data_3PL9 # _model_server_result.job_id DW2HMJVltwqkXPiJOZS-1g _model_server_result.datetime_utc '2024-11-24 23:56:26' _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 3pl9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":620}' # _entry.id 3PL9 # _exptl.entry_id 3PL9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 568.871 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL" _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 120 _cell.entry_id 3PL9 _cell.length_a 68.793 _cell.length_b 68.793 _cell.length_c 425.778 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PL9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id O _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 metalc ? metalc1 A OE1 GLU 96 A GLU 96 1_555 B MG CLA . A CLA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc2 A OE1 GLU 159 A GLU 159 1_555 H MG CLA . A CLA 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc3 A OE1 GLU 197 A GLU 197 1_555 I MG CLA . A CLA 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc4 A OE1 GLN 214 A GLN 214 1_555 L MG CLA . A CLA 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc5 U O HOH . A HOH 245 1_555 F MG CHL . A CHL 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc6 U O HOH . A HOH 247 1_555 G MG CHL . A CHL 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc7 U O HOH . A HOH 248 1_555 E MG CHL . A CHL 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc8 U O HOH . A HOH 307 1_555 D MG CLA . A CLA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc9 J MG CLA . A CLA 611 1_555 R O3P G3P . A G3P 630 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc10 J MG CLA . A CLA 611 1_555 R O2P G3P . A G3P 630 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc11 N MG CLA . A CLA 615 1_555 R O4P G3P . A G3P 630 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? # _chem_comp.formula 'C40 H56 O2' _chem_comp.formula_weight 568.871 _chem_comp.id LUT _chem_comp.mon_nstd_flag . _chem_comp.name "(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "(3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL;LUTEIN" # 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 LUT sing 546 n n C1 C6 LUT sing 547 n n C1 C16 LUT sing 548 n n C1 C17 LUT sing 549 n n C2 C3 LUT sing 550 n n C2 H21 LUT sing 551 n n C2 H22 LUT sing 552 n n C3 C4 LUT sing 553 n n C3 O3 LUT sing 554 n n C3 H3 LUT sing 555 n n C4 C5 LUT sing 556 n n C4 H41 LUT sing 557 n n C4 H42 LUT sing 558 n n C5 C6 LUT doub 559 n n C5 C18 LUT sing 560 n n C6 C7 LUT sing 561 n n C7 C8 LUT doub 562 e n C7 H7 LUT sing 563 n n C8 C9 LUT sing 564 n n C8 H8 LUT sing 565 n n C9 C10 LUT doub 566 e n C9 C19 LUT sing 567 n n C10 C11 LUT sing 568 n n C10 H10 LUT sing 569 n n C11 C12 LUT doub 570 e n C11 H11 LUT sing 571 n n C12 C13 LUT sing 572 n n C12 H12 