data_6SM3 # _model_server_result.job_id U1mR-NA42TIAhF2aidTeNQ _model_server_result.datetime_utc '2025-07-07 02:58:41' _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 6sm3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 6SM3 # _exptl.entry_id 6SM3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 1233.719 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE' _entity.pdbx_number_of_molecules 1 _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 6SM3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6SM3 _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 PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 231.3556 231.009 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 SG CYS 1 A CYS 20 1_555 D CAW 5PL . A 5PL 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? covale ? covale2 A N CYS 1 A CYS 20 1_555 E C1 PLM . A PLM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale3 A N CYS 1 A CYS 20 1_555 E O2 PLM . A PLM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.224 ? # _chem_comp.formula 'C67 H129 N2 O15 P' _chem_comp.formula_weight 1233.719 _chem_comp.id 5PL _chem_comp.mon_nstd_flag . _chem_comp.name '(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE' _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 OCO CBL 5PL doub 1 n n CBL CBM 5PL sing 2 n n CBL OCL 5PL sing 3 n n CBM CBN 5PL sing 4 n n OCL CBI 5PL sing 5 n n CBN CBO 5PL sing 6 n n CBO CBP 5PL sing 7 n n CBP CAA 5PL sing 8 n n CAA CBR 5PL sing 9 n n CBR CBS 5PL sing 10 n n CBS CBT 5PL sing 11 n n CBT CAL 5PL sing 12 n n CAL CAO 5PL sing 13 n n CAO CAS 5PL sing 14 n n CAS C7 5PL sing 15 n n C7 C8 5PL sing 16 n n CBI CBH 5PL sing 17 n n CBH CAW 5PL sing 18 n n CBH OCK 5PL sing 19 n n CAW OCJ 5PL sing 20 n n CBV CBW 5PL sing 21 n n CBV CBU 5PL sing 22 n n CBW CBX 5PL sing 23 n n CBX CBY 5PL sing 24 n n CBY CBZ 5PL sing 25 n n CAE CAF 5PL sing 26 n n CAE CBZ 5PL sing 27 n n CAF CAG 5PL sing 28 n n CAG CAK 5PL sing 29 n n CAK CBK 5PL sing 30 n n CBK CBQ 5PL sing 31 n n CBQ C13 5PL sing 32 n n C13 C14 5PL sing 33 n n OCJ PCR 5PL sing 34 n n PCR OCI 5PL sing 35 n n PCR OCM 5PL doub 36 n n PCR OCG 5PL sing 37 n n OCG CAN 5PL sing 38 n n CAN CAM 5PL sing 39 n n CAN CAP 5PL sing 40 n n CAM O1 5PL sing 41 n n CBU OCK 5PL sing 42 n n CBU OCN 5PL doub 43 n n O1 C1 5PL sing 44 n n C1 C2 5PL sing 45 n n C1 O5 5PL sing 46 n n C2 N2 5PL sing 47 n n C2 C3 5PL sing 48 n n N2 CAQ 5PL sing 49 n n CAQ OCP 5PL doub 50 n n CAQ CAR 5PL sing 51 n n C3 O3 5PL sing 52 n n C3 C4 5PL sing 53 n n C4 O4 5PL sing 54 n n C4 C5 5PL sing 55 n n C5 C6 5PL sing 56 n n C5 O5 5PL sing 57 n n C6 O6 5PL sing 58 n n CAP OCH 5PL doub 59 n n CAP NCB 5PL sing 60 n n NCB CAX 5PL sing 61 n n CAX CAY 5PL sing 62 n n CAY CAZ 5PL sing 63 n n CAZ CBA 5PL sing 64 n n CBA CBB 5PL sing 65 n n CBB CBC 5PL sing 66 n n CBC CBD 5PL sing 67 n n CBD CBE 5PL sing 68 n n CBE CBF 5PL sing 69 n n CBF CBG 5PL sing 70 n n CBG CAT 5PL sing 71 n n CAT CAU 5PL sing 72 