data_5NMI # _model_server_result.job_id W1bTOGib8lWl29x1ZJlRyg _model_server_result.datetime_utc '2024-11-23 12:16:41' _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 5nmi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"LA","auth_seq_id":405}' # _entry.id 5NMI # _exptl.entry_id 5NMI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 749.073 _entity.id 13 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine _entity.pdbx_number_of_molecules 6 _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 120 _cell.entry_id 5NMI _cell.length_a 129.477 _cell.length_b 129.477 _cell.length_c 720.294 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NMI _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 22-meric _pdbx_struct_assembly.oligomeric_count 22 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 13 Z N N ? 13 DA N N ? 13 GA N N ? 13 LA N N ? 13 PA N N ? 13 QA 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 disulf ? disulf1 E SG CYS 222 E CYS 144 1_555 E SG CYS 238 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 H SG CYS 37 H CYS 24 1_555 H SG CYS 81 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 H SG CYS 53 H CYS 40 1_555 H SG CYS 67 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 S SG CYS 37 U CYS 24 1_555 S SG CYS 81 U CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 S SG CYS 53 U CYS 40 1_555 S SG CYS 67 U CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 C NE2 HIS 76 C HIS 83 1_555 W FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc2 C NE2 HIS 90 C HIS 97 1_555 X FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? metalc ? metalc3 C NE2 HIS 175 C HIS 182 1_555 W FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? metalc ? metalc4 C NE2 HIS 189 C HIS 196 1_555 X FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? covale ? covale1 D SG CYS 36 D CYS 37 1_555 CA CAB HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.624 ? covale ? covale2 D SG CYS 39 D CYS 40 1_555 CA CAC HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.665 ? metalc ? metalc5 D NE2 HIS 40 D HIS 41 1_555 CA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? metalc ? metalc6 D SD MET 159 D MET 160 1_555 CA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc7 E SG CYS 217 E CYS 139 1_555 FA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc8 E ND1 HIS 219 E HIS 141 1_555 FA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? metalc ? metalc9 E SG CYS 236 E CYS 158 1_555 FA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc10 E ND1 HIS 239 E HIS 161 1_555 FA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.877 ? metalc ? metalc11 N NE2 HIS 76 P HIS 83 1_555 IA FE HEM . P HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? metalc ? metalc12 N NE2 HIS 90 P HIS 97 1_555 JA FE HEM . P HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? metalc ? metalc13 N NE2 HIS 175 P HIS 182 1_555 IA FE HEM . P HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.764 ? metalc ? metalc14 N NE2 HIS 189 P HIS 196 1_555 JA FE HEM . P HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? covale ? covale3 O SG CYS 36 Q CYS 37 1_555 OA CAB HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.626 ? covale ? covale4 O SG CYS 39 Q CYS 40 1_555 OA CAC HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.678 ? metalc ? metalc15 O NE2 HIS 40 Q HIS 41 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? metalc ? metalc16 O SD MET 159 Q MET 160 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? # _chem_comp.formula 'C41 H83 N O8 P 1' _chem_comp.formula_weight 749.073 _chem_comp.id PEE _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DOPE # _atom_sites.entry_id 5NMI _atom_sites.fract_transf_matrix[1][1] 0.007723 _atom_sites.fract_transf_matrix[1][2] 0.004459 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008918 _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] 0.001388 _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 W 11 HEM C 1 501 501 HEM HEM . X 11 HEM C 1 502 502 HEM HEM . Y 12 MJM C 1 503 503 MJM MJM . Z 13 PEE C 1 504 504 PEE PEE . AA 14 CDL C 1 505 505 CDL CDL . BA 14 CDL C 1 506 501 CDL CDL . CA 15 HEC D 1 501 501 HEC HEC . DA 13 PEE D 1 502 502 PEE PEE . EA 14 CDL D 1 503 503 CDL CDL . FA 16 FES E 1 501 501 FES FES . GA 13 PEE E 1 502 502 PEE PEE . HA 14 CDL P 1 401 503 CDL CDL . IA 11 HEM P 1 402 501 HEM HEM . JA 11 HEM P 1 403 502 HEM HEM . KA 12 MJM P 1 404 503 MJM MJM . LA 13 PEE P 1 405 504 PEE PEE . MA 14 CDL P 1 406 505 CDL CDL . NA 14 CDL P 1 407 501 CDL CDL . OA 15 HEC Q 1 501 501 HEC HEC . PA 13 PEE R 1 201 502 PEE PEE . QA 13 PEE R 1 202 502 PEE PEE . # 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 C2 PEE . . . LA 13 41.378 54.956 -29.65 1 52.82 ? C2 PEE 405 P 1 HETATM 2 C C1 PEE . . . LA 13 42.097 55.953 -28.727 1 53.16 ? C1 PEE 405 P 1 HETATM 3 N N PEE . . . LA 13 40.44 60.105 -25.392 1 62.03 ? N PEE 405 P 1 HETATM 4 C C3 PEE . . . LA 13 41.273 55.425 -31.125 1 57.78 ? C3 PEE 405 P 1 HETATM 5 C C4 PEE . . . LA 13 41.858 58.075 -25.503 1 54.46 ? C4 PEE 405 P 1 HETATM 6 C C5 PEE . . . LA 13 41.735 59.567 -25.852 1 57.86 ? C5 PEE 405 P 1 HETATM 7 C C10 PEE . . . LA 13 41.182 52.594 -28.912 1 47.19 ? C10 PEE 405 P 1 HETATM 8 C C11 PEE . . . LA 13 41.975 51.283 -28.66 1 44.88 ? C11 PEE 405 P 1 HETATM 9 C C12 PEE . . . LA 13 41.102 50.025 -28.519 1 45.23 ? C12 PEE 405 P 1 HETATM 10 C C13 PEE . . . LA 13 41.706 48.827 -29.258 1 42.49 ? C13 PEE 405 P 1 HETATM 11 C C14 PEE . . . LA 13 40.756 47.624 -29.396 1 41.98 ? C14 PEE 405 P 1 HETATM 12 C C15 PEE . . . LA 13 40.332 47.306 -30.844 1 43.01 ? C15 PEE 405 P 1 HETATM 13 C C16 PEE . . . LA 13 40.415 45.814 -31.209 1 47.26 ? C16 PEE 405 P 1 HETATM 14 C C17 PEE . . . LA 13 39.931 45.474 -32.634 1 51.52 ? C17 PEE 405 P 1 HETATM 15 C C18 PEE . . . LA 13 40.183 44.019 -32.987 1 56.25 ? C18 PEE 405 P 1 HETATM 16 C C19 PEE . . . LA 13 41.361 43.414 -33.203 1 57.03 ? C19 PEE 405 P 1 HETATM 17 C C20 PEE . . . LA 13 41.665 41.933 -33.145 1 57.62 ? C20 PEE 405 P 1 HETATM 18 C C21 PEE . . . LA 13 42.74 41.566 -32.134 1 56.61 ? C21 PEE 405 P 1 HETATM 19 C C22 PEE . . . LA 13 43.965 41.08 -32.408 1 62.1 ? C22 PEE 405 P 1 HETATM 20 C C23 PEE . . . LA 13 44.46 39.642 -32.242 1 65.6 ? C23 PEE 405 P 1 HETATM 21 C C30 PEE . . . LA 13 39.179 54.437 -31.898 1 66.54 ? C30 PEE 405 P 1 HETATM 22 C C31 PEE . . . LA 13 38.525 53.623 -33.042 1 69.37 ? C31 PEE 405 P 1 HETATM 23 C C32 PEE . . . LA 13 37.958 52.257 -32.603 1 72.25 ? C32 PEE 405 P 1 HETATM 24 C C33 PEE . . . LA 13 37.802 51.288 -33.788 1 75.55 ? C33 PEE 405 P 1 HETATM 25 C C34 PEE . . . LA 13 37.083 49.985 -33.39 1 78.69 ? C34 PEE 405 P 1 HETATM 26 C C35 PEE . . . LA 13 36.605 49.196 -34.621 1 81.44 ? C35 PEE 405 P 1 HETATM 27 C C36 PEE . . . LA 13 37.572 48.059 -35.001 1 81.44 ? C36 PEE 405 P 1 HETATM 28 C C37 PEE . . . LA 13 36.905 47.009 -35.913 1 81.03 ? C37 PEE 405 P 1 HETATM 29 C C38 PEE . . . LA 13 37.832 46.56 -37.062 1 80.31 ? C38 PEE 405 P 1 HETATM 30 O O4 PEE . . . LA 13 39.982 52.713 -28.575 1 49.09 ? O4 PEE 405 P 1 HETATM 31 O O5 PEE . . . LA 13 38.501 55.016 -31.02 1 67.88 ? O5 PEE 405 P 1 HETATM 32 O O2 PEE . . . LA 13 41.965 53.6 -29.54 1 50.26 ? O2 PEE 405 P 1 HETATM 33 O O3 PEE . . . LA 13 40.593 54.433 -31.966 1 63.34 ? O3 PEE 405 P 1 HETATM 34 O O1P PEE . . . LA 13 43.235 54.997 -25.032 1 55.94 ? O1P PEE 405 P 1 HETATM 35 O O2P PEE . . . LA 13 44.723 55.688 -27.061 1 55.27 ? O2P PEE 405 P 1 HETATM 36 O O3P PEE . . . LA 13 42.114 55.506 -27.344 1 54.15 ? O3P PEE 405 P 1 HETATM 37 O O4P PEE . . . LA 13 43.149 57.489 -25.888 1 53.31 ? O4P PEE 405 P 1 HETATM 38 P P PEE . . . LA 13 43.314 55.923 -26.346 1 50.49 ? P PEE 405 P 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #