data_6IRT # _model_server_result.job_id XlvSiR7LOt4CfERWAXXtmA _model_server_result.datetime_utc '2024-12-24 01:01:04' _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 6irt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":601}' # _entry.id 6IRT # _exptl.entry_id 6IRT _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 704.998 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE _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 6IRT _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IRT _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 ? _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 ? 4 G N N ? 4 H N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 C 1 NAG A 632 NAG 3 n C NAG 2 C 2 NAG A 633 NAG 3 n D NAG 1 D 1 NAG A 634 NAG 3 n D NAG 2 D 2 NAG A 635 NAG 3 n E NAG 1 E 1 NAG A 636 NAG 3 n E NAG 2 E 2 NAG A 637 NAG 3 n F NAG 1 F 1 NAG A 638 NAG 3 n F NAG 2 F 2 NAG A 639 NAG # 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 A SG CYS 225 A CYS 211 1_555 B SG CYS 184 B CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A ND2 ASN 380 A ASN 366 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.506 ? covale ? covale2 A ND2 ASN 396 A ASN 382 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 ? covale ? covale3 A ND2 ASN 439 A ASN 425 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.524 ? covale ? covale4 A ND2 ASN 521 A ASN 507 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _chem_comp.formula 'C39 H77 O8 P' _chem_comp.formula_weight 704.998 _chem_comp.id 3PH _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'PHOSPHATIDIC ACID' # 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 O13 P 3PH sing 1 n n O13 H13 3PH sing 2 n n P O14 3PH sing 3 n n P O12 3PH doub 4 n n P O11 3PH sing 5 n n O11 C1 3PH sing 6 n n C1 C2 3PH sing 7 n n C1 H11 3PH sing 8 n n C1 H12 3PH sing 9 n n C2 O21 3PH sing 10 n n C2 C3 3PH sing 11 n n C2 H2 3PH sing 12 n n O21 C21 3PH sing 13 n n C21 O22 3PH doub 14 n n C21 C22 3PH sing 15 n n C22 C23 3PH sing 16 n n C22 H221 3PH sing 17 n n C22 H222 3PH sing 18 n n C23 C24 3PH sing 19 n n C23 H231 3PH sing 20 n n C23 H232 3PH sing 21 n n C24 C25 3PH sing 22 n n C24 H241 3PH sing 23 n n C24 H242 3PH sing 24 n n C25 C26 3PH sing 25 n n C25 H251 3PH sing 26 n n C25 H252 3PH sing 27 n n C26 C27 3PH sing 28 n n C26 H261 3PH sing 29 n n C26 H262 3PH sing 30 n n C27 C28 3PH sing 31 n n C27 H271 3PH sing 32 n n C27 H272 3PH sing 33 n n C28 C29 3PH sing 34 n n C28 H281 3PH sing 35 n n C28 H282 3PH sing 36 n n C29 C2A 3PH sing 37 n n C29 H291 3PH sing 38 n n C29 H292 3PH sing 39 n n C2A C2B 3PH sing 40 n n C2A H2A1 3PH sing 41 n n C2A H2A2 3PH sing 42 n n C2B C2C 3PH sing 43 n n C2B H2B1 3PH sing 44 n n C2B H2B2 3PH sing 45 n n C2C C2D 3PH sing 46 n n C2C H2C1 3PH sing 47 n n C2C H2C2 3PH sing 48 n n C2D C2E 3PH sing 49 n n C2D H2D1 3PH sing 50 n n C2D H2D2 3PH sing 51 n n C2E C2F 3PH sing 52 n n C2E H2E1 3PH sing 53 n n C2E H2E2 3PH sing 54 n n C2F C2G 3PH sing 55 n n C2F H2F1 3PH sing 56 