data_3VR9 # _model_server_result.job_id aVsWYsTUE64m_DWkIQob6A _model_server_result.datetime_utc '2024-11-28 09:30:04' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3vr9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":201}' # _entry.id 3VR9 # _exptl.entry_id 3VR9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 709.933 _entity.id 12 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 3VR9 _cell.length_a 124.011 _cell.length_b 135.333 _cell.length_c 220.498 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VR9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,I,J,K,L,M,N,O,P 1 1 E,F,G,H,Q,R,S,T,U,V,W,X 2 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 12 P N N ? 12 X N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A NE2 HIS 79 A HIS 79 1_555 J C8M FAD . A FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.668 ? covale ? covale2 E NE2 HIS 79 E HIS 79 1_555 R C8M FAD . E FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc6 B SG CYS 185 B CYS 185 1_555 L FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc7 B SG CYS 188 B CYS 188 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc8 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc9 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc10 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc11 B SG CYS 249 B CYS 249 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc12 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc13 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc14 F SG CYS 89 F CYS 89 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc15 F SG CYS 94 F CYS 94 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc16 F SG CYS 97 F CYS 97 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc17 F SG CYS 109 F CYS 109 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc18 F SG CYS 182 F CYS 182 1_555 T FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc19 F SG CYS 185 F CYS 185 1_555 T FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc20 F SG CYS 188 F CYS 188 1_555 T FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc21 F SG CYS 192 F CYS 192 1_555 U FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc22 F SG CYS 239 F CYS 239 1_555 U FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc23 F SG CYS 245 F CYS 245 1_555 U FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc24 F SG CYS 249 F CYS 249 1_555 T FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc25 G NE2 HIS 131 G HIS 131 1_555 W FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc26 W FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? # _chem_comp.formula 'C39 H68 N O8 P' _chem_comp.formula_weight 709.933 _chem_comp.id EPH _chem_comp.mon_nstd_flag . _chem_comp.name L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 C2 EPH sing 83 n n C1 O2 EPH sing 84 n n C1 H11 EPH sing 85 n n C1 H12A EPH sing 86 n n C2 C37 EPH sing 87 n n C2 O1 EPH sing 88 n n C2 H2 EPH sing 89 n n C4 O2 EPH sing 90 n n C4 O4 EPH doub 91 n n C4 C18 EPH sing 92 n n C18 C19 EPH sing 93 n n C18 H181 EPH sing 94 n n C18 H182 EPH sing 95 n n C19 C20 EPH sing 96 n n C19 H191 EPH sing 97 n n C19 H192 EPH sing 98 n n C20 C21 EPH sing 99 n n C20 H201 EPH sing 100 n n C20 H202 EPH sing 101 n n C21 C22 EPH sing 102 n n C21 H211 EPH sing 103 n n C21 H212 EPH sing 104 n n C22 C23 EPH sing 105 n n C22 H221 EPH sing 106 n n C22 H222 EPH sing 107 n n C23 C24 EPH sing 108 n n C23 H231 EPH sing 109 n n C23 H232 EPH sing 110 n n C24 C25 EPH doub 111 e n C24 H24 EPH sing 112 n n C25 C26 EPH sing 113 n n C25 H25 EPH sing 114 n n C26 C27 EPH sing 115 n n C26 H261 EPH sing 116 n n C26 H262 EPH sing 117 n n C27 C28 EPH sing 118 n n C27 H271 EPH sing 119 n n C27 H272 EPH sing 120 n n C28 C29 EPH doub 121 e n C28 H28 EPH sing 122 n n C29 C30 EPH sing 123 n n C29 H29 EPH sing 124 n n C30 C31 EPH sing 125 n n C30 H301 EPH sing 126 n n C30 H302 EPH sing 127 n n C31 C32 EPH sing 128 n n C31 H311 EPH sing 129 n n C31 H312 EPH sing 130 n n C32 C33 EPH doub 131 e n C32 H32 EPH sing 132 n n C33 C34 EPH sing 133 n n C33 H33 EPH sing 134 n n C34 H341 EPH sing 135 n n C34 H342 EPH sing 136 n n C34 H343 EPH sing 137 n n C37 O5 EPH sing 138 n n C37 H371 EPH sing 139 n n C37 H372 EPH sing 140 n n O5 P1 EPH sing 141 n n C3 O1 EPH sing 142 n n C3 O3 EPH doub 143 n n C3 C5 EPH sing 144 n n C5 C6 EPH sing 145 n n C5 H51 EPH sing 146 n n C5 H52 EPH sing 147 n n C6 C7 EPH sing 148 n n C6 H61 EPH sing 149 n n C6 H62 EPH sing 150 n n C7 C8 EPH sing 151 n n C7 H71 EPH sing 152 n n C7 H72 EPH sing 153 n n C8 C9 EPH sing 154 n n C8 H81 EPH sing 155 n n C8 H82 EPH sing 156 n n C9 C10 EPH sing 157 n n C9 H91 EPH sing 158 n n C9 H92 EPH sing 159 n n C10 C11 EPH sing 160 n n C10 H101 EPH sing 161 n n C10 H102 EPH sing 162 n n C11 C12 EPH sing 163 n n C11 H111 EPH sing 164 n n C11 H112 EPH sing 165 n n C12 C13 EPH doub 166 e n C12 H12 EPH sing 167 n n C13 C14 EPH sing 168 n n C13 H13 EPH sing 169 n n C14 C15 EPH sing 170 n n C14 H141 EPH sing 171 n n C14 H142 EPH sing 172 n n C15 C16 EPH doub 173 e n C15 H15 EPH sing 174 n n C16 C17 EPH sing 175 n n C16 H16 EPH sing 176 n n C17 C35 EPH sing 177 n n C17 H171 EPH sing 178 n n C17 H172 EPH sing 179 n n C35 C36 EPH sing 180 n n C35 H351 EPH sing 181 n n C35 H352 EPH sing 182 n n C36 H361 EPH sing 183 n n C36 H362 EPH sing 184 n n C36 H363 EPH sing 185 n n P1 O6 EPH sing 186 n n P1 O7 EPH doub 187 n n P1 O8 EPH sing 188 n n O6 HO6 EPH sing 189 n n O8 C38 EPH sing 190 n n C38 C39 EPH sing 191 n n C38 H381 EPH sing 192 n n C38 H382 EPH sing 193 n n C39 N1 EPH sing 194 n n C39 H391 EPH sing 195 n n C39 H392 EPH sing 196 n n N1 HN11 EPH sing 197 n n N1 HN12 EPH sing 198 n n # _atom_sites.entry_id 3VR9 _atom_sites.fract_transf_matrix[1][1] 0.008064 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007389 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.004535 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code I 5 MLI A 1 701 300 MLI MLI . J 6 FAD A 1 702 301 FAD FAD . K 7 FES B 1 301 302 FES FES . L 8 SF4 B 1 302 303 SF4 FS4 . M 9 F3S B 1 303 304 F3S F3S . N 10 HEM C 1 201 305 HEM HEM . O 11 FTN C 1 202 810 FTN FTN . P 12 EPH D 1 201 306 EPH EPH . Q 5 MLI E 1 701 300 MLI MLI . R 6 FAD E 1 702 301 FAD FAD . S 7 FES F 1 301 302 FES FES . T 8 SF4 F 1 302 303 SF4 FS4 . U 9 F3S F 1 303 304 F3S F3S . V 11 FTN F 1 304 810 FTN FTN . W 10 HEM G 1 201 305 HEM HEM . X 12 EPH H 1 201 306 EPH EPH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 EPH . . . X 12 -117.895 -8.51 59.417 1 119.69 ? C1 EPH 201 H 1 HETATM 2 C C2 EPH . . . X 12 -118.949 -8.999 60.402 1 121.62 ? C2 EPH 201 H 1 HETATM 3 C C4 EPH . . . X 12 -115.515 -9.367 59.083 1 114.25 ? C4 EPH 