data_3L72 # _model_server_result.job_id Vyjurewk2k3vteuRLGeJ9Q _model_server_result.datetime_utc '2024-10-14 05:24:52' _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 3l72 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"RA","auth_seq_id":501}' # _entry.id 3L72 # _exptl.entry_id 3L72 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 17 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _entity.pdbx_number_of_molecules 2 _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 3L72 _cell.length_a 172.614 _cell.length_b 181.548 _cell.length_c 241.033 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3L72 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,SA,TA,UA,VA,WA,XA,YA,ZA,AB _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 17 CA N N ? 17 RA 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 disulf ? disulf1 E SG CYS 144 E CYS 144 1_555 E SG CYS 160 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 H SG CYS 23 H CYS 24 1_555 H SG CYS 67 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 H SG CYS 39 H CYS 40 1_555 H SG CYS 53 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 O SG CYS 144 R CYS 144 1_555 O SG CYS 160 R CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 R SG CYS 23 U CYS 24 1_555 R SG CYS 67 U CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf6 R SG CYS 39 U CYS 40 1_555 R SG CYS 53 U CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 C NE2 HIS 84 C HIS 84 1_555 U FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc2 C NE2 HIS 98 C HIS 98 1_555 V FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc3 C NE2 HIS 183 C HIS 183 1_555 U FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc4 C NE2 HIS 197 C HIS 197 1_555 V FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc5 D NE2 HIS 41 D HIS 41 1_555 CA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc6 D SD MET 160 D MET 160 1_555 CA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc7 E SG CYS 139 E CYS 139 1_555 GA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc8 E ND1 HIS 141 E HIS 141 1_555 GA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc9 E SG CYS 158 E CYS 158 1_555 GA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc10 E ND1 HIS 161 E HIS 161 1_555 GA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc11 M NE2 HIS 84 P HIS 84 1_555 IA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc12 M NE2 HIS 98 P HIS 98 1_555 JA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc13 M NE2 HIS 183 P HIS 183 1_555 IA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc14 M NE2 HIS 197 P HIS 197 1_555 JA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc15 N NE2 HIS 41 Q HIS 41 1_555 RA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc16 N SD MET 160 Q MET 160 1_555 RA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc17 O SG CYS 139 R CYS 139 1_555 VA FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc18 O ND1 HIS 141 R HIS 141 1_555 VA FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc19 O SG CYS 158 R CYS 158 1_555 VA FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc20 O ND1 HIS 161 R HIS 161 1_555 VA FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? # _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 449 n n FE NB HEC sing 450 n n FE NC HEC sing 451 n n FE ND HEC sing 452 n n CHA C1A HEC doub 453 n n CHA C4D HEC sing 454 n n CHA HHA HEC sing 455 n n CHB C4A HEC doub 456 n n CHB C1B HEC sing 457 n n CHB HHB HEC sing 458 n n CHC C4B HEC doub 459 n n CHC C1C HEC sing 460 n n CHC HHC HEC sing 461 n n CHD C4C HEC doub 462 n