251 LYS C OXT sing N N 252 LYS CB CG sing N N 253 LYS CB HB2 sing N N 254 LYS CB HB3 sing N N 255 LYS CG CD sing N N 256 LYS CG HG2 sing N N 257 LYS CG HG3 sing N N 258 LYS CD CE sing N N 259 LYS CD HD2 sing N N 260 LYS CD HD3 sing N N 261 LYS CE NZ sing N N 262 LYS CE HE2 sing N N 263 LYS CE HE3 sing N N 264 LYS NZ HZ1 sing N N 265 LYS NZ HZ2 sing N N 266 LYS NZ HZ3 sing N N 267 LYS OXT HXT sing N N 268 MET N CA sing N N 269 MET N H sing N N 270 MET N H2 sing N N 271 MET CA C sing N N 272 MET CA CB sing N N 273 MET CA HA sing N N 274 MET C O doub N N 275 MET C OXT sing N N 276 MET CB CG sing N N 277 MET CB HB2 sing N N 278 MET CB HB3 sing N N 279 MET CG SD sing N N 280 MET CG HG2 sing N N 281 MET CG HG3 sing N N 282 MET SD CE sing N N 283 MET CE HE1 sing N N 284 MET CE HE2 sing N N 285 MET CE HE3 sing N N 286 MET OXT HXT sing N N 287 PHE N CA sing N N 288 PHE N H sing N N 289 PHE N H2 sing N N 290 PHE CA C sing N N 291 PHE CA CB sing N N 292 PHE CA HA sing N N 293 PHE C O doub N N 294 PHE C OXT sing N N 295 PHE CB CG sing N N 296 PHE CB HB2 sing N N 297 PHE CB HB3 sing N N 298 PHE CG CD1 doub Y N 299 PHE CG CD2 sing Y N 300 PHE CD1 CE1 sing Y N 301 PHE CD1 HD1 sing N N 302 PHE CD2 CE2 doub Y N 303 PHE CD2 HD2 sing N N 304 PHE CE1 CZ doub Y N 305 PHE CE1 HE1 sing N N 306 PHE CE2 CZ sing Y N 307 PHE CE2 HE2 sing N N 308 PHE CZ HZ sing N N 309 PHE OXT HXT sing N N 310 PRO N CA sing N N 311 PRO N CD sing N N 312 PRO N H sing N N 313 PRO CA C sing N N 314 PRO CA CB sing N N 315 PRO CA HA sing N N 316 PRO C O doub N N 317 PRO C OXT sing N N 318 PRO CB CG sing N N 319 PRO CB HB2 sing N N 320 PRO CB HB3 sing N N 321 PRO CG CD sing N N 322 PRO CG HG2 sing N N 323 PRO CG HG3 sing N N 324 PRO CD HD2 sing N N 325 PRO CD HD3 sing N N 326 PRO OXT HXT sing N N 327 SER N CA sing N N 328 SER N H sing N N 329 SER N H2 sing N N 330 SER CA C sing N N 331 SER CA CB sing N N 332 SER CA HA sing N N 333 SER C O doub N N 334 SER C OXT sing N N 335 SER CB OG sing N N 336 SER CB HB2 sing N N 337 SER CB HB3 sing N N 338 SER OG HG sing N N 339 SER OXT HXT sing N N 340 SV1 O1 C8 doub N N 341 SV1 C8 C7 sing N N 342 SV1 C8 O2 sing N N 343 SV1 C7 C6 sing N N 344 SV1 C6 C5 sing Y N 345 SV1 C6 C1 doub Y N 346 SV1 C5 C4 doub Y N 347 SV1 C4 C3 sing Y N 348 SV1 C3 N sing N N 349 SV1 C3 C2 doub Y N 350 SV1 C2 C1 sing Y N 351 SV1 C1 C sing N N 352 SV1 C O doub N N 353 SV1 O2 C9 sing N N 354 SV1 C9 C10 sing N N 355 SV1 C10 C11 sing N N 356 SV1 C11 C16 sing Y N 357 SV1 C11 C12 doub Y N 358 SV1 C16 C15 doub Y N 359 SV1 C15 C14 sing Y N 360 SV1 C14 C13 doub Y N 361 SV1 C13 C12 sing Y N 362 SV1 C H sing N N 363 SV1 C7 H71 sing N N 364 SV1 C7 H72 sing N N 365 SV1 C5 H5 sing N N 366 SV1 C4 H4 sing N N 367 SV1 N HN1 sing N N 368 SV1 N HN2 sing