201 H 1 HETATM 4 O O2 EPH . . . X 12 -116.88 -9.548 59.231 1 117.54 ? O2 EPH 201 H 1 HETATM 5 O O4 EPH . . . X 12 -114.896 -8.62 59.807 1 114.03 ? O4 EPH 201 H 1 HETATM 6 C C18 EPH . . . X 12 -114.917 -10.127 58.075 1 111.36 ? C18 EPH 201 H 1 HETATM 7 C C19 EPH . . . X 12 -113.397 -10.07 57.746 1 106.83 ? C19 EPH 201 H 1 HETATM 8 C C20 EPH . . . X 12 -112.622 -11.369 57.937 1 103.3 ? C20 EPH 201 H 1 HETATM 9 C C21 EPH . . . X 12 -112.707 -12.416 56.833 1 99.35 ? C21 EPH 201 H 1 HETATM 10 C C22 EPH . . . X 12 -111.994 -13.72 57.226 1 96.45 ? C22 EPH 201 H 1 HETATM 11 C C23 EPH . . . X 12 -112.844 -15.004 57.345 1 95.39 ? C23 EPH 201 H 1 HETATM 12 C C24 EPH . . . X 12 -112.305 -15.951 58.378 1 95.63 ? C24 EPH 201 H 1 HETATM 13 C C25 EPH . . . X 12 -113.222 -17.064 58.91 1 95.71 ? C25 EPH 201 H 1 HETATM 14 C C26 EPH . . . X 12 -112.543 -17.776 60.244 1 96.85 ? C26 EPH 201 H 1 HETATM 15 C C27 EPH . . . X 12 -112.745 -18.772 61.408 1 97.34 ? C27 EPH 201 H 1 HETATM 16 C C28 EPH . . . X 12 -111.705 -19.528 61.765 1 96.64 ? C28 EPH 201 H 1 HETATM 17 C C29 EPH . . . X 12 -111.846 -20.66 63.037 1 95.46 ? C29 EPH 201 H 1 HETATM 18 C C30 EPH . . . X 12 -110.648 -20.619 63.977 1 95.31 ? C30 EPH 201 H 1 HETATM 19 C C31 EPH . . . X 12 -110.075 -21.985 64.3 1 95.1 ? C31 EPH 201 H 1 HETATM 20 C C37 EPH . . . X 12 -120.108 -8.002 60.495 1 125.06 ? C37 EPH 201 H 1 HETATM 21 O O5 EPH . . . X 12 -121.107 -8.358 61.5 1 129.2 ? O5 EPH 201 H 1 HETATM 22 C C3 EPH . . . X 12 -118.426 -10.242 62.543 1 117.75 ? C3 EPH 201 H 1 HETATM 23 O O1 EPH . . . X 12 -118.29 -9.169 61.707 1 120.36 ? O1 EPH 201 H 1 HETATM 24 O O3 EPH . . . X 12 -119.46 -10.578 63.073 1 117.81 ? O3 EPH 201 H 1 HETATM 25 C C5 EPH . . . X 12 -117.106 -11.012 62.763 1 114.87 ? C5 EPH 201 H 1 HETATM 26 C C6 EPH . . . X 12 -116.276 -10.207 63.813 1 112.24 ? C6 EPH 201 H 1 HETATM 27 C C7 EPH . . . X 12 -114.776 -10.185 63.531 1 109.86 ? C7 EPH 201 H 1 HETATM 28 C C8 EPH . . . X 12 -113.999 -9.12 64.3 1 108.11 ? C8 EPH 201 H 1 HETATM 29 C C9 EPH . . . X 12 -114.239 -7.694 63.747 1 106.87 ? C9 EPH 201 H 1 HETATM 30 C C10 EPH . . . X 12 -113.086 -6.985 63.008 1 105.55 ? C10 EPH 201 H 1 HETATM 31 C C11 EPH . . . X 12 -112.188 -6.351 63.927 1 104.48 ? C11 EPH 201 H 1 HETATM 32 C C12 EPH . . . X 12 -110.914 -5.56 63.452 1 103.03 ? C12 EPH 201 H 1 HETATM 33 C C13 EPH . . . X 12 -109.54 -5.913 64.031 1 100.13 ? C13 EPH 201 H 1 HETATM 34 C C14 EPH . . . X 12 -108.439 -4.942 63.61 1 98.56 ? C14 EPH 201 H 1 HETATM 35 C C15 EPH . . . X 12 -108.175 -3.46 63.5 1 98.31 ? C15 EPH 201 H 1 HETATM 36 C C16 EPH . . . X 12 -107.204 -2.314 63.205 1 96.8 ? C16 EPH 201 H 1 HETATM 37 C C17 EPH . . . X 12 -107.832 -1.139 62.719 1 96.74 ? C17 EPH 201 H 1 HETATM 38 P P1 EPH . . . X 12 -122.302 -7.342 62.028 1 131.82 ? P1 EPH 201 H 1 HETATM 39 O O6 EPH . . . X 12 -121.707 -6.253 62.972 1 131.97 ? O6 EPH 201 H 1 HETATM 40 O O7 EPH . . . X 12 -122.947 -6.643 60.716 1 130.7 ? O7 EPH 201 H 1 HETATM 41 O O8 EPH . . . X 12 -123.383 -8.264 62.794 1 131.42 ? O8 EPH 201 H 1 HETATM 42 C C38 EPH . . . X 12 -124.814 -8.338 62.464 1 130.85 ? C38 EPH 201 H 1 HETATM 43 C C39 EPH . . . X 12 -125.772 -8.347 63.649 1 130.16 ? C39 EPH 201 H 1 HETATM 44 N N1 EPH . . . X 12 -125.566 -9.694 64.175 1 130.08 ? N1 EPH 201 H 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 44 #