data_4MD2 # _model_server_result.job_id HoEoxHN_sktNxir80p5NCw _model_server_result.datetime_utc '2024-11-02 19:32:23' _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 4md2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1004}' # _entry.id 4MD2 # _exptl.entry_id 4MD2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 653.157 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,3-DI-PHYTANYL-GLYCEROL _entity.pdbx_number_of_molecules 18 _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 4MD2 _cell.length_a 60.91 _cell.length_b 60.91 _cell.length_c 110.09 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4MD2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 30.455 52.749607 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -30.455 52.749607 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P N N ? 2 Q N N ? 2 R N N ? 2 S N N ? 2 T N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 216 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 216 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id U _struct_conn.ptnr2_label_atom_id C15 _struct_conn.ptnr2_label_comp_id RET _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id RET _struct_conn.ptnr2_auth_seq_id 1020 _struct_conn.ptnr2_symmetry 1_555 _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 1.465 _struct_conn.pdbx_value_order doub # _chem_comp.formula 'C43 H88 O3' _chem_comp.formula_weight 653.157 _chem_comp.id L2P _chem_comp.mon_nstd_flag . _chem_comp.name 2,3-DI-PHYTANYL-GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL # 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 O1 L2P sing 139 n n C1 C2 L2P sing 140 n n C1 H12 L2P sing 141 n n C1 H11 L2P sing 142 n n O1 C11 L2P sing 143 n n C2 O2 L2P sing 144 n n C2 C3 L2P sing 145 n n C2 H2 L2P sing 146 n n O2 C41 L2P sing 147 n n C3 O3 L2P sing 148 n n C3 H32 L2P sing 149 n n C3 H31 L2P sing 150 n n O3 H3O L2P sing 151 n n C11 C12 L2P sing 152 n n C11 H112 L2P sing 153 n n C11 H111 L2P sing 154 n n C12 C13 L2P sing 155 n n C12 H122 L2P sing 156 n n C12 H121 L2P sing 157 n n C13 C14 L2P sing 158 n n C13 C15 L2P sing 159 n n C13 H13 L2P sing 160 n n C14 H143 L2P sing 161 n n C14 H142 L2P sing 162 n n C14 H141 L2P sing 163 n n C15 C16 L2P sing 164 n n C15 H152 L2P sing 165 n n C15 H151 L2P sing 166 n n C16 C17 L2P sing 167 n n C16 H162 L2P sing 168 n n C16 H161 L2P sing 169 n n C17 C18 L2P sing 170 n n C17 H172 L2P sing 171 n n C17 H171 L2P sing 172 n n C18 C19 L2P sing 173 n n C18 C20 L2P sing 174 n n C18 H18 L2P sing 175 n n C19 H193 L2P sing 176 n n C19 H192 L2P sing 177 n n C19 H191 L2P sing 178 n n C20 C21 L2P sing 179 n n C20 H202 L2P sing 180 n n C20 H201 L2P sing 181 n n C21 C22 L2P sing 182 n n C21 H212 L2P sing 183 n n C21 H211 L2P sing 184 n n C22 C23 L2P