data_8HPD # _model_server_result.job_id W9ypuyvjLZ-_Cqoa-yqgOg _model_server_result.datetime_utc '2024-11-13 01:29:49' _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 8hpd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","auth_seq_id":309}' # _entry.id 8HPD # _exptl.entry_id 8HPD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 907.472 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CHLOROPHYLL B' _entity.pdbx_number_of_molecules 24 _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 8HPD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8HPD _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,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,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB _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 ? 7 G N N ? 7 H N N ? 7 K N N ? 7 L N N ? 7 M N N ? 7 N N N ? 7 O N N ? 7 T N N ? 7 Z N N ? 7 AA N N ? 7 DA N N ? 7 EA N N ? 7 FA N N ? 7 GA N N ? 7 HA N N ? 7 MA N N ? 7 SA N N ? 7 TA N N ? 7 WA N N ? 7 XA N N ? 7 YA N N ? 7 ZA N N ? 7 AB N N ? 7 FB 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 metalc ? metalc1 A O TRP 37 A TRP 11 1_555 G MG CHL . A CHL 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc2 A O VAL 134 A VAL 108 1_555 K MG CHL . A CHL 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? metalc ? metalc3 A OD1 ASN 198 A ASN 172 1_555 R MG CLA . A CLA 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? metalc ? metalc4 B O TRP 39 B TRP 11 1_555 Z MG CHL . B CHL 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? metalc ? metalc5 B OE2 GLU 81 B GLU 53 1_555 AA MG CHL . B CHL 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc6 B O VAL 136 B VAL 108 1_555 DA MG CHL . B CHL 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? metalc ? metalc7 B OE2 GLU 198 B GLU 170 1_555 IA MG CLA . B CLA 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? metalc ? metalc8 B OD1 ASN 201 B ASN 173 1_555 KA MG CLA . B CLA 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? metalc ? metalc9 C O TRP 41 C TRP 11 1_555 SA MG CHL . C CHL 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.912 ? metalc ? metalc10 C O ILE 138 C ILE 108 1_555 WA MG CHL . C CHL 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? metalc ? metalc11 C OD1 ASN 202 C ASN 172 1_555 DB MG CLA . C CLA 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? # _chem_comp.formula 'C55 H70 Mg N4 O6 2' _chem_comp.formula_weight 907.472 _chem_comp.id CHL _chem_comp.mon_nstd_flag . _chem_comp.name 'CHLOROPHYLL B' _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 MG NA CHL sing 305 n n MG NB CHL sing 306 n n MG NC CHL sing 307 n n MG ND CHL sing 308 n n CHA C1A CHL sing 309 n n CHA C4D CHL doub 310 n n CHA CBD CHL sing 311 n n CHB C4A CHL doub 312 n n CHB C1B CHL sing 313 n n CHC C4B CHL sing 314 n n CHC C1C CHL doub 315 n n CHD C4C CHL