n n CAU CAV 5PL sing 73 n n CAV CBJ 5PL sing 74 n n CBJ C18 5PL sing 75 n n C8 C9 5PL sing 76 n n C9 C10 5PL sing 77 n n C9 C12 5PL sing 78 n n C14 C15 5PL sing 79 n n C15 C16 5PL sing 80 n n C15 C17 5PL sing 81 n n C18 C19 5PL sing 82 n n C19 C20 5PL sing 83 n n C20 C21 5PL sing 84 n n C21 C22 5PL sing 85 n n CBM HBM1 5PL sing 86 n n CBM HBM2 5PL sing 87 n n CBN HBN1 5PL sing 88 n n CBN HBN2 5PL sing 89 n n CBI HBI1 5PL sing 90 n n CBI HBI2 5PL sing 91 n n CBO HBO1 5PL sing 92 n n CBO HBO2 5PL sing 93 n n CBP HBP1 5PL sing 94 n n CBP HBP2 5PL sing 95 n n CAA HAA1 5PL sing 96 n n CAA HAA2 5PL sing 97 n n CBR HBR1 5PL sing 98 n n CBR HBR2 5PL sing 99 n n CBS HBS1 5PL sing 100 n n CBS HBS2 5PL sing 101 n n CBT HBT1 5PL sing 102 n n CBT HBT2 5PL sing 103 n n CAL HAL1 5PL sing 104 n n CAL HAL2 5PL sing 105 n n CAO HAO1 5PL sing 106 n n CAO HAO2 5PL sing 107 n n CAS HAS1 5PL sing 108 n n CAS HAS2 5PL sing 109 n n C7 H71C 5PL sing 110 n n C7 H72C 5PL sing 111 n n C8 H81C 5PL sing 112 n n C8 H82C 5PL sing 113 n n CBH HBH 5PL sing 114 n n CAW HAW1 5PL sing 115 n n CAW HAW2 5PL sing 116 n n CBV HBV1 5PL sing 117 n n CBV HBV2 5PL sing 118 n n CBW HBW1 5PL sing 119 n n CBW HBW2 5PL sing 120 n n CBX HBX1 5PL sing 121 n n CBX HBX2 5PL sing 122 n n CBY HBY1 5PL sing 123 n n CBY HBY2 5PL sing 124 n n CBZ HBZ1 5PL sing 125 n n CBZ HBZ2 5PL sing 126 n n CAE HAE1 5PL sing 127 n n CAE HAE2 5PL sing 128 n n CAF HAF1 5PL sing 129 n n CAF HAF2 5PL sing 130 n n CAG HAG1 5PL sing 131 n n CAG HAG2 5PL sing 132 n n CAK HAK1 5PL sing 133 n n CAK HAK2 5PL sing 134 n n CBK HBK1 5PL sing 135 n n CBK HBK2 5PL sing 136 n n CBQ HBQ1 5PL sing 137 n n CBQ HBQ2 5PL sing 138 n n C13 H131 5PL sing 139 n n C13 H132 5PL sing 140 n n C14 H141 5PL sing 141 n n C14 H142 5PL sing 142 n n OCI HCI 5PL sing 143 n n CAN HAN 5PL sing 144 n n CAM HAM1 5PL sing 145 n n CAM HAM2 5PL sing 146 n n C1 H1 5PL sing 147 n n C2 H2 5PL sing 148 n n N2 HA 5PL sing 149 n n C3 H3 5PL sing 150 n n CAR HAR1 5PL sing 151 n n CAR HAR2 5PL sing 152 n n CAR HAR3 5PL sing 153 n n O3 HB 5PL sing 154 n n C4 H4 5PL sing 155 n n O4 HC 5PL sing 156 n n C5 H5 5PL sing 157 n n C6 H61C 5PL sing 158 n n C6 H62C 5PL sing 159 n n O6 H6 5PL sing 160 n n NCB HCB 5PL sing 161 n n CAX HAX1 5PL sing 162 n n CAX HAX2 5PL sing 163 n n CAY HAY1 5PL sing 164 n n CAY HAY2 5PL sing 165 n n CAZ HAZ1 5PL sing 166 n n CAZ HAZ2 5PL sing 167 n n CBA HBA1 5PL sing 168 n n CBA HBA2 5PL sing 169 n n CBB HBB1 5PL sing 170 n n CBB HBB2 5PL sing 171 n n CBC HBC1 5PL sing 172 n n CBC HBC2 5PL sing 173 n n CBD HBD1 5PL sing 174 n n CBD HBD2 5PL sing 175 n n CBE HBE1 5PL sing 176 n n CBE HBE2 5PL sing 177 n n CBF HBF1 5PL sing 178 n n CBF HBF2 5PL sing 179 n n CBG HBG1 5PL sing 180 n n CBG HBG2 5PL sing 181 n n CAT HAT1 5PL sing 182 n n CAT HAT2 5PL sing 183 n n CAU HAU1 5PL sing 184 n n CAU HAU2 5PL sing 185 n n CAV HAV1 5PL sing 186 n n CAV HAV2 5PL sing 187 n n CBJ HBJ1 5PL sing 188 n n CBJ HBJ2 5PL sing 189 n