sing 185 n n C22 H222 L2P sing 186 n n C22 H221 L2P sing 187 n n C23 C24 L2P sing 188 n n C23 C25 L2P sing 189 n n C23 H23 L2P sing 190 n n C24 H243 L2P sing 191 n n C24 H242 L2P sing 192 n n C24 H241 L2P sing 193 n n C25 C26 L2P sing 194 n n C25 H252 L2P sing 195 n n C25 H251 L2P sing 196 n n C26 C27 L2P sing 197 n n C26 H262 L2P sing 198 n n C26 H261 L2P sing 199 n n C27 C28 L2P sing 200 n n C27 H272 L2P sing 201 n n C27 H271 L2P sing 202 n n C28 C29 L2P sing 203 n n C28 C30 L2P sing 204 n n C28 H28 L2P sing 205 n n C29 H293 L2P sing 206 n n C29 H292 L2P sing 207 n n C29 H291 L2P sing 208 n n C30 H303 L2P sing 209 n n C30 H302 L2P sing 210 n n C30 H301 L2P sing 211 n n C41 C42 L2P sing 212 n n C41 H412 L2P sing 213 n n C41 H411 L2P sing 214 n n C42 C43 L2P sing 215 n n C42 H422 L2P sing 216 n n C42 H421 L2P sing 217 n n C43 C44 L2P sing 218 n n C43 C45 L2P sing 219 n n C43 H43 L2P sing 220 n n C44 H443 L2P sing 221 n n C44 H442 L2P sing 222 n n C44 H441 L2P sing 223 n n C45 C46 L2P sing 224 n n C45 H452 L2P sing 225 n n C45 H451 L2P sing 226 n n C46 C47 L2P sing 227 n n C46 H462 L2P sing 228 n n C46 H461 L2P sing 229 n n C47 C48 L2P sing 230 n n C47 H472 L2P sing 231 n n C47 H471 L2P sing 232 n n C48 C49 L2P sing 233 n n C48 C50 L2P sing 234 n n C48 H48 L2P sing 235 n n C49 H493 L2P sing 236 n n C49 H492 L2P sing 237 n n C49 H491 L2P sing 238 n n C50 C51 L2P sing 239 n n C50 H502 L2P sing 240 n n C50 H501 L2P sing 241 n n C51 C52 L2P sing 242 n n C51 H512 L2P sing 243 n n C51 H511 L2P sing 244 n n C52 C53 L2P sing 245 n n C52 H522 L2P sing 246 n n C52 H521 L2P sing 247 n n C53 C54 L2P sing 248 n n C53 C55 L2P sing 249 n n C53 H53 L2P sing 250 n n C54 H543 L2P sing 251 n n C54 H542 L2P sing 252 n n C54 H541 L2P sing 253 n n C55 C56 L2P sing 254 n n C55 H552 L2P sing 255 n n C55 H551 L2P sing 256 n n C56 C57 L2P sing 257 n n C56 H562 L2P sing 258 n n C56 H561 L2P sing 259 n n C57 C58 L2P sing 260 n n C57 H572 L2P sing 261 n n C57 H571 L2P sing 262 n n C58 C59 L2P sing 263 n n C58 C60 L2P sing 264 n n C58 H58 L2P sing 265 n n C59 H593 L2P sing 266 n n C59 H592 L2P sing 267 n n C59 H591 L2P sing 268 n n C60 H603 L2P sing 269 n n C60 H602 L2P sing 270 n n C60 H601 L2P sing 271 n n # _atom_sites.entry_id 4MD2 _atom_sites.fract_transf_matrix[1][1] 0.016418 _atom_sites.fract_transf_matrix[1][2] 0.009479 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018957 _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] 0.009083 _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 B 2 L2P A 1 1001 1001 L2P L2P . C 3 SQL A 1 1002 1002 SQL SQN . D 2 L2P A 1 1003 1003 L2P L2P . E 2 L2P A 1 1004 1004 L2P L2P . F 2 L2P A 1 1005 1005 L2P L2P . G 2 L2P A 1 1006 1006 L2P L2P . H 2 L2P A 1 1007 1007 L2P L2P . I 2 L2P A 1 1008 1008 