sing 316 n n CHD C1D CHL doub 317 n n NA C1A CHL doub 318 n n NA C4A CHL sing 319 n n C1A C2A CHL sing 320 n n C2A C3A CHL sing 321 n n C2A CAA CHL sing 322 n n C3A C4A CHL sing 323 n n C3A CMA CHL sing 324 n n CAA CBA CHL sing 325 n n CBA CGA CHL sing 326 n n CGA O1A CHL doub 327 n n CGA O2A CHL sing 328 n n O2A C1 CHL sing 329 n n NB C1B CHL sing 330 n y NB C4B CHL sing 331 n y C1B C2B CHL doub 332 n y C2B C3B CHL sing 333 n y C2B CMB CHL sing 334 n n C3B C4B CHL doub 335 n y C3B CAB CHL sing 336 n n CAB CBB CHL doub 337 n n NC C1C CHL sing 338 n n NC C4C CHL doub 339 n n C1C C2C CHL sing 340 n n C2C C3C CHL doub 341 n n C2C CMC CHL sing 342 n n C3C C4C CHL sing 343 n n C3C CAC CHL sing 344 n n CMC OMC CHL doub 345 n n CAC CBC CHL sing 346 n n ND C1D CHL sing 347 n n ND C4D CHL sing 348 n n C1D C2D CHL sing 349 n n C2D C3D CHL doub 350 n n C2D CMD CHL sing 351 n n C3D C4D CHL sing 352 n n C3D CAD CHL sing 353 n n CAD OBD CHL doub 354 n n CAD CBD CHL sing 355 n n CBD CGD CHL sing 356 n n CGD O1D CHL doub 357 n n CGD O2D CHL sing 358 n n O2D CED CHL sing 359 n n C1 C2 CHL sing 360 n n C2 C3 CHL doub 361 e n C3 C4 CHL sing 362 n n C3 C5 CHL sing 363 n n C5 C6 CHL sing 364 n n C6 C7 CHL sing 365 n n C7 C8 CHL sing 366 n n C8 C9 CHL sing 367 n n C8 C10 CHL sing 368 n n C10 C11 CHL sing 369 n n C11 C12 CHL sing 370 n n C12 C13 CHL sing 371 n n C13 C14 CHL sing 372 n n C13 C15 CHL sing 373 n n C15 C16 CHL sing 374 n n C16 C17 CHL sing 375 n n C17 C18 CHL sing 376 n n C18 C19 CHL sing 377 n n C18 C20 CHL sing 378 n n CHB H1 CHL sing 379 n n CHC H2 CHL sing 380 n n CHD H3 CHL sing 381 n n CMA H4 CHL sing 382 n n CMA H5 CHL sing 383 n n CMA H6 CHL sing 384 n n CAA H7 CHL sing 385 n n CAA H8 CHL sing 386 n n CBA H9 CHL sing 387 n n CBA H10 CHL sing 388 n n CMB H11 CHL sing 389 n n CMB H12 CHL sing 390 n n CMB H13 CHL sing 391 n n CAB H14 CHL sing 392 n n CBB H15 CHL sing 393 n n CBB H16 CHL sing 394 n n CMC H17 CHL sing 395 n n CAC H18 CHL sing 396 n n CAC H19 CHL sing 397 n n CBC H20 CHL sing 398 n n CBC H21 CHL sing 399 n n CBC H22 CHL sing 400 n n CMD H23 CHL sing 401 n n CMD H24 CHL sing 402 n n CMD H25 CHL sing 403 n n CBD H26 CHL sing 404 n n CED H27 CHL sing 405 n n CED H28 CHL sing 406 n n CED H29 CHL sing 407 n n C1 H30 CHL sing 408 n n C1 H31 CHL sing 409 n n C2 H32 CHL sing 410 n n C4 H33 CHL sing 411 n n C4 H34 CHL sing 412 n n C4 H35 CHL sing 413 n n C5 H36 CHL sing 414 n n C5 H37 CHL sing 415 n n C6 H38 CHL sing 416 n n C6 H39 CHL sing 417 n n C7 H40 CHL sing 418 n n C7 H41 CHL sing 419 n n C8 H42 CHL sing 420 n n C9 H43 CHL sing 421 n n C9 H44 CHL sing 422 n n C9 H45 CHL sing 423 n n C10 H46 CHL sing 424 n n C10 H47 CHL sing 425 n n C11 H48 CHL sing 426 n n C11 H49 CHL sing 427 n n C12 H50 CHL sing 428 n n C12 H51 CHL sing 429 n n C13 H52 CHL sing 430 n n C14 H53 CHL sing 431 n n C14 H54 CHL sing 432 