n CHD C1D HEC sing 463 n n CHD HHD HEC sing 464 n n NA C1A HEC sing 465 n y NA C4A HEC sing 466 n y C1A C2A HEC sing 467 n y C2A C3A HEC doub 468 n y C2A CAA HEC sing 469 n n C3A C4A HEC sing 470 n y C3A CMA HEC sing 471 n n CMA HMA1 HEC sing 472 n n CMA HMA2 HEC sing 473 n n CMA HMA3 HEC sing 474 n n CAA CBA HEC sing 475 n n CAA HAA1 HEC sing 476 n n CAA HAA2 HEC sing 477 n n CBA CGA HEC sing 478 n n CBA HBA1 HEC sing 479 n n CBA HBA2 HEC sing 480 n n CGA O1A HEC doub 481 n n CGA O2A HEC sing 482 n n O2A H2A HEC sing 483 n n NB C1B HEC sing 484 n y NB C4B HEC sing 485 n y C1B C2B HEC doub 486 n y C2B C3B HEC sing 487 n y C2B CMB HEC sing 488 n n C3B C4B HEC sing 489 n y C3B CAB HEC doub 490 e n CMB HMB1 HEC sing 491 n n CMB HMB2 HEC sing 492 n n CMB HMB3 HEC sing 493 n n CAB CBB HEC sing 494 n n CAB HAB HEC sing 495 n n CBB HBB1 HEC sing 496 n n CBB HBB2 HEC sing 497 n n CBB HBB3 HEC sing 498 n n NC C1C HEC sing 499 n y NC C4C HEC sing 500 n y C1C C2C HEC doub 501 n y C2C C3C HEC sing 502 n y C2C CMC HEC sing 503 n n C3C C4C HEC sing 504 n y C3C CAC HEC doub 505 e n CMC HMC1 HEC sing 506 n n CMC HMC2 HEC sing 507 n n CMC HMC3 HEC sing 508 n n CAC CBC HEC sing 509 n n CAC HAC HEC sing 510 n n CBC HBC1 HEC sing 511 n n CBC HBC2 HEC sing 512 n n CBC HBC3 HEC sing 513 n n ND C1D HEC sing 514 n y ND C4D HEC sing 515 n y C1D C2D HEC doub 516 n y C2D C3D HEC sing 517 n y C2D CMD HEC sing 518 n n C3D C4D HEC doub 519 n y C3D CAD HEC sing 520 n n CMD HMD1 HEC sing 521 n n CMD HMD2 HEC sing 522 n n CMD HMD3 HEC sing 523 n n CAD CBD HEC sing 524 n n CAD HAD1 HEC sing 525 n n CAD HAD2 HEC sing 526 n n CBD CGD HEC sing 527 n n CBD HBD1 HEC sing 528 n n CBD HBD2 HEC sing 529 n n CGD O1D HEC doub 530 n n CGD O2D HEC sing 531 n n O2D H2D HEC sing 532 n n # _atom_sites.entry_id 3L72 _atom_sites.fract_transf_matrix[1][1] 0.005793 _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] 0.005508 _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] 0.004149 _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 U 11 HEM C 1 501 501 HEM HEM . V 11 HEM C 1 502 502 HEM HEM . W 12 IKR C 1 2001 2001 IKR IKR . X 13 UQ C 1 2002 2002 UQ UQ . Y 14 CDL C 1 2004 2004 CDL CDL . Z 15 PEE C 1 2007 2007 PEE PEE . AA 15 PEE C 1 2008 2008 PEE PEE . BA 16 GOL C 1 2011 2011 GOL GOL . CA 17 HEC D 1 501 501 HEC HEC . DA 14 CDL D 1 2003 2003 CDL CDL . EA 18 BOG D 1 2009 2009 BOG BOG . FA 18 BOG D 1 2091 2091 BOG BOG . GA 19 FES E 1 501 501 FES FES . HA 15 PEE E 1 2005 2005 PEE PEE . IA 11 HEM P 1 501 501 HEM HEM . JA 11 HEM P 1 502 502 HEM HEM . KA 18 BOG P 1 2010 2010 BOG BOG . LA 12 IKR P 1 3001 3001 IKR IKR . MA 13 UQ P 1 3002 3002 UQ UQ . NA 14 CDL P 1 3004 3004 CDL CDL . OA 15 PEE P 1 3007 3007 PEE PEE . PA 15 PEE P 1 3008 3008 PEE PEE . QA 16 GOL P 1 3011 3011 GOL GOL . RA 17 HEC Q 1 501 501 HEC HEC . SA 14 CDL Q 1 3003 3003 CDL CDL . TA 18 BOG Q 1 3009 3009 BOG BOG . UA 18 BOG Q 1 3091 3091 BOG BOG . VA 19 FES R 1 501 501 FES FES . WA 15 PEE R 1 3005 3005 PEE PEE . XA 20 HOH C 1 381 2 HOH HOH . XA 20 HOH C 2 382 4 HOH HOH . XA 20 HOH C 3 383 108 HOH HOH . XA 20 HOH C 4 384 119 HOH HOH . XA 20 HOH C 5 385 168 HOH HOH . XA 20 HOH C 6 386 222 HOH HOH . XA 20 HOH C 7 1008 1008 HOH HOH . XA 20 HOH C 8 1238 1238 HOH HOH . YA 20 HOH E 1 1289 1289 HOH HOH . ZA 20 HOH P 1 381 1 HOH HOH . ZA 20 HOH P 2 382 6 HOH HOH . ZA 20 HOH P 3 383 28 HOH HOH . ZA 20 HOH P 4 384 35 HOH HOH . ZA 20 HOH P 5 385 109 HOH HOH . ZA 20 HOH P 6 386 214 HOH HOH . ZA 20 HOH P 7 959 959 HOH HOH . ZA 20 HOH P 8 1239 1239 HOH HOH . AB 20 HOH R 1 1230 1230 