L2P L2P . J 2 L2P A 1 1009 1009 L2P L2P . K 2 L2P A 1 1010 1010 L2P L2P . L 2 L2P A 1 1011 1011 L2P L2P . M 2 L2P A 1 1012 1012 L2P L2P . N 2 L2P A 1 1013 1013 L2P L2P . O 2 L2P A 1 1014 1014 L2P L2P . P 2 L2P A 1 1015 1015 L2P L2P . Q 2 L2P A 1 1016 1016 L2P L2P . R 2 L2P A 1 1017 1017 L2P L2P . S 2 L2P A 1 1018 1018 L2P L2P . T 2 L2P A 1 1019 1019 L2P L2P . U 4 RET A 1 1020 216 RET LYR . V 5 HOH A 1 1101 401 HOH HOH . V 5 HOH A 2 1102 402 HOH HOH . V 5 HOH A 3 1103 403 HOH HOH . V 5 HOH A 4 1104 404 HOH HOH . V 5 HOH A 5 1105 405 HOH HOH . V 5 HOH A 6 1106 406 HOH HOH . V 5 HOH A 7 1107 407 HOH HOH . V 5 HOH A 8 1108 409 HOH HOH . V 5 HOH A 9 1109 411 HOH HOH . V 5 HOH A 10 1110 412 HOH HOH . V 5 HOH A 11 1111 414 HOH HOH . V 5 HOH A 12 1112 415 HOH HOH . V 5 HOH A 13 1113 416 HOH HOH . V 5 HOH A 14 1114 418 HOH HOH . V 5 HOH A 15 1115 419 HOH HOH . V 5 HOH A 16 1116 420 HOH HOH . V 5 HOH A 17 1117 421 HOH HOH . V 5 HOH A 18 1118 423 HOH HOH . V 5 HOH A 19 1119 424 HOH HOH . V 5 HOH A 20 1120 425 HOH HOH . V 5 HOH A 21 1121 427 HOH HOH . V 5 HOH A 22 1122 428 HOH HOH . V 5 HOH A 23 1123 430 HOH HOH . V 5 HOH A 24 1124 431 HOH HOH . V 5 HOH A 25 1125 432 HOH HOH . V 5 HOH A 26 1126 501 HOH HOH . V 5 HOH A 27 1127 502 HOH HOH . V 5 HOH A 28 1128 511 HOH HOH . V 5 HOH A 29 1129 512 HOH HOH . V 5 HOH A 30 1130 513 HOH HOH . V 5 HOH A 31 1131 514 HOH HOH . V 5 HOH A 32 1132 521 HOH HOH . V 5 HOH A 33 1133 522 HOH HOH . V 5 HOH A 34 1134 524 HOH HOH . V 5 HOH A 35 1135 526 HOH HOH . V 5 HOH A 36 1136 527 HOH HOH . V 5 HOH A 37 1137 530 HOH HOH . V 5 HOH A 38 1138 533 HOH HOH . V 5 HOH A 39 1139 538 HOH HOH . V 5 HOH A 40 1140 539 HOH HOH . V 5 HOH A 41 1141 544 HOH HOH . V 5 HOH A 42 1142 545 HOH HOH . V 5 HOH A 43 1143 649 HOH HOH . V 5 HOH A 44 1144 653 HOH HOH . V 5 HOH A 45 1145 655 HOH HOH . V 5 HOH A 46 1146 657 HOH HOH . V 5 HOH A 47 1147 658 HOH HOH . V 5 HOH A 48 1148 660 HOH HOH . V 5 HOH A 49 1149 670 HOH HOH . V 5 HOH A 50 1150 671 HOH HOH . # 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 C20 L2P . . . E 2 0.296 29.567 71.042 1 56.68 ? C20 L2P 1004 A 1 HETATM 2 C C21 L2P . . . E 2 1.725 29.824 70.547 1 78.01 ? C21 L2P 1004 A 1 HETATM 3 C C22 L2P . . . E 2 1.867 30.47 69.143 1 58.73 ? C22 L2P 1004 A 1 HETATM 4 C C23 L2P . . . E 2 1.471 29.676 67.881 1 32.64 ? C23 L2P 1004 A 1 HETATM 5 C C25 L2P . . . E 2 1.691 30.547 66.621 1 49.68 ? C25 L2P 1004 A 1 HETATM 6 C C26 L2P . . . E 2 1.566 29.692 65.346 1 46.58 ? C26 L2P 1004 A 1 HETATM 7 C C27 L2P . . . E 2 1.769 30.497 64.051 1 58.45 ? C27 L2P 1004 A 1 HETATM 8 C C28 L2P . . . E 2 1.798 29.602 62.799 1 43.45 ? C28 L2P 1004 A 1 HETATM 9 C C29 L2P . . . E 2 1.987 30.436 61.525 1 39.38 ? C29 L2P 1004 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 9 #