LUT sing 573 n n C13 C14 LUT doub 574 e n C13 C20 LUT sing 575 n n C14 C15 LUT sing 576 n n C14 H14 LUT sing 577 n n C15 C35 LUT doub 578 e n C15 H15 LUT sing 579 n n C16 H161 LUT sing 580 n n C16 H162 LUT sing 581 n n C16 H163 LUT sing 582 n n C17 H171 LUT sing 583 n n C17 H172 LUT sing 584 n n C17 H173 LUT sing 585 n n C18 H181 LUT sing 586 n n C18 H182 LUT sing 587 n n C18 H183 LUT sing 588 n n C19 H191 LUT sing 589 n n C19 H192 LUT sing 590 n n C19 H193 LUT sing 591 n n C20 H201 LUT sing 592 n n C20 H202 LUT sing 593 n n C20 H203 LUT sing 594 n n O3 HO3 LUT sing 595 n n C21 C22 LUT sing 596 n n C21 C26 LUT sing 597 n n C21 C36 LUT sing 598 n n C21 C37 LUT sing 599 n n C22 C23 LUT sing 600 n n C22 H221 LUT sing 601 n n C22 H222 LUT sing 602 n n C23 C24 LUT sing 603 n n C23 O23 LUT sing 604 n n C23 H23 LUT sing 605 n n C24 C25 LUT doub 606 n n C24 H24 LUT sing 607 n n C25 C26 LUT sing 608 n n C25 C38 LUT sing 609 n n C26 C27 LUT sing 610 n n C26 H26 LUT sing 611 n n C27 C28 LUT doub 612 e n C27 H27 LUT sing 613 n n C28 C29 LUT sing 614 n n C28 H28 LUT sing 615 n n C29 C30 LUT doub 616 e n C29 C39 LUT sing 617 n n C30 C31 LUT sing 618 n n C30 H30 LUT sing 619 n n C31 C32 LUT doub 620 e n C31 H31 LUT sing 621 n n C32 C33 LUT sing 622 n n C32 H32 LUT sing 623 n n C33 C34 LUT doub 624 e n C33 C40 LUT sing 625 n n C34 C35 LUT sing 626 n n C34 H34 LUT sing 627 n n C35 H35 LUT sing 628 n n C36 H361 LUT sing 629 n n C36 H362 LUT sing 630 n n C36 H363 LUT sing 631 n n C37 H371 LUT sing 632 n n C37 H372 LUT sing 633 n n C37 H373 LUT sing 634 n n C38 H381 LUT sing 635 n n C38 H382 LUT sing 636 n n C38 H383 LUT sing 637 n n C39 H391 LUT sing 638 n n C39 H392 LUT sing 639 n n C39 H393 LUT sing 640 n n C40 H401 LUT sing 641 n n C40 H402 LUT sing 642 n n C40 H403 LUT sing 643 n n O23 H1 LUT sing 644 n n # _atom_sites.entry_id 3PL9 _atom_sites.fract_transf_matrix[1][1] 0.014536 _atom_sites.fract_transf_matrix[1][2] 0.008393 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016785 _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] 0.002349 _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 CLA A 1 602 602 CLA CLA . C 2 CLA A 1 603 603 CLA CLA . D 2 CLA A 1 604 604 CLA CLA . E 3 CHL A 1 606 606 CHL CHL . F 3 CHL A 1 607 607 CHL CHL . G 3 CHL A 1 608 608 CHL CHL . H 2 CLA A 1 609 609 CLA CLA . I 2 CLA A 1 610 610 CLA CLA . J 2 CLA A 1 611 611 CLA CLA . K 2 CLA A 1 612 612 CLA CLA . L 2 CLA A 1 613 613 CLA CLA . M 3 CHL A 1 614 614 CHL CHL . N 2 CLA A 1 615 615 CLA CLA . O 4 LUT A 1 620 620 LUT LUT . P 5 XAT A 1 622 622 XAT XAT . Q 6 NEX A 1 623 623 NEX NEX . R 7 G3P A 1 630 630 G3P G3P . S 8 HTG A 1 631 631 HTG HTG . T 8 HTG A 1 632 632 HTG HTG . U 9 HOH A 1 244 244 HOH HOH . U 9 HOH A 2 245 245 HOH HOH . U 9 HOH A 3 246 246 HOH HOH . U 9 HOH A 4 247 247 HOH HOH . U 9 HOH A 5 248 248 HOH HOH . U 9 HOH A 6 249 249 HOH HOH . U 9 HOH A 7 250 250 HOH HOH . U 9 HOH A 8 251 251 HOH HOH . U 9 HOH A 9 252 252 HOH HOH . U 9 HOH A 10 253 253 HOH HOH . U 9 HOH A 11 254 254 HOH HOH . U 9 HOH A 12 255 255 HOH HOH . U 9 HOH A 13 256 256 HOH HOH . U 9 HOH A 14 257 257 HOH HOH . U 9 HOH A 15 258 258 HOH HOH . U 9 HOH A 16 259 259 HOH HOH . U 9 HOH A 17 260 260 HOH HOH . U 9 HOH A 18 261 261 HOH HOH . U 9 HOH A 19 262 262 HOH HOH . U 9 HOH A 20 263 263 HOH HOH . U 9 HOH A 21 264 264 HOH HOH . U 9 HOH A 22 265 265 HOH HOH . U 9 HOH A 23 266 266 HOH HOH . U 9 HOH A 24 267 267 HOH HOH . U 9 HOH A 25 268 268 HOH HOH . U 9 HOH A 26 269 269 HOH HOH . U 9 HOH A 27 270 270 HOH HOH . U 9 HOH A 28 271 271 HOH HOH . U 9 HOH A 29 272 272 HOH HOH . U 9 HOH A 30 273 273 HOH HOH . U 9 HOH A 31 274 274 HOH HOH . U 9 HOH A 32 275 275 HOH HOH . U 9 HOH A 33 276 276 HOH HOH . U 9 HOH A 34 277 277 HOH HOH . U 9 HOH A 35 278 278 HOH HOH . U 9 HOH A 36 279 279 HOH HOH . U 9 HOH A 37 280 280 HOH HOH . U 9 HOH A 38 281 281 HOH HOH . U 9 HOH A 39 282 282 HOH HOH . U 9 HOH A 40 283 283 HOH HOH . U 9 HOH A 41 284 284 HOH HOH . U 9 HOH A 42 285 285 HOH HOH . U 9 HOH A 43 286 286 HOH HOH . U 9 HOH A 44 287 287 HOH HOH . U 9 HOH A 45 288 288 HOH HOH . U 9 HOH A 46 289 289 HOH HOH . U 9 HOH A 47 290 290 HOH HOH . U 9 HOH A 48 291 291 HOH HOH . U 9 HOH A 49 292 292 HOH HOH . U 9 HOH A 50 293 293 HOH HOH . U 9 HOH A 51 294 294 HOH HOH . U 9 HOH A 52 295 295 HOH HOH . U 9 HOH A 53 296 296 HOH HOH . U 9 HOH A 54 297 297 HOH HOH . U 9 HOH A 55 298 298 HOH HOH . U 9 HOH A 56 299 299 HOH HOH . U 9 HOH A 57 300 300 HOH HOH . U 9 HOH A 58 301 301 HOH HOH . U 9 HOH A 59 302 302 HOH HOH . U 9 HOH A 60 303 303 HOH HOH . U 9 HOH A 61 304 304 HOH HOH . U 9 HOH A 62 305 305 HOH HOH . U 9 HOH A 63 306 306 HOH HOH . U 9 HOH A 64 307 307 HOH HOH . U 9 HOH A 65 308 308 HOH HOH . U 9 HOH A 66 309 309 HOH HOH . U 9 HOH A 67 310 310 HOH HOH . U 9 HOH A 68 311 311 HOH HOH . U 9 HOH A 69 312 312 HOH HOH . U 9 HOH A 70 313 313 HOH HOH . U 9 HOH A 71 314 314 HOH HOH . U 9 HOH A 72 315 315 HOH HOH . U 9 HOH A 73 316 316 HOH HOH . U 9 HOH A 74 317 317 HOH HOH . U 9 HOH A 75 318 318 HOH HOH . U 9 HOH A 76 319 319 HOH HOH . U 9 HOH A 77 320 320 HOH HOH . U 9 HOH A 78 321 321 HOH HOH . U 9 HOH A 79 322 322 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 C1 LUT . . . O 4 41.31 5.597 7.08 1 31.25 ? C1 LUT 620 A 1 HETATM 2 C C2 LUT . . . O 4 42.518 6.553 7.117 1 31.48 ? C2 LUT 620 A 1 HETATM 3 C C3 LUT . . . O 4 43.689 6.252 8.057 1 30.21 ? C3 LUT 620 A 1 HETATM 4 C C4 LUT . . . O 4 43.523 5.037 8.976 1 28.14 ? C4 LUT 620 A 1 HETATM 5 C C5 LUT . . . O 4 42.491 4.004 8.669 1 24.55 ? C5 LUT 620 A 1 HETATM 6 C C6 LUT . . . O 4 41.447 4.201 7.804 1 28.71 ? C6 LUT 620 A 1 