N N 369 SV1 C2 H2 sing N N 370 SV1 C9 H91C sing N N 371 SV1 C9 H92C sing N N 372 SV1 C10 H101 sing N N 373 SV1 C10 H102 sing N N 374 SV1 C16 H16 sing N N 375 SV1 C12 H12 sing N N 376 SV1 C15 H15 sing N N 377 SV1 C14 H14 sing N N 378 SV1 C13 H13 sing N N 379 THR N CA sing N N 380 THR N H sing N N 381 THR N H2 sing N N 382 THR CA C sing N N 383 THR CA CB sing N N 384 THR CA HA sing N N 385 THR C O doub N N 386 THR C OXT sing N N 387 THR CB OG1 sing N N 388 THR CB CG2 sing N N 389 THR CB HB sing N N 390 THR OG1 HG1 sing N N 391 THR CG2 HG21 sing N N 392 THR CG2 HG22 sing N N 393 THR CG2 HG23 sing N N 394 THR OXT HXT sing N N 395 TRP N CA sing N N 396 TRP N H sing N N 397 TRP N H2 sing N N 398 TRP CA C sing N N 399 TRP CA CB sing N N 400 TRP CA HA sing N N 401 TRP C O doub N N 402 TRP C OXT sing N N 403 TRP CB CG sing N N 404 TRP CB HB2 sing N N 405 TRP CB HB3 sing N N 406 TRP CG CD1 doub Y N 407 TRP CG CD2 sing Y N 408 TRP CD1 NE1 sing Y N 409 TRP CD1 HD1 sing N N 410 TRP CD2 CE2 doub Y N 411 TRP CD2 CE3 sing Y N 412 TRP NE1 CE2 sing Y N 413 TRP NE1 HE1 sing N N 414 TRP CE2 CZ2 sing Y N 415 TRP CE3 CZ3 doub Y N 416 TRP CE3 HE3 sing N N 417 TRP CZ2 CH2 doub Y N 418 TRP CZ2 HZ2 sing N N 419 TRP CZ3 CH2 sing Y N 420 TRP CZ3 HZ3 sing N N 421 TRP CH2 HH2 sing N N 422 TRP OXT HXT sing N N 423 TYR N CA sing N N 424 TYR N H sing N N 425 TYR N H2 sing N N 426 TYR CA C sing N N 427 TYR CA CB sing N N 428 TYR CA HA sing N N 429 TYR C O doub N N 430 TYR C OXT sing N N 431 TYR CB CG sing N N 432 TYR CB HB2 sing N N 433 TYR CB HB3 sing N N 434 TYR CG CD1 doub Y N 435 TYR CG CD2 sing Y N 436 TYR CD1 CE1 sing Y N 437 TYR CD1 HD1 sing N N 438 TYR CD2 CE2 doub Y N 439 TYR CD2 HD2 sing N N 440 TYR CE1 CZ doub Y N 441 TYR CE1 HE1 sing N N 442 TYR CE2 CZ sing Y N 443 TYR CE2 HE2 sing N N 444 TYR CZ OH sing N N 445 TYR OH HH sing N N 446 TYR OXT HXT sing N N 447 VAL N CA sing N N 448 VAL N H sing N N 449 VAL N H2 sing N N 450 VAL CA C sing N N 451 VAL CA CB sing N N 452 VAL CA HA sing N N 453 VAL C O doub N N 454 VAL C OXT sing N N 455 VAL CB CG1 sing N N 456 VAL CB CG2 sing N N 457 VAL CB HB sing N N 458 VAL CG1 HG11 sing N N 459 VAL CG1 HG12 sing N N 460 VAL CG1 HG13 sing N N 461 VAL CG2 HG21 sing N N 462 VAL CG2 HG22 sing N N 463 VAL CG2 HG23 sing N N 464 VAL OXT HXT sing N N 465 # _pdbx_chem_comp_identifier.comp_id BNG _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1.0 _pdbx_chem_comp_identifier.identifier b-nonylglucoside # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '2-phenylethyl 2-(4-azanyl-2-methanoyl-phenyl)ethanoate' SV1 3 'CHLORIDE ION' CL 4 'nonyl beta-D-glucopyranoside' BNG 5 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 2XOV _pdbx_initial_refinement_model.details 'PDB ENTRY 2XOV' #