n n C14 H55 CHL sing 433 n n C15 H56 CHL sing 434 n n C16 H57 CHL sing 435 n n C17 H58 CHL sing 436 n n C17 H59 CHL sing 437 n n C18 H60 CHL sing 438 n n C19 H61 CHL sing 439 n n C19 H62 CHL sing 440 n n C19 H63 CHL sing 441 n n C20 H64 CHL sing 442 n n C20 H65 CHL sing 443 n n C20 H66 CHL sing 444 n n C2A H67 CHL sing 445 n n C3A H68 CHL sing 446 n n C15 H69 CHL sing 447 n n C16 H70 CHL sing 448 n n # _atom_sites.entry_id 8HPD _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 0UR A 1 301 520 0UR 0UR . E 5 0IE A 1 302 521 0IE 0IE . F 6 NEX A 1 303 523 NEX NEX . G 7 CHL A 1 304 601 CHL CHL . H 7 CHL A 1 305 602 CHL CHL . I 8 CLA A 1 306 603 CLA CLA . J 8 CLA A 1 307 604 CLA CLA . K 7 CHL A 1 308 605 CHL CHL . L 7 CHL A 1 309 606 CHL CHL . M 7 CHL A 1 310 607 CHL CHL . N 7 CHL A 1 311 608 CHL CHL . O 7 CHL A 1 312 609 CHL CHL . P 8 CLA A 1 313 610 CLA CLA . Q 8 CLA A 1 314 611 CLA CLA . R 8 CLA A 1 315 612 CLA CLA . S 8 CLA A 1 316 613 CLA CLA . T 7 CHL A 1 317 614 CHL CHL . U 9 LHG A 1 318 630 LHG LHG . V 4 0UR B 1 301 520 0UR 0UR . W 5 0IE B 1 302 521 0IE 0IE . X 5 0IE B 1 303 522 0IE 0IE . Y 6 NEX B 1 304 523 NEX NEX . Z 7 CHL B 1 305 601 CHL CHL . AA 7 CHL B 1 306 602 CHL CHL . BA 8 CLA B 1 307 603 CLA CLA . CA 8 CLA B 1 308 604 CLA CLA . DA 7 CHL B 1 309 605 CHL CHL . EA 7 CHL B 1 310 606 CHL CHL . FA 7 CHL B 1 311 607 CHL CHL . GA 7 CHL B 1 312 608 CHL CHL . HA 7 CHL B 1 313 609 CHL CHL . IA 8 CLA B 1 314 610 CLA CLA . JA 8 CLA B 1 315 611 CLA CLA . KA 8 CLA B 1 316 612 CLA CLA . LA 8 CLA B 1 317 613 CLA CLA . MA 7 CHL B 1 318 614 CHL CHL . NA 9 LHG B 1 319 630 LHG LHG . OA 4 0UR C 1 301 520 0UR 0UR . PA 5 0IE C 1 302 521 0IE 0IE . QA 5 0IE C 1 303 522 0IE 0IE . RA 6 NEX C 1 304 523 NEX NEX . SA 7 CHL C 1 305 601 CHL CHL . TA 7 CHL C 1 306 602 CHL CHL . UA 8 CLA C 1 307 603 CLA CLA . VA 8 CLA C 1 308 604 CLA CLA . WA 7 CHL C 1 309 605 CHL CHL . XA 7 CHL C 1 310 606 CHL CHL . YA 7 CHL C 1 311 607 CHL CHL . ZA 7 CHL C 1 312 608 CHL CHL . AB 7 CHL C 1 313 609 CHL CHL . BB 8 CLA C 1 314 610 CLA CLA . CB 8 CLA C 1 315 611 CLA CLA . DB 8 CLA C 1 316 612 CLA CLA . EB 8 CLA C 1 317 613 CLA CLA . FB 7 CHL C 1 318 614 CHL CHL . GB 9 LHG C 1 319 630 LHG LHG . # 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 MG MG CHL . . . DA 7 121.066 97.638 122.594 1 97.39 ? MG CHL 309 B 1 HETATM 2 C CHA CHL . . . DA 7 122.557 96.581 119.537 1 97.39 ? CHA CHL 309 B 1 HETATM 3 C CHB CHL . . . DA 7 118.591 95.311 122.031 1 97.39 ? CHB CHL 309 B 1 HETATM 4 C CHC CHL . . . DA 7 119.385 98.854 125.475 1 97.39 ? CHC CHL 309 B 1 HETATM 5 C CHD CHL . . . DA 7 123.847 99.808 123.316 1 97.39 ? CHD CHL 309 B 1 HETATM 6 N NA CHL . . . DA 7 120.61 96.376 121.122 1 97.39 ? NA CHL 309 B 1 HETATM 7 C C1A CHL . . . DA 7 121.237 96.09 120.025 1 97.39 ? C1A CHL 309 B 1 HETATM 8 C C2A CHL . . . DA 7 120.532 95.144 119.106 1 97.39 ? C2A