n n C2F H2F2 3PH sing 57 n n C2G C2H 3PH sing 58 n n C2G H2G1 3PH sing 59 n n C2G H2G2 3PH sing 60 n n C2H C2I 3PH sing 61 n n C2H H2H1 3PH sing 62 n n C2H H2H2 3PH sing 63 n n C2I H2I1 3PH sing 64 n n C2I H2I2 3PH sing 65 n n C2I H2I3 3PH sing 66 n n C3 O31 3PH sing 67 n n C3 H31 3PH sing 68 n n C3 H32 3PH sing 69 n n O31 C31 3PH sing 70 n n C31 O32 3PH doub 71 n n C31 C32 3PH sing 72 n n C32 C33 3PH sing 73 n n C32 H321 3PH sing 74 n n C32 H322 3PH sing 75 n n C33 C34 3PH sing 76 n n C33 H331 3PH sing 77 n n C33 H332 3PH sing 78 n n C34 C35 3PH sing 79 n n C34 H341 3PH sing 80 n n C34 H342 3PH sing 81 n n C35 C36 3PH sing 82 n n C35 H351 3PH sing 83 n n C35 H352 3PH sing 84 n n C36 C37 3PH sing 85 n n C36 H361 3PH sing 86 n n C36 H362 3PH sing 87 n n C37 C38 3PH sing 88 n n C37 H371 3PH sing 89 n n C37 H372 3PH sing 90 n n C38 C39 3PH sing 91 n n C38 H381 3PH sing 92 n n C38 H382 3PH sing 93 n n C39 C3A 3PH sing 94 n n C39 H391 3PH sing 95 n n C39 H392 3PH sing 96 n n C3A C3B 3PH sing 97 n n C3A H3A1 3PH sing 98 n n C3A H3A2 3PH sing 99 n n C3B C3C 3PH sing 100 n n C3B H3B1 3PH sing 101 n n C3B H3B2 3PH sing 102 n n C3C C3D 3PH sing 103 n n C3C H3C1 3PH sing 104 n n C3C H3C2 3PH sing 105 n n C3D C3E 3PH sing 106 n n C3D H3D1 3PH sing 107 n n C3D H3D2 3PH sing 108 n n C3E C3F 3PH sing 109 n n C3E H3E1 3PH sing 110 n n C3E H3E2 3PH sing 111 n n C3F C3G 3PH sing 112 n n C3F H3F1 3PH sing 113 n n C3F H3F2 3PH sing 114 n n C3G C3H 3PH sing 115 n n C3G H3G1 3PH sing 116 n n C3G H3G2 3PH sing 117 n n C3H C3I 3PH sing 118 n n C3H H3H1 3PH sing 119 n n C3H H3H2 3PH sing 120 n n C3I H3I1 3PH sing 121 n n C3I H3I2 3PH sing 122 n n C3I H3I3 3PH sing 123 n n O14 H77 3PH sing 124 n n # _atom_sites.entry_id 6IRT _atom_sites.fract_transf_matrix[1][1] 0.00358 _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] 0.00358 _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] 0.00358 _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 G 4 3PH B 1 601 1 3PH 3PH . H 4 3PH B 1 602 2 3PH 3PH . I 5 AUU B 1 603 1 AUU LIG . # 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 O O13 3PH . . . G 4 120.221 149.592 116.382 1 75.09 ? O13 3PH 601 B 1 HETATM 2 P P 3PH . . . G 4 121.575 149.257 115.804 1 75.09 ? P 3PH 601 B 1 HETATM 3 O O14 3PH . . . G 4 122.069 150.236 114.766 1 75.09 ? O14 3PH 601 B 1 HETATM 4 O O12 3PH . . . G 4 121.749 147.806 115.425 1 75.09 ? O12 3PH 601 B 1 HETATM 5 O O11 3PH . . . G 4 122.586 149.46 117.042 1 75.09 ? O11 3PH 601 B 1 HETATM 6 C C1 3PH . . . G 4 123.684 148.571 117.233 1 75.09 ? C1 3PH 601 B 1 HETATM 7 C C2 3PH . . . G 4 123.724 148.116 118.688 1 75.09 ? C2 3PH 601 B 1 HETATM 8 O O21 3PH . . . G 4 122.411 147.759 119.112 1 75.09 ? O21 3PH 601 B 1 HETATM 9 C C21 3PH . . . G 4 122.191 146.325 119.028 1 75.09 ? C21 3PH 601 B 1 HETATM 10 O O22 3PH . . . G 4 122.708 145.697 118.119 1 75.09 ? O22 3PH 601 B 1 HETATM 11 C C22 3PH . . . G 4 121.333 145.626 120.055 1 75.09 ? C22 3PH 601 B 1 HETATM 12 C C23 3PH . . . G 4 122.178 145.288 121.278 1 75.09 ? C23 3PH 601 B 1 HETATM 13 C C24 3PH . . . G 4 121.304 144.806 122.43 1 75.09 ? C24 3PH 601 B 1 HETATM 14 C C25 3PH . . . G 4 121.451 143.302 122.633 1 75.09 ? C25 3PH 601 B 1 HETATM 15 C C26 3PH . . . G 4 120.962 142.887 124.016 1 75.09 ? C26 3PH 601 B 1 HETATM 16 C C27 3PH . . . G 4 120.321 141.505 123.978 1 75.09 ? C27 3PH 601 B 1 HETATM 17 C C28 3PH . . . G 4 121.11 140.56 123.079 1 75.09 ? C28 3PH 601 B 1 HETATM 18 C C29 3PH . . . G 4 120.242 139.397 122.612 1 75.09 ? C29 3PH 601 B 1 HETATM 19 C C2A 3PH . . . G 4 121.03 138.092 122.609 1 75.09 ? C2A 3PH 601 B 1 HETATM 20 C C2B 3PH . . . G 4 120.188 136.946 122.061 1 75.09 ? C2B 3PH 601 B 1 HETATM 21 C C2C 3PH . . . G 4 121.033 135.694 121.861 1 75.09 ? C2C 3PH 601 B 1 HETATM 22 C C2D 3PH . . . G 4 120.172 134.517 121.419 1 75.09 ? C2D 3PH 601 B 1 HETATM 23 C C2E 3PH . . . G 4 120.973 133.546 120.56 1 75.09 ? C2E 3PH 601 B 1 HETATM 24 C C2F 3PH . . . G 4 122.226 133.079 121.29 1 75.09 ? C2F 3PH 601 B 1 HETATM 25 C C2G 3PH . . . G 4 121.873 132.419 122.618 1 75.09 ? C2G 3PH 601 B 1 HETATM 26 C C2H 3PH . . . G 4 122.903 131.361 122.992 1 75.09 ? C2H 3PH 601 B 1 HETATM 27 C C2I 3PH . . . G 4 122.587 130.749 124.339 1 75.09 ? C2I 3PH 601 B 1 HETATM 28 C C3 3PH . . . G 4 124.253 149.247 119.562 1 75.09 ? C3 3PH 601 B 1 HETATM 29 O O31 3PH . . . G 4 125.204 148.725 120.489 1 75.09 ? O31 3PH 601 B 1 HETATM 30 C C31 3PH . . . G 4 125.147 149.119 121.887 1 75.09 ? C31 3PH 601 B 1 HETATM 31 O O32 3PH . . . G 4 124.595 150.164 122.189 1 75.09 ? O32 3PH 601 B 1 HETATM 32 C C32 3PH . . . G 4 125.767 148.241 122.948 1 75.09 ? C32 3PH 601 B 1 HETATM 33 C C33 3PH . . . G 4 124.762 147.181 123.381 1 75.09 ? C33 3PH 601 B 1 HETATM 34 C C34 3PH . . . G 4 125.453 146.047 124.13 1 75.09 ? C34 3PH 601 B 1 HETATM 35 C C35 3PH . . . G 4 125.243 146.177 125.634 1 75.09 ? C35 3PH 601 B 1 HETATM 36 C C36 3PH . . . G 4 125.874 145.006 126.377 1 75.09 ? C36 3PH 601 B 1 HETATM 37 C C37 3PH . . . G 4 124.872 143.873 126.564 1 75.09 ? C37 3PH 601 B 1 HETATM 38 C C38 3PH . . . G 4 125.352 142.881 127.618 1 75.09 ? C38 3PH 601 B 1 HETATM 39 C C39 3PH . . . G 4 124.635 141.545 127.474 1 75.09 ? C39 3PH 601 B 1 HETATM 40 C C3A 3PH . . . G 4 123.199 141.744 127.004 1 75.09 ? C3A 3PH 601 B 1 HETATM 41 C C3B 3PH . . . G 4 122.332 142.312 128.122 1 75.09 ? C3B 3PH 601 B 1 HETATM 42 C C3C 3PH . . . G 4 122.279 141.36 129.31 1 75.09 ? C3C 3PH 601 B 1 HETATM 43 C C3D 3PH . . . G 4 122.111 142.125 130.617 1 75.09 ? C3D 3PH 601 B 1 HETATM 44 C C3E 3PH . . . G 4 123.459 142.369 131.285 1 75.09 ? C3E 3PH 601 B 1 HETATM 45 C C3F 3PH . . . G 4 123.277 142.916 132.696 1 75.09 ? C3F 3PH 601 B 1 HETATM 46 C C3G 3PH . . . G 4 122.313 142.05 133.498 1 75.09 ? C3G 3PH 601 B 1 HETATM 47 C C3H 3PH . . . G 4 122.72 140.583 133.44 1 75.09 ? C3H 3PH 601 B 1 HETATM 48 C C3I 3PH . . . G 4 123.176 140.093 134.797 1 75.09 ? C3I 3PH 601 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 430 _model_server_stats.encode_time_ms 39 _model_server_stats.element_count 48 #