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 . . . RA 17 37.115 170.524 106.196 1 74.58 ? FE HEC 501 Q 1 HETATM 2 C CHA HEC . . . RA 17 39.532 169.191 104.099 1 71.37 ? CHA HEC 501 Q 1 HETATM 3 C CHB HEC . . . RA 17 37.527 167.878 108.23 1 69.07 ? CHB HEC 501 Q 1 HETATM 4 C CHC HEC . . . RA 17 34.796 171.744 108.313 1 71.09 ? CHC HEC 501 Q 1 HETATM 5 C CHD HEC . . . RA 17 36.875 173.097 104.185 1 72.57 ? CHD HEC 501 Q 1 HETATM 6 N NA HEC . . . RA 17 38.251 168.871 106.139 1 72.14 ? NA HEC 501 Q 1 HETATM 7 C C1A HEC . . . RA 17 39.216 168.463 105.207 1 70.69 ? C1A HEC 501 Q 1 HETATM 8 C C2A HEC . . . RA 17 39.885 167.228 105.623 1 69.63 ? C2A HEC 501 Q 1 HETATM 9 C C3A HEC . . . RA 17 39.221 166.849 106.72 1 70.31 ? C3A HEC 501 Q 1 HETATM 10 C C4A HEC . . . RA 17 38.277 167.876 107.084 1 70.47 ? C4A HEC 501 Q 1 HETATM 11 C CMA HEC . . . RA 17 39.504 165.572 107.493 1 71.96 ? CMA HEC 501 Q 1 HETATM 12 C CAA HEC . . . RA 17 41.166 166.523 105.191 1 68.27 ? CAA HEC 501 Q 1 HETATM 13 C CBA HEC . . . RA 17 41.622 166.599 103.744 1 68.64 ? CBA HEC 501 Q 1 HETATM 14 C CGA HEC . . . RA 17 42.922 165.85 103.504 1 69.15 ? CGA HEC 501 Q 1 HETATM 15 O O1A HEC . . . RA 17 43.365 165.795 102.335 1 69.39 ? O1A HEC 501 Q 1 HETATM 16 O O2A HEC . . . RA 17 43.502 165.317 104.478 1 68.37 ? O2A HEC 501 Q 1 HETATM 17 N NB HEC . . . RA 17 36.32 169.951 107.908 1 70.82 ? NB HEC 501 Q 1 HETATM 18 C C1B HEC . . . RA 17 36.616 168.823 108.606 1 69.08 ? C1B HEC 501 Q 1 HETATM 19 C C2B HEC . . . RA 17 35.781 168.68 109.748 1 68.9 ? C2B HEC 501 Q 1 HETATM 20 C C3B HEC . . . RA 17 34.994 169.735 109.787 1 69.7 ? C3B HEC 501 Q 1 HETATM 21 C C4B HEC . . . RA 17 35.342 170.545 108.649 1 70.08 ? C4B HEC 501 Q 1 HETATM 22 C CMB HEC . . . RA 17 35.782 167.563 110.782 1 68.55 ? CMB HEC 501 Q 1 HETATM 23 C CAB HEC . . . RA 17 33.945 170.144 110.808 1 72.33 ? CAB HEC 501 Q 1 HETATM 24 C CBB HEC . . . RA 17 34.383 170.014 112.262 1 74.12 ? CBB HEC 501 Q 1 HETATM 25 N NC HEC . . . RA 17 36.09 172.118 106.281 1 73.24 ? NC HEC 501 Q 1 HETATM 26 C C1C HEC . . . RA 17 35.137 172.491 107.208 1 72.57 ? C1C HEC 501 Q 1 HETATM 27 C C2C HEC . . . RA 17 34.384 173.641 106.709 1 73.42 ? C2C HEC 501 Q 1 HETATM 28 C C3C HEC . . . RA 17 34.953 173.99 105.539 1 74.84 ? C3C HEC 501 Q 1 HETATM 29 C C4C HEC . . . RA 17 36.077 173.093 105.321 1 73.75 ? C4C HEC 501 Q 1 HETATM 30 C CMC HEC . . . RA 17 33.101 174.288 107.219 1 71.91 ? CMC HEC 501 Q 1 HETATM 31 C CAC HEC . . . RA 17 34.529 174.952 104.422 1 76.98 ? CAC HEC 501 Q 1 HETATM 32 C CBC HEC . . . RA 17 35.004 176.334 104.916 1 76.89 ? CBC HEC 501 Q 1 HETATM 33 N ND HEC . . . RA 17 38.002 171.021 104.5 1 72.39 ? ND HEC 501 Q 1 HETATM 34 C C1D HEC . . . RA 17 37.755 172.138 103.788 1 71.85 ? C1D HEC 501 Q 1 HETATM 35 C C2D HEC . . . RA 17 38.592 172.214 102.621 1 72.22 ? C2D HEC 501 Q 1 HETATM 36 C C3D HEC . . . RA 17 39.412 171.142 102.62 1 72.57 ? C3D HEC 501 Q 1 HETATM 37 C C4D HEC . . . RA 17 38.992 170.385 103.777 1 71.76 ? C4D HEC 501 Q 1 HETATM 38 C CMD HEC . . . RA 17 38.599 173.311 101.561 1 72.11 ? CMD HEC 501 Q 1 HETATM 39 C CAD HEC . . . RA 17 40.496 170.831 101.566 1 73.49 ? CAD HEC 501 Q 1 HETATM 40 C CBD HEC . . . RA 17 41.938 171.141 101.962 1 76.02 ? CBD HEC 501 Q 1 HETATM 41 C CGD HEC . . . RA 17 42.943 170.797 100.864 1 77.69 ? CGD HEC 501 Q 1 HETATM 42 O O1D HEC . . . RA 17 42.847 169.676 100.326 1 78.52 ? O1D HEC 501 Q 1 HETATM 43 O O2D HEC . . . RA 17 43.829 171.63 100.543 1 78 ? O2D HEC 501 Q 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 49 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 43 #