CHL 309 B 1 HETATM 9 C C3A CHL . . . DA 7 119.194 95.024 119.764 1 97.39 ? C3A CHL 309 B 1 HETATM 10 C C4A CHL . . . DA 7 119.488 95.621 121.097 1 97.39 ? C4A CHL 309 B 1 HETATM 11 C CMA CHL . . . DA 7 118.138 95.849 119.046 1 97.39 ? CMA CHL 309 B 1 HETATM 12 C CAA CHL . . . DA 7 121.241 93.798 119.064 1 97.39 ? CAA CHL 309 B 1 HETATM 13 C CBA CHL . . . DA 7 120.431 92.777 118.274 1 97.39 ? CBA CHL 309 B 1 HETATM 14 N NB CHL . . . DA 7 119.324 97.17 123.56 1 97.39 ? NB CHL 309 B 1 HETATM 15 C C1B CHL . . . DA 7 118.479 96.211 123.181 1 97.39 ? C1B CHL 309 B 1 HETATM 16 C C2B CHL . . . DA 7 117.306 96.112 124.085 1 97.39 ? C2B CHL 309 B 1 HETATM 17 C C3B CHL . . . DA 7 117.547 97.159 125.096 1 97.39 ? C3B CHL 309 B 1 HETATM 18 C C4B CHL . . . DA 7 118.84 97.757 124.666 1 97.39 ? C4B CHL 309 B 1 HETATM 19 C CMB CHL . . . DA 7 116.141 95.163 123.991 1 97.39 ? CMB CHL 309 B 1 HETATM 20 C CAB CHL . . . DA 7 116.529 97.314 126.162 1 97.39 ? CAB CHL 309 B 1 HETATM 21 C CBB CHL . . . DA 7 116.907 97.506 127.412 1 97.39 ? CBB CHL 309 B 1 HETATM 22 N NC CHL . . . DA 7 121.519 99.016 124.063 1 97.39 ? NC CHL 309 B 1 HETATM 23 C C1C CHL . . . DA 7 120.719 99.348 125.102 1 97.39 ? C1C CHL 309 B 1 HETATM 24 C C2C CHL . . . DA 7 121.319 100.376 125.993 1 97.39 ? C2C CHL 309 B 1 HETATM 25 C C3C CHL . . . DA 7 122.618 100.653 125.361 1 97.39 ? C3C CHL 309 B 1 HETATM 26 C C4C CHL . . . DA 7 122.648 99.763 124.177 1 97.39 ? C4C CHL 309 B 1 HETATM 27 C CMC CHL . . . DA 7 120.997 101.131 127.229 1 97.39 ? CMC CHL 309 B 1 HETATM 28 O OMC CHL . . . DA 7 119.967 100.899 127.837 1 97.39 ? OMC CHL 309 B 1 HETATM 29 C CAC CHL . . . DA 7 123.685 101.615 125.815 1 97.39 ? CAC CHL 309 B 1 HETATM 30 C CBC CHL . . . DA 7 124.491 100.964 126.915 1 97.39 ? CBC CHL 309 B 1 HETATM 31 N ND CHL . . . DA 7 122.824 98.149 121.713 1 97.39 ? ND CHL 309 B 1 HETATM 32 C C1D CHL . . . DA 7 123.771 98.983 122.108 1 97.39 ? C1D CHL 309 B 1 HETATM 33 C C2D CHL . . . DA 7 124.816 98.954 121.067 1 97.39 ? C2D CHL 309 B 1 HETATM 34 C C3D CHL . . . DA 7 124.355 98.003 120.03 1 97.39 ? C3D CHL 309 B 1 HETATM 35 C C4D CHL . . . DA 7 123.115 97.545 120.498 1 97.39 ? C4D CHL 309 B 1 HETATM 36 C CMD CHL . . . DA 7 126.143 99.631 120.854 1 97.39 ? CMD CHL 309 B 1 HETATM 37 C CAD CHL . . . DA 7 124.667 97.356 118.726 1 97.39 ? CAD CHL 309 B 1 HETATM 38 O OBD CHL . . . DA 7 125.754 97.615 118.094 1 97.39 ? OBD CHL 309 B 1 HETATM 39 C CBD CHL . . . DA 7 123.528 96.466 118.429 1 97.39 ? CBD CHL 309 B 1 HETATM 40 C CGD CHL . . . DA 7 122.885 96.886 117.142 1 97.39 ? CGD CHL 309 B 1 HETATM 41 O O1D CHL . . . DA 7 122.149 97.858 117.103 1 97.39 ? O1D CHL 309 B 1 HETATM 42 O O2D CHL . . . DA 7 123.133 96.133 115.924 1 97.39 ? O2D CHL 309 B 1 HETATM 43 C CED CHL . . . DA 7 122.148 96.098 114.895 1 97.39 ? CED CHL 309 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #