data_3VRM # _model_server_result.job_id -YBtYdw7iEzuDWLGcn2BlA _model_server_result.datetime_utc '2025-03-30 07:34:25' _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 3vrm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 3VRM # _exptl.entry_id 3VRM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _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 90 _cell.entry_id 3VRM _cell.length_a 61.421 _cell.length_b 105.521 _cell.length_c 141.988 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VRM _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 347 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 347 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id HEM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HEM _struct_conn.ptnr2_auth_seq_id 501 _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 2.378 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C34 H32 Fe N4 O4' _chem_comp.formula_weight 616.487 _chem_comp.id HEM _chem_comp.mon_nstd_flag . _chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms HEME # 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 CHA C1A HEM sing 129 n n CHA C4D HEM doub 130 n n CHA HHA HEM sing 131 n n CHB C4A HEM sing 132 n n CHB C1B HEM doub 133 n n CHB HHB HEM sing 134 n n CHC C4B HEM sing 135 n n CHC C1C HEM doub 136 n n CHC HHC HEM sing 137 n n CHD C4C HEM doub 138 n n CHD C1D HEM sing 139 n n CHD HHD HEM sing 140 n n C1A C2A HEM doub 141 n y C1A NA HEM sing 142 n y C2A C3A HEM sing 143 n y C2A CAA HEM sing 144 n n C3A C4A HEM doub 145 n y C3A CMA HEM sing 146 n n C4A NA HEM sing 147 n y CMA HMA HEM sing 148 n n CMA HMAA HEM sing 149 n n CMA HMAB HEM sing 150 n n CAA CBA HEM sing 151 n n CAA HAA HEM sing 152 n n CAA HAAA HEM sing 153 n n CBA CGA HEM sing 154 n n CBA HBA HEM sing 155 n n CBA HBAA HEM sing 156 n n CGA O1A HEM doub 157 n n CGA O2A HEM sing 158 n n C1B C2B HEM sing 159 n n C1B NB HEM sing 160 n n C2B C3B HEM doub 161 n n C2B CMB HEM sing 162 n n C3B C4B HEM sing 163 n n C3B CAB HEM sing 164 n n C4B NB HEM doub 165 n n CMB HMB HEM sing 166 n n CMB HMBA HEM sing 167 n n CMB HMBB HEM sing 168 n n CAB CBB HEM doub 169 n n CAB HAB HEM sing 170 n n CBB HBB HEM sing 171 n n CBB HBBA HEM sing 172 n n C1C C2C HEM sing 173 n y C1C NC HEM sing 174 n y C2C C3C HEM doub 175 n y C2C CMC HEM sing 176 n n C3C C4C HEM sing 177 n y C3C CAC HEM sing 178 n n C4C NC HEM sing 179 n y CMC HMC HEM sing 180 n n CMC HMCA HEM sing 181 n n CMC HMCB HEM sing 182 n n CAC CBC HEM doub 183 n n CAC HAC HEM sing 184 n n CBC HBC HEM sing 185 n n CBC HBCA HEM sing 186 n n C1D C2D HEM sing 187 n n C1D ND HEM doub 188 n n C2D C3D HEM doub 189 n n C2D CMD HEM sing 190 n n C3D C4D HEM sing 191 n n C3D CAD HEM sing 192 n n C4D ND HEM sing 193 n n CMD HMD HEM sing 194 n n CMD HMDA HEM sing 195 n n CMD HMDB HEM sing 196 n n CAD CBD HEM sing 197 n n CAD HAD HEM sing 198 n n CAD HADA HEM sing 199 n n CBD CGD HEM sing 200 n n CBD HBD HEM sing 201 n n CBD HBDA HEM sing 202 n n CGD O1D HEM doub 203 n n CGD O2D HEM sing 204 n n O2A H2A HEM sing 205 n n O2D H2D HEM sing 206 n n FE NA HEM sing 207 n n FE NB HEM sing 208 n n FE NC HEM sing 209 n n FE ND HEM sing 210 n n # _atom_sites.entry_id 3VRM _atom_sites.fract_transf_matrix[1][1] 0.016281 _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] 0.009477 _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] 0.007043 _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 HEM A 1 501 411 HEM HEM . C 3 VD3 A 1 502 421 VD3 VD3 . D 4 HOH A 1 601 501 HOH HOH . D 4 HOH A 2 602 502 HOH HOH . D 4 HOH A 3 603 503 HOH HOH . D 4 HOH A 4 604 504 HOH HOH . D 4 HOH A 5 605 505 HOH HOH . D 4 HOH A 6 606 506 HOH HOH . D 4 HOH A 7 607 507 HOH HOH . D 4 HOH A 8 608 508 HOH HOH . D 4 HOH A 9 609 509 HOH HOH . D 4 HOH A 10 610 510 HOH HOH . D 4 HOH A 11 611 511 HOH HOH . D 4 HOH A 12 612 512 HOH HOH . D 4 HOH A 13 613 513 HOH HOH . D 4 HOH A 14 614 514 HOH HOH . D 4 HOH A 15 615 515 HOH HOH . D 4 HOH A 16 616 516 HOH HOH . D 4 HOH A 17 617 517 HOH HOH . D 4 HOH A 18 618 518 HOH HOH . D 4 HOH A 19 619 519 HOH HOH . D 4 HOH A 20 620 520 HOH HOH . D 4 HOH A 21 621 521 HOH HOH . D 4 HOH A 22 622 522 HOH HOH . D 4 HOH A 23 623 523 HOH HOH . D 4 HOH A 