data_6XVF # _model_server_result.job_id UMBsdXDF3qU1g1BeKFyTRA _model_server_result.datetime_utc '2024-11-27 06:04:15' _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 6xvf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":501}' # _entry.id 6XVF # _exptl.entry_id 6XVF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 19 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _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 6XVF _cell.length_a 209.869 _cell.length_b 209.869 _cell.length_c 342.418 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XVF _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 eicosameric _pdbx_struct_assembly.oligomeric_count 20 _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,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA _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 'crystal symmetry operation' 10_445 -y-1,-x-1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -104.9345 -181.751885 57.069667 # _struct_asym.details ? _struct_asym.entity_id 19 _struct_asym.id Y _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 disulf ? disulf1 E SG CYS 144 E CYS 144 1_555 E SG CYS 160 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 H SG CYS 11 H CYS 24 1_555 H SG CYS 55 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 H SG CYS 27 H CYS 40 1_555 H SG CYS 41 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc1 C NE2 HIS 82 C HIS 83 1_555 P FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc2 C NE2 HIS 96 C HIS 97 1_555 Q FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc3 C NE2 HIS 181 C HIS 182 1_555 P FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc4 C NE2 HIS 195 C HIS 196 1_555 Q FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc5 D NE2 HIS 40 D HIS 41 1_555 Y FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc6 D SD MET 159 D MET 160 1_555 Y FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc7 E SG CYS 158 E CYS 158 1_555 BA FE1 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? # _chem_comp.formula 'C34 H34 Fe N4 O4' _chem_comp.formula_weight 618.503 _chem_comp.id HEC _chem_comp.mon_nstd_flag . _chem_comp.name 'HEME C' _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 FE NA HEC sing 447 n n FE NB HEC sing 448 n n FE NC HEC sing 449 n n FE ND HEC sing 450 n n CHA C1A HEC doub 451 n n CHA C4D HEC sing 452 n n CHA HHA HEC sing 453 n n CHB C4A HEC doub 454 n n CHB C1B HEC sing 455 n n CHB HHB HEC sing 456 n n CHC C4B HEC doub 457 n n CHC C1C HEC sing 458 n n CHC HHC HEC sing 459 n n CHD C4C HEC doub 460 n n CHD C1D HEC sing 461 n n CHD HHD HEC sing 462 n n NA C1A HEC sing 463 n y NA C4A HEC sing 464 n y C1A C2A HEC sing 465 n y C2A C3A HEC doub 466 n y C2A CAA HEC sing 467 n n C3A C4A HEC sing 468 n y C3A CMA HEC sing 469 n n CMA HMA1 HEC sing 470 n n CMA HMA2 HEC sing 471 n n CMA HMA3 HEC sing 472 n n CAA CBA HEC sing 473 n n CAA HAA1 HEC sing 474 n n CAA HAA2 HEC sing 475 n n CBA CGA HEC sing 476 n n CBA HBA1 HEC sing 477 n n CBA HBA2 HEC sing 478 n n CGA O1A HEC doub 479 n n CGA O2A HEC sing 480 n n O2A H2A HEC sing 481 n n NB C1B HEC sing 482 n y NB C4B HEC sing 483 n y C1B C2B HEC doub 484 n y C2B C3B HEC sing 485 n y C2B CMB HEC sing 486 n n C3B C4B HEC sing 487 n y C3B CAB HEC doub 488 e n CMB HMB1 HEC sing 489 n n CMB HMB2 HEC sing 490 n n CMB HMB3 HEC sing 491 n n CAB CBB HEC sing 492 n n CAB HAB HEC sing 493 n n CBB HBB1 HEC sing 494 n n CBB HBB2 HEC sing 495 n n CBB HBB3 HEC sing 496 n n NC C1C HEC sing 497 n y NC C4C HEC sing 498 n y C1C C2C HEC doub 499 n y C2C C3C HEC sing 500 n y C2C CMC HEC sing 501 n n C3C C4C HEC sing 502 n y C3C CAC HEC doub 503 e n CMC HMC1 HEC sing 504 n n CMC HMC2 HEC sing 505 n n CMC HMC3 HEC sing 506 n n CAC CBC HEC sing 507 n n CAC HAC HEC sing 508 n n CBC HBC1 HEC sing 509 n n CBC HBC2 HEC sing 510 n n CBC HBC3 HEC sing 511 n n ND C1D HEC sing 512 n y ND C4D HEC sing 513 n y C1D C2D HEC doub 514 n y C2D C3D HEC sing 515 n y C2D CMD HEC sing 516 n n C3D C4D HEC doub 517 n y C3D CAD HEC sing 518 n n CMD HMD1 HEC sing 519 n n CMD HMD2 HEC sing 520 n n CMD HMD3 HEC sing 521 n n CAD CBD HEC sing 522 n n CAD HAD1 HEC sing 523 n n CAD HAD2 HEC sing 524 n n CBD CGD HEC sing 525 n n CBD HBD1 HEC sing 526 n n CBD HBD2 HEC sing 527 n n CGD O1D HEC doub 528 n n CGD O2D HEC sing 529 n n O2D H2D HEC sing 530 n n # _atom_sites.entry_id 6XVF _atom_sites.fract_transf_matrix[1][1] 0.004765 _atom_sites.fract_transf_matrix[1][2] 0.002751 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005502 _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] 0.00292 _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 K 11 PG4 A 1 501 501 PG4 PG4 . L 12 6PE A 1 502 502 6PE 6PE . M 13 PO4 A 1 503 503 PO4 PO4 . N 14 CDL A 1 504 401 CDL CDL . O 13 PO4 B 1 501 501 PO4 PO4 . P 15 HEM C 1 401 402 HEM HEM . Q 15 HEM C 1 402 403 HEM HEM . R 16 LMT C 1 403 405 LMT LMT . S 11 PG4 C 1 404 406 PG4 PG4 . T 11 PG4 C 1 405 407 PG4 PG4 . U 14 CDL C 1 406 408 CDL CDL . V 17 PEE C 1 407 409 PEE PEE . W 18 JAG C 1 408 404 JAG JAG . X 13 PO4 C 1 409 410 PO4 PO4 . Y 19 HEC D 1 501 501 HEC HEC . Z 13 PO4 D 1 502 502 PO4 PO4 . AA 14 CDL D 1 503 503 CDL CDL . BA 20 FES E 1 201 201 FES FES . CA 21 PX4 E 1 202 202 PX4 PX4 . DA 13 PO4 E 1 203 203 PO4 PO4 . EA 17 PEE E 1 204 204 PEE PEE . FA 14 CDL E 1 205 205 CDL CDL . GA 13 PO4 F 1 501 501 PO4 PO4 . HA 13 PO4 G 1 101 101 PO4 PO4 . IA 13 PO4 G 1 102 102 PO4 PO4 . JA 13 PO4 G 1 103 103 PO4 PO4 . KA 22 HOH A 1 601 504 HOH HOH . KA 22 HOH A 2 602 508 HOH HOH . KA 22 HOH A 3 603 507 HOH HOH . KA 22 HOH A 4 604 505 HOH HOH . KA 22 HOH A 5 605 509 HOH HOH . KA 22 HOH A 6 606 506 HOH HOH . LA 22 HOH B 1 601 502 HOH HOH . LA 22 HOH B 2 602 503 HOH HOH . MA 22 HOH C 1 501 412 HOH HOH . MA 22 HOH C 2 502 414 HOH HOH . MA 22 HOH C 3 503 411 HOH HOH . MA 22 HOH C 4 504 413 HOH HOH . NA 22 HOH D 1 601 505 HOH HOH . NA 22 HOH D 2 602 504 HOH HOH . OA 22 HOH F 1 601 502 HOH HOH . PA 22 HOH G 1 201 104 HOH HOH . QA 22 HOH I 1 101 101 HOH HOH . QA 22 HOH I 2 102 102 HOH HOH . RA 22 HOH J 1 101 101 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 FE FE HEC . . . Y 19 -17.864 -82.601 38.276 1 189.47 ? FE HEC 501 D 1 HETATM 2 C CHA HEC . . . Y 19 -20.231 -82.593 40.826 1 190.67 ? CHA HEC 501 D 1 HETATM 3 C CHB HEC . . . Y 19 -19.382 -79.835 36.877 1 185.53 ? CHB HEC 501 D 1 HETATM 4 C CHC HEC . . . Y 19 -15.2 -82.245 36.129 1 193.38 ? CHC HEC 501 D 1 HETATM 5 C CHD HEC . . . Y 19 -16.496 -85.48 39.605 1 196.13 ? CHD HEC 501 D 1 HETATM 6 N NA HEC . . . Y 19 -19.53 -81.409 38.765 1 188.25 ? NA HEC 501 D 1 HETATM 7 C C1A HEC . . . Y 19 -20.378 -81.536 39.813 1 188.76 ? C1A HEC 501 D 1 HETATM 8 C C2A HEC . . . Y 19 -21.469 -80.527 39.904 1 186.56 ? C2A HEC 501 D 1 HETATM 9 C C3A HEC . . . Y 19 -21.216 -79.698 38.714 1 186.62 ? C3A HEC 501 D 1 HETATM 10 C C4A HEC . . . Y 19 -20.007 -80.331 38.114 1 187.03 ? C4A HEC 501 D 1 HETATM 11 C CMA HEC . . . Y 19 -21.987 -78.493 38.234 1 186.78 ? CMA HEC 501 D 1 HETATM 12 C CAA HEC . . . Y 19 -22.575 -80.416 40.936 1 184.24 ? CAA HEC 501 D 1 HETATM 13 C CBA HEC . . . Y 19 -22.312 -79.393 42.033 1 184.81 ? CBA HEC 501 D 1 HETATM 14 C CGA HEC . . . Y 19 -23.546 -79.313 42.912 1 185.11 ? CGA HEC 501 D 1 HETATM 15 O O1A HEC . . . Y 19 -23.983 -80.346 43.47 1 185.14 ? O1A HEC 501 D 1 HETATM 16 O O2A HEC . . . Y 19 -24.106 -78.206 43.055 1 186.76 ? O2A HEC 501 D 1 HETATM 17 N NB HEC . . . Y 19 -17.367 -81.259 36.737 1 187.66 ? NB HEC 501 D 1 HETATM 18 C C1B HEC . . . Y 19 -18.077 -80.194 36.307 1 186.07 ? C1B HEC 501 D 1 HETATM 19 C C2B HEC . . . Y 19 -17.485 -79.394 35.21 1 185.8 ? C2B HEC 501 D 1 HETATM 20 C C3B HEC . . . Y 19 -16.228 -80.123 34.996 1 187.03 ? C3B HEC 501 D 1 HETATM 21 C C4B HEC . . . Y 19 -16.267 -81.241 35.972 1 188.49 ? C4B HEC 501 D 1 HETATM 22 C CMB HEC . . . Y 19 -18.066 -78.172 34.54 1 184.94 ? CMB HEC 501 D 1 HETATM 23 C CAB HEC . . . Y 19 -15.132 -79.846 34.019 1 187.71 ? CAB HEC 501 D 1 HETATM 24 C CBB HEC . . . Y 19 -15.121 -78.704 33.025 1 186.44 ? CBB HEC 501 D 1 HETATM 25 N NC HEC . . . Y 19 -16.12 -83.697 37.918 1 194.07 ? NC HEC 501 D 1 HETATM 26 C C1C HEC . . . Y 19 -15.139 -83.421 37.03 1 196.15 ? C1C HEC 501 D 1 HETATM 27 C C2C HEC . . . Y 19 -13.989 -84.381 37.036 1 199.35 ? C2C HEC 501 D 1 HETATM 28 C C3C HEC . . . Y 19 -14.406 -85.337 38.092 1 198.85 ? C3C HEC 501 D 1 HETATM 29 C C4C HEC . . . Y 19 -15.709 -84.814 38.555 1 196.43 ? C4C HEC 501 D 1 HETATM 30 C CMC HEC . . . Y 19 -12.756 -84.332 36.163 1 202.4 ? CMC HEC 501 D 1 HETATM 31 C CAC HEC . . . Y 19 -13.758 -86.566 38.646 1 199.76 ? CAC HEC 501 D 1 HETATM 32 C CBC HEC . . . Y 19 -12.43 -87.145 38.214 1 202.55 ? CBC HEC 501 D 1 HETATM 33 N ND HEC . . . Y 19 -18.291 -83.834 39.934 1 191.33 ? ND HEC 501 D 1 HETATM 34 C C1D HEC . . . Y 19 -17.653 -84.948 40.338 1 194.03 ? C1D HEC 501 D 1 HETATM 35 C C2D HEC . . . Y 19 -18.198 -85.608 41.561 1 194.62 ? C2D HEC 501 D 1 HETATM 36 C C3D HEC . . . Y 19 -19.327 -84.742 41.931 1 192.54 ? C3D HEC 501 D 1 HETATM 37 C C4D HEC . . . Y 19 -19.267 -83.702 40.863 1 191.55 ? C4D HEC 501 D 1 HETATM 38 C CMD HEC . . . Y 19 -17.728 -86.864 42.253 1 197.26 ? CMD HEC 501 D 1 HETATM 39 C CAD HEC . . . Y 19 -20.285 -84.883 43.102 1 191.58 ? CAD HEC 501 D 1 HETATM 40 C CBD HEC . . . Y 19 -19.796 -83.989 44.247 1 192.94 ? CBD HEC 501 D 1 HETATM 41 C CGD HEC . . . Y 19 -20.577 -84.124 45.548 1 192.6 ? CGD HEC 501 D 1 HETATM 42 O O1D HEC . . . Y 19 -20.004 -83.803 46.613 1 191.5 ? O1D HEC 501 D 1 HETATM 43 O O2D HEC . . . Y 19 -21.759 -84.532 45.553 1 192.12 ? O2D HEC 501 D 1 # _model_server_stats.io_time_ms 79 _model_server_stats.parse_time_ms 66 _model_server_stats.create_model_time_ms 76 _model_server_stats.query_time_ms 828 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 43 #