HETATM 7 C C7 LUT . . . O 4 40.434 3.163 7.506 1 29.62 ? C7 LUT 620 A 1 HETATM 8 C C8 LUT . . . O 4 39.307 2.901 8.186 1 32.01 ? C8 LUT 620 A 1 HETATM 9 C C9 LUT . . . O 4 38.318 1.851 7.914 1 32.36 ? C9 LUT 620 A 1 HETATM 10 C C10 LUT . . . O 4 37.164 1.885 8.616 1 34.05 ? C10 LUT 620 A 1 HETATM 11 C C11 LUT . . . O 4 36.023 1.027 8.438 1 32.83 ? C11 LUT 620 A 1 HETATM 12 C C12 LUT . . . O 4 34.878 1.312 9.079 1 30.73 ? C12 LUT 620 A 1 HETATM 13 C C13 LUT . . . O 4 33.569 0.67 8.971 1 28.12 ? C13 LUT 620 A 1 HETATM 14 C C14 LUT . . . O 4 32.563 1.217 9.682 1 26.44 ? C14 LUT 620 A 1 HETATM 15 C C15 LUT . . . O 4 31.19 0.839 9.708 1 29.88 ? C15 LUT 620 A 1 HETATM 16 C C16 LUT . . . O 4 40.923 5.415 5.596 1 33.94 ? C16 LUT 620 A 1 HETATM 17 C C17 LUT . . . O 4 40.2 6.434 7.729 1 27.53 ? C17 LUT 620 A 1 HETATM 18 C C18 LUT . . . O 4 42.84 2.794 9.445 1 32.09 ? C18 LUT 620 A 1 HETATM 19 C C19 LUT . . . O 4 38.596 0.887 6.801 1 34.41 ? C19 LUT 620 A 1 HETATM 20 C C20 LUT . . . O 4 33.418 -0.5 8.045 1 26.88 ? C20 LUT 620 A 1 HETATM 21 O O3 LUT . . . O 4 44.012 7.401 8.824 1 32.14 ? O3 LUT 620 A 1 HETATM 22 C C21 LUT . . . O 4 18.423 0.127 11.595 1 32.74 ? C21 LUT 620 A 1 HETATM 23 C C22 LUT . . . O 4 17.034 -0.55 11.525 1 37.65 ? C22 LUT 620 A 1 HETATM 24 C C23 LUT . . . O 4 16.567 -1.206 12.828 1 39.89 ? C23 LUT 620 A 1 HETATM 25 C C24 LUT . . . O 4 17.713 -1.914 13.577 1 38.09 ? C24 LUT 620 A 1 HETATM 26 C C25 LUT . . . O 4 19.022 -1.704 13.291 1 36.22 ? C25 LUT 620 A 1 HETATM 27 C C26 LUT . . . O 4 19.541 -0.767 12.207 1 33.13 ? C26 LUT 620 A 1 HETATM 28 C C27 LUT . . . O 4 20.739 0.021 12.694 1 34.44 ? C27 LUT 620 A 1 HETATM 29 C C28 LUT . . . O 4 21.969 -0.014 12.136 1 33.12 ? C28 LUT 620 A 1 HETATM 30 C C29 LUT . . . O 4 23.124 0.853 12.465 1 33.51 ? C29 LUT 620 A 1 HETATM 31 C C30 LUT . . . O 4 24.285 0.66 11.8 1 30.55 ? C30 LUT 620 A 1 HETATM 32 C C31 LUT . . . O 4 25.529 1.362 11.994 1 26.84 ? C31 LUT 620 A 1 HETATM 33 C C32 LUT . . . O 4 26.635 1.057 11.285 1 25.79 ? C32 LUT 620 A 1 HETATM 34 C C33 LUT . . . O 4 27.992 1.62 11.376 1 24.14 ? C33 LUT 620 A 1 HETATM 35 C C34 LUT . . . O 4 28.943 1.11 10.565 1 26.44 ? C34 LUT 620 A 1 HETATM 36 C C35 LUT . . . O 4 30.333 1.483 10.505 1 31.52 ? C35 LUT 620 A 1 HETATM 37 C C36 LUT . . . O 4 18.272 1.448 12.411 1 27.92 ? C36 LUT 620 A 1 HETATM 38 C C37 LUT . . . O 4 18.793 0.505 10.153 1 29.2 ? C37 LUT 620 A 1 HETATM 39 C C38 LUT . . . O 4 19.966 -2.494 14.122 1 34.84 ? C38 LUT 620 A 1 HETATM 40 C C39 LUT . . . O 4 22.937 1.885 13.528 1 35.27 ? C39 LUT 620 A 1 HETATM 41 C C40 LUT . . . O 4 28.242 2.679 12.384 1 21.19 ? C40 LUT 620 A 1 HETATM 42 O O23 LUT . . . O 4 15.496 -2.104 12.564 1 39.05 ? O23 LUT 620 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 25 _model_server_stats.element_count 42 #