n C18 H181 5PL sing 190 n n C18 H182 5PL sing 191 n n C9 H9 5PL sing 192 n n C10 H101 5PL sing 193 n n C10 H102 5PL sing 194 n n C10 H103 5PL sing 195 n n C12 H121 5PL sing 196 n n C12 H122 5PL sing 197 n n C12 H123 5PL sing 198 n n C15 H15 5PL sing 199 n n C16 H161 5PL sing 200 n n C16 H162 5PL sing 201 n n C16 H163 5PL sing 202 n n C17 H171 5PL sing 203 n n C17 H172 5PL sing 204 n n C17 H173 5PL sing 205 n n C19 H191 5PL sing 206 n n C19 H192 5PL sing 207 n n C20 H201 5PL sing 208 n n C20 H202 5PL sing 209 n n C21 H211 5PL sing 210 n n C21 H212 5PL sing 211 n n C22 H221 5PL sing 212 n n C22 H222 5PL sing 213 n n C22 H223 5PL sing 214 n n # _atom_sites.entry_id 6SM3 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 D 4 5PL A 1 601 2 5PL 5PL . E 5 PLM A 1 602 2 PLM PLM . # 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 OCO 5PL . . . D 4 123.57 89.158 125.097 1 18.02 ? OCO 5PL 601 A 1 HETATM 2 C CBL 5PL . . . D 4 122.547 89.699 124.823 1 18.02 ? CBL 5PL 601 A 1 HETATM 3 C CBM 5PL . . . D 4 121.494 89.969 125.917 1 18.02 ? CBM 5PL 601 A 1 HETATM 4 O OCL 5PL . . . D 4 122.304 90.078 123.49 1 18.02 ? OCL 5PL 601 A 1 HETATM 5 C CBN 5PL . . . D 4 122.153 90.148 127.31 1 18.02 ? CBN 5PL 601 A 1 HETATM 6 C CBO 5PL . . . D 4 121.192 90.95 128.232 1 18.02 ? CBO 5PL 601 A 1 HETATM 7 C CBP 5PL . . . D 4 121.715 90.95 129.69 1 18.02 ? CBP 5PL 601 A 1 HETATM 8 C CAA 5PL . . . D 4 120.589 91.416 130.65 1 18.02 ? CAA 5PL 601 A 1 HETATM 9 C CBR 5PL . . . D 4 121.21 92.02 131.944 1 18.02 ? CBR 5PL 601 A 1 HETATM 10 C CBS 5PL . . . D 4 120.093 92.591 132.868 1 18.02 ? CBS 5PL 601 A 1 HETATM 11 C CBT 5PL . . . D 4 120.68 92.921 134.267 1 18.02 ? CBT 5PL 601 A 1 HETATM 12 C CBI 5PL . . . D 4 122.745 91.387 123.167 1 18.02 ? CBI 5PL 601 A 1 HETATM 13 C CBH 5PL . . . D 4 121.742 92.025 122.196 1 18.02 ? CBH 5PL 601 A 1 HETATM 14 C CAW 5PL . . . D 4 122.193 91.791 120.751 1 18.02 ? CAW 5PL 601 A 1 HETATM 15 C CBV 5PL . . . D 4 120.903 94.188 124.752 1 18.02 ? CBV 5PL 601 A 1 HETATM 16 C CBW 5PL . . . D 4 119.582 94.173 125.536 1 18.02 ? CBW 5PL 601 A 1 HETATM 17 C CBX 5PL . . . D 4 119.838 94.648 126.984 1 18.02 ? CBX 5PL 601 A 1 HETATM 18 C CBY 5PL . . . D 4 118.508 95.06 127.632 1 18.02 ? CBY 5PL 601 A 1 HETATM 19 C CAE 5PL . . . D 4 117.7 95.331 130 1 18.02 ? CAE 5PL 601 A 1 HETATM 20 C CAF 5PL . . . D 4 117.726 96.232 131.253 1 18.02 ? CAF 5PL 601 A 1 HETATM 21 C CAG 5PL . . . D 4 117.002 95.485 132.411 1 18.02 ? CAG 5PL 601 A 1 HETATM 22 C CAK 5PL . . . D 4 117.03 96.33 133.703 1 18.02 ? CAK 5PL 601 A 1 HETATM 23 C CBZ 5PL . . . D 4 118.77 95.778 128.983 1 18.02 ? CBZ 5PL 601 A 1 HETATM 24 C CBU 5PL . . . D 4 120.631 93.81 123.288 1 18.02 ? CBU 5PL 601 A 1 HETATM 25 O OCK 5PL . . . D 4 121.681 93.392 122.441 1 18.02 ? OCK 5PL 601 A 1 HETATM 26 O OCN 5PL . . . D 4 119.542 93.89 122.87 1 18.02 ? OCN 5PL 601 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 391 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #