data_5GNL
#
_model_server_result.job_id            NWvAB9h4xn_koYeu2LuBmw 
_model_server_result.datetime_utc      '2024-11-18 06:30:39' 
_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          5gnl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":501}' 
#
_entry.id    5GNL 
#
_exptl.entry_id    5GNL 
_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         120 
_cell.entry_id            5GNL 
_cell.length_a            61.67 
_cell.length_b            61.67 
_cell.length_c            98.166 
_cell.Z_PDB               3 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5GNL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        144 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31' 
#
_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 
_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 
#
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 SG CYS 347 A CYS 347 1_555 B FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? 
metalc ? metalc2 B FE HEM . A HEM 501 1_555 D O HOH . A HOH 665 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? 
#
_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                     5GNL 
_atom_sites.fract_transf_matrix[1][1]    0.016215 
_atom_sites.fract_transf_matrix[1][2]    0.009362 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018724 
_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]    0.010187 
_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 1 501 412 HEM HEM . 
C 3 PG0 A 1 502 420 PG0 PG0 . 
D 4 HOH A 1 601 43 HOH HOH . 
D 4 HOH A 2 602 76 HOH HOH . 
D 4 HOH A 3 603 96 HOH HOH . 
D 4 HOH A 4 604 78 HOH HOH . 
D 4 HOH A 5 605 117 HOH HOH . 
D 4 HOH A 6 606 83 HOH HOH . 
D 4 HOH A 7 607 8 HOH HOH . 
D 4 HOH A 8 608 9 HOH HOH . 
D 4 HOH A 9 609 12 HOH HOH . 
D 4 HOH A 10 610 66 HOH HOH . 
D 4 HOH A 11 611 19 HOH HOH . 
D 4 HOH A 12 612 20 HOH HOH . 
D 4 HOH A 13 613 48 HOH HOH . 
D 4 HOH A 14 614 7 HOH HOH . 
D 4 HOH A 15 615 91 HOH HOH . 
D 4 HOH A 16 616 75 HOH HOH . 
D 4 HOH A 17 617 69 HOH HOH . 
D 4 HOH A 18 618 72 HOH HOH . 
D 4 HOH A 19 619 29 HOH HOH . 
D 4 HOH A 20 620 22 HOH HOH . 
D 4 HOH A 21 621 28 HOH HOH . 
D 4 HOH A 22 622 85 HOH HOH . 
D 4 HOH A 23 623 88 HOH HOH . 
D 4 HOH A 24 624 55 HOH HOH . 
D 4 HOH A 25 625 70 HOH HOH . 
D 4 HOH A 26 626 36 HOH HOH . 
D 4 HOH A 27 627 79 HOH HOH . 
D 4 HOH A 28 628 31 HOH HOH . 
D 4 HOH A 29 629 49 HOH HOH . 
D 4 HOH A 30 630 33 HOH HOH . 
D 4 HOH A 31 631 2 HOH HOH . 
D 4 HOH A 32 632 27 HOH HOH . 
D 4 HOH A 33 633 56 HOH HOH . 
D 4 HOH A 34 634 64 HOH HOH . 
D 4 HOH A 35 635 5 HOH HOH . 
D 4 HOH A 36 636 65 HOH HOH . 
D 4 HOH A 37 637 26 HOH HOH . 
D 4 HOH A 38 638 35 HOH HOH . 
D 4 HOH A 39 639 4 HOH HOH . 
D 4 HOH A 40 640 57 HOH HOH . 
D 4 HOH A 41 641 73 HOH HOH . 
D 4 HOH A 42 642 32 HOH HOH . 
D 4 HOH A 43 643 1 HOH HOH . 
D 4 HOH A 44 644 84 HOH HOH . 
D 4 HOH A 45 645 108 HOH HOH . 
D 4 HOH A 46 646 3 HOH HOH . 
D 4 HOH A 47 647 54 HOH HOH . 
D 4 HOH A 48 648 115 HOH HOH . 
D 4 HOH A 49 649 30 HOH HOH . 
D 4 HOH A 50 650 45 HOH HOH . 
D 4 HOH A 51 651 11 HOH HOH . 
D 4 HOH A 52 652 38 HOH HOH . 
D 4 HOH A 53 653 40 HOH HOH . 
D 4 HOH A 54 654 95 HOH HOH . 
D 4 HOH A 55 655 104 HOH HOH . 
D 4 HOH A 56 656 110 HOH HOH . 
D 4 HOH A 57 657 15 HOH HOH . 
D 4 HOH A 58 658 60 HOH HOH . 
D 4 HOH A 59 659 34 HOH HOH . 
D 4 HOH A 60 660 21 HOH HOH . 
D 4 HOH A 61 661 39 HOH HOH . 
D 4 HOH A 62 662 92 HOH HOH . 
D 4 HOH A 63 663 98 HOH HOH . 
D 4 HOH A 64 664 24 HOH HOH . 
D 4 HOH A 65 665 13 HOH HOH . 
D 4 HOH A 66 666 114 HOH HOH . 
D 4 HOH A 67 667 47 HOH HOH . 
D 4 HOH A 68 668 102 HOH HOH . 
D 4 HOH A 69 669 52 HOH HOH . 
D 4 HOH A 70 670 17 HOH HOH . 
D 4 HOH A 71 671 44 HOH HOH . 
D 4 HOH A 72 672 74 HOH HOH . 
D 4 HOH A 73 673 41 HOH HOH . 
D 4 HOH A 74 674 46 HOH HOH . 
D 4 HOH A 75 675 105 HOH HOH . 
D 4 HOH A 76 676 42 HOH HOH . 
D 4 HOH A 77 677 100 HOH HOH . 
D 4 HOH A 78 678 81 HOH HOH . 
D 4 HOH A 79 679 77 HOH HOH . 
D 4 HOH A 80 680 93 HOH HOH . 
D 4 HOH A 81 681 16 HOH HOH . 
D 4 HOH A 82 682 58 HOH HOH . 
D 4 HOH A 83 683 10 HOH HOH . 
D 4 HOH A 84 684 99 HOH HOH . 
D 4 HOH A 85 685 71 HOH HOH . 
D 4 HOH A 86 686 111 HOH HOH . 
D 4 HOH A 87 687 107 HOH HOH . 
D 4 HOH A 88 688 37 HOH HOH . 
D 4 HOH A 89 689 67 HOH HOH . 
D 4 HOH A 90 690 62 HOH HOH . 
D 4 HOH A 91 691 109 HOH HOH . 
D 4 HOH A 92 692 112 HOH HOH . 
D 4 HOH A 93 693 23 HOH HOH . 
D 4 HOH A 94 694 14 HOH HOH . 
D 4 HOH A 95 695 50 HOH HOH . 
D 4 HOH A 96 696 6 HOH HOH . 
D 4 HOH A 97 697 61 HOH HOH . 
D 4 HOH A 98 698 103 HOH HOH . 
D 4 HOH A 99 699 53 HOH HOH . 
D 4 HOH A 100 700 25 HOH HOH . 
D 4 HOH A 101 701 51 HOH HOH . 
D 4 HOH A 102 702 89 HOH HOH . 
D 4 HOH A 103 703 18 HOH HOH . 
D 4 HOH A 104 704 101 HOH HOH . 
D 4 HOH A 105 705 80 HOH HOH . 
D 4 HOH A 106 706 106 HOH HOH . 
D 4 HOH A 107 707 86 HOH HOH . 
D 4 HOH A 108 708 68 HOH HOH . 
D 4 HOH A 109 709 94 HOH HOH . 
D 4 HOH A 110 710 59 HOH HOH . 
D 4 HOH A 111 711 87 HOH HOH . 
D 4 HOH A 112 712 82 HOH HOH . 
D 4 HOH A 113 713 63 HOH HOH . 
D 4 HOH A 114 714 97 HOH HOH . 
D 4 HOH A 115 715 116 HOH HOH . 
D 4 HOH A 116 716 90 HOH HOH . 
D 4 HOH A 117 717 113 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 3.793 6.934 3.996 1 27.17 ? CHA HEM 501 A 1 
HETATM 2 C CHB HEM . . . B 2 -0.755 7.523 2.467 1 26.89 ? CHB HEM 501 A 1 
HETATM 3 C CHC HEM . . . B 2 -0.574 12.223 3.824 1 27.8 ? CHC HEM 501 A 1 
HETATM 4 C CHD HEM . . . B 2 4.049 11.654 5.061 1 28.61 ? CHD HEM 501 A 1 
HETATM 5 C C1A HEM . . . B 2 2.529 6.687 3.514 1 27.79 ? C1A HEM 501 A 1 
HETATM 6 C C2A HEM . . . B 2 2.054 5.409 3.067 1 28.54 ? C2A HEM 501 A 1 
HETATM 7 C C3A HEM . . . B 2 0.772 5.581 2.639 1 28.07 ? C3A HEM 501 A 1 
HETATM 8 C C4A HEM . . . B 2 0.46 6.96 2.816 1 27.88 ? C4A HEM 501 A 1 
HETATM 9 C CMA HEM . . . B 2 -0.187 4.549 2.06 1 26.14 ? CMA HEM 501 A 1 
HETATM 10 C CAA HEM . . . B 2 2.835 4.097 3.117 1 29.53 ? CAA HEM 501 A 1 
HETATM 11 C CBA HEM . . . B 2 3.753 3.875 1.916 1 31.21 ? CBA HEM 501 A 1 
HETATM 12 C CGA HEM . . . B 2 4.318 2.462 1.871 1 33.6 ? CGA HEM 501 A 1 
HETATM 13 O O1A HEM . . . B 2 4.085 1.612 2.748 1 30 ? O1A HEM 501 A 1 
HETATM 14 O O2A HEM . . . B 2 5.047 2.114 0.921 1 34.89 ? O2A HEM 501 A 1 
HETATM 15 C C1B HEM . . . B 2 -1.095 8.872 2.69 1 28.11 ? C1B HEM 501 A 1 
HETATM 16 C C2B HEM . . . B 2 -2.368 9.42 2.365 1 26.84 ? C2B HEM 501 A 1 
HETATM 17 C C3B HEM . . . B 2 -2.343 10.749 2.759 1 28.32 ? C3B HEM 501 A 1 
HETATM 18 C C4B HEM . . . B 2 -0.989 10.988 3.301 1 27.83 ? C4B HEM 501 A 1 
HETATM 19 C CMB HEM . . . B 2 -3.537 8.681 1.754 1 26.79 ? CMB HEM 501 A 1 
HETATM 20 C CAB HEM . . . B 2 -3.384 11.812 2.637 1 28.47 ? CAB HEM 501 A 1 
HETATM 21 C CBB HEM . . . B 2 -4.698 11.624 2.699 1 29.43 ? CBB HEM 501 A 1 
HETATM 22 C C1C HEM . . . B 2 0.694 12.501 4.335 1 28.67 ? C1C HEM 501 A 1 
HETATM 23 C C2C HEM . . . B 2 1.122 13.74 4.874 1 29.22 ? C2C HEM 501 A 1 
HETATM 24 C C3C HEM . . . B 2 2.463 13.578 5.222 1 31.18 ? C3C HEM 501 A 1 
HETATM 25 C C4C HEM . . . B 2 2.819 12.223 4.885 1 29.85 ? C4C HEM 501 A 1 
HETATM 26 C CMC HEM . . . B 2 0.245 14.973 5.029 1 30 ? CMC HEM 501 A 1 
HETATM 27 C CAC HEM . . . B 2 3.403 14.559 5.838 1 33.93 ? CAC HEM 501 A 1 
HETATM 28 C CBC HEM . . . B 2 3.002 15.669 6.464 1 36.69 ? CBC HEM 501 A 1 
HETATM 29 C C1D HEM . . . B 2 4.317 10.309 4.833 1 29.06 ? C1D HEM 501 A 1 
HETATM 30 C C2D HEM . . . B 2 5.67 9.771 5.079 1 28.23 ? C2D HEM 501 A 1 
HETATM 31 C C3D HEM . . . B 2 5.603 8.458 4.792 1 26.83 ? C3D HEM 501 A 1 
HETATM 32 C C4D HEM . . . B 2 4.215 8.211 4.35 1 27.25 ? C4D HEM 501 A 1 
HETATM 33 C CMD HEM . . . B 2 6.874 10.551 5.568 1 28.48 ? CMD HEM 501 A 1 
HETATM 34 C CAD HEM . . . B 2 6.735 7.45 4.874 1 28.2 ? CAD HEM 501 A 1 
HETATM 35 C CBD HEM . . . B 2 6.709 6.629 6.17 1 27.43 ? CBD HEM 501 A 1 
HETATM 36 C CGD HEM . . . B 2 7.894 5.696 6.244 1 28.88 ? CGD HEM 501 A 1 
HETATM 37 O O1D HEM . . . B 2 8.483 5.32 5.188 1 30.22 ? O1D HEM 501 A 1 
HETATM 38 O O2D HEM . . . B 2 8.299 5.286 7.361 1 28.87 ? O2D HEM 501 A 1 
HETATM 39 N NA HEM . . . B 2 1.54 7.621 3.354 1 27.92 ? NA HEM 501 A 1 
HETATM 40 N NB HEM . . . B 2 -0.327 9.826 3.248 1 26.93 ? NB HEM 501 A 1 
HETATM 41 N NC HEM . . . B 2 1.724 11.606 4.377 1 28.54 ? NC HEM 501 A 1 
HETATM 42 N ND HEM . . . B 2 3.458 9.336 4.431 1 29.06 ? ND HEM 501 A 1 
HETATM 43 FE FE HEM . . . B 2 1.637 9.563 3.886 1 29.62 ? FE HEM 501 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#