24 624 524 HOH HOH . D 4 HOH A 25 625 525 HOH HOH . D 4 HOH A 26 626 526 HOH HOH . D 4 HOH A 27 627 527 HOH HOH . D 4 HOH A 28 628 528 HOH HOH . D 4 HOH A 29 629 529 HOH HOH . D 4 HOH A 30 630 530 HOH HOH . D 4 HOH A 31 631 531 HOH HOH . D 4 HOH A 32 632 532 HOH HOH . D 4 HOH A 33 633 533 HOH HOH . D 4 HOH A 34 634 534 HOH HOH . D 4 HOH A 35 635 535 HOH HOH . D 4 HOH A 36 636 536 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 CHA HEM . . . B 2 9.823 21.999 10.912 1 39.97 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . B 2 12.887 23.612 14.54 1 37.51 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . B 2 11.126 28.08 14.066 1 44.86 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . B 2 7.617 26.328 10.909 1 39.41 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . B 2 10.849 22.154 11.922 1 38.24 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . B 2 11.757 21.01 12.166 1 40.52 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . B 2 12.655 21.493 13.237 1 37.97 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . B 2 12.186 22.866 13.512 1 38.12 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . B 2 13.795 20.786 13.914 1 33.79 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . B 2 11.763 19.671 11.445 1 39.19 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . B 2 11.065 18.622 12.312 1 44.28 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . B 2 11.258 17.177 11.822 1 49.7 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . B 2 10.768 16.267 12.541 1 49.68 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . B 2 11.87 16.916 10.74 1 47.93 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . B 2 12.694 25.019 14.731 1 39.87 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . B 2 13.426 25.764 15.78 1 41.56 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . B 2 12.868 27.102 15.607 1 41.51 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . B 2 11.91 26.949 14.516 1 43.66 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . B 2 14.447 25.281 16.753 1 41.1 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . B 2 13.171 28.331 16.364 1 45.84 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . B 2 14.443 28.654 16.577 1 45.52 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . B 2 10.014 27.97 13.139 1 40.77 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . B 2 9.248 29.184 12.737 1 42.23 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . B 2 8.242 28.662 11.806 1 42.71 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . B 2 8.433 27.194 11.73 1 38.47 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . B 2 9.448 30.624 13.1 1 38.09 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . B 2 7.278 29.558 11.131 1 44.51 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . B 2 6.168 29.143 10.565 1 52.84 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . B 2 7.975 24.929 10.628 1 39.4 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . B 2 7.072 24.089 9.797 1 39.87 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . B 2 7.729 22.802 9.82 1 41.85 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . B 2 8.908 23.083 10.645 1 42.27 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . B 2 5.784 24.429 9.102 1 42.34 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . B 2 7.335 21.527 9.128 1 43.81 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . B 2 8.083 21.629 7.812 1 43.74 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . B 2 7.791 20.49 6.896 1 47.67 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . B 2 7.464 19.374 7.387 1 55.26 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . B 2 7.911 20.728 5.671 1 47.96 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . B 2 10.967 23.302 12.817 1 38.81 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . B 2 11.787 25.706 13.999 1 42.72 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . B 2 9.466 26.714 12.651 1 39.87 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . B 2 9.039 24.316 11.188 1 38.67 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . B 2 10.603 25.17 12.334 1 45.57 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 43 #