data_3GYS
#
_model_server_result.job_id            u46rkUkaQg84V2L1lebvFQ 
_model_server_result.datetime_utc      '2024-12-11 03:07:25' 
_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          3gys 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":148}' 
#
_entry.id    3GYS 
#
_exptl.entry_id    3GYS 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_entity.pdbx_number_of_molecules    8 
_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            3GYS 
_cell.length_a            86.022 
_cell.length_b            96.465 
_cell.length_c            146.345 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3GYS 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
PISA dimeric 2 software_defined_assembly 4 
PISA dimeric 2 software_defined_assembly 5 
PISA dimeric 2 software_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,I,J,K,L,Q,R,S 1 1 
E,F,G,H,M,N,O,P,T,U,V,W 2 1 
A,B,I,J,Q 3 1 
C,D,K,L,R,S 4 1 
E,F,M,N,T,U 5 1 
G,H,O,P,V,W 6 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
? 3 I N N 
? 3 J N N 
? 3 K N N 
? 3 L N N 
? 3 M N N 
? 3 N N N 
? 3 O N N 
? 3 P 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 NE2 HIS 87 A HIS 87 1_555 I FE HEM . A HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? 
metalc ? metalc2 Q O HOH . A HOH 142 1_555 I FE HEM . A HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? 
metalc ? metalc3 B NE2 HIS 91 B HIS 92 1_555 J FE HEM . B HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc4 C NE2 HIS 87 C HIS 87 1_555 K FE HEM . C HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc5 R O HOH . C HOH 142 1_555 K FE HEM . C HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc6 D NE2 HIS 91 D HIS 92 1_555 L FE HEM . D HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc7 E NE2 HIS 87 E HIS 87 1_555 M FE HEM . E HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
metalc ? metalc8 T O HOH . E HOH 142 1_555 M FE HEM . E HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc9 F NE2 HIS 91 F HIS 92 1_555 N FE HEM . F HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc10 U O HOH . F HOH 147 1_555 N FE HEM . F HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc11 G NE2 HIS 87 G HIS 87 1_555 O FE HEM . G HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc12 O FE HEM . G HEM 143 1_555 V O HOH . G HOH 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc13 H NE2 HIS 91 H HIS 92 1_555 P FE HEM . H HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
#
_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                     3GYS 
_atom_sites.fract_transf_matrix[1][1]    0.011625 
_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]    0.010366 
_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]    0.006833 
_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
I 3 HEM A 1 143 143 HEM HEM . 
J 3 HEM B 1 148 148 HEM HEM . 
K 3 HEM C 1 143 143 HEM HEM . 
L 3 HEM D 1 148 148 HEM HEM . 
M 3 HEM E 1 143 143 HEM HEM . 
N 3 HEM F 1 148 148 HEM HEM . 
O 3 HEM G 1 143 143 HEM HEM . 
P 3 HEM H 1 148 148 HEM HEM . 
Q 4 HOH A 1 142 10 HOH HOH . 
R 4 HOH C 1 142 1 HOH HOH . 
S 4 HOH D 1 147 5 HOH HOH . 
T 4 HOH E 1 142 6 HOH HOH . 
U 4 HOH F 1 147 4 HOH HOH . 
U 4 HOH F 2 149 8 HOH HOH . 
V 4 HOH G 1 142 2 HOH HOH . 
V 4 HOH G 2 144 3 HOH HOH . 
W 4 HOH H 1 147 9 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 . . . J 3 17.386 -32.469 20.994 1 46.69 ? CHA HEM 148 B 1 
HETATM 2 C CHB HEM . . . J 3 14.329 -30.857 24.397 1 44.16 ? CHB HEM 148 B 1 
HETATM 3 C CHC HEM . . . J 3 10.399 -31.323 21.539 1 41.91 ? CHC HEM 148 B 1 
HETATM 4 C CHD HEM . . . J 3 13.398 -33.432 18.281 1 45.64 ? CHD HEM 148 B 1 
HETATM 5 C C1A HEM . . . J 3 16.911 -31.996 22.208 1 48.22 ? C1A HEM 148 B 1 
HETATM 6 C C2A HEM . . . J 3 17.681 -31.749 23.418 1 50.12 ? C2A HEM 148 B 1 
HETATM 7 C C3A HEM . . . J 3 16.828 -31.315 24.355 1 47.31 ? C3A HEM 148 B 1 
HETATM 8 C C4A HEM . . . J 3 15.491 -31.252 23.779 1 45.01 ? C4A HEM 148 B 1 
HETATM 9 C CMA HEM . . . J 3 17.254 -30.944 25.797 1 46.05 ? CMA HEM 148 B 1 
HETATM 10 C CAA HEM . . . J 3 19.213 -31.983 23.645 1 55.16 ? CAA HEM 148 B 1 
HETATM 11 C CBA HEM . . . J 3 20.139 -31.12 22.775 1 59.59 ? CBA HEM 148 B 1 
HETATM 12 C CGA HEM . . . J 3 21.563 -31.659 22.715 1 61.15 ? CGA HEM 148 B 1 
HETATM 13 O O1A HEM . . . J 3 21.795 -32.883 22.987 1 61.38 ? O1A HEM 148 B 1 
HETATM 14 O O2A HEM . . . J 3 22.471 -30.839 22.374 1 61.35 ? O2A HEM 148 B 1 
HETATM 15 C C1B HEM . . . J 3 13.028 -30.788 23.92 1 42.88 ? C1B HEM 148 B 1 
HETATM 16 C C2B HEM . . . J 3 11.894 -30.169 24.601 1 41.32 ? C2B HEM 148 B 1 
HETATM 17 C C3B HEM . . . J 3 10.814 -30.298 23.833 1 41.55 ? C3B HEM 148 B 1 
HETATM 18 C C4B HEM . . . J 3 11.209 -30.996 22.62 1 42 ? C4B HEM 148 B 1 
HETATM 19 C CMB HEM . . . J 3 11.935 -29.489 25.988 1 41.43 ? CMB HEM 148 B 1 
HETATM 20 C CAB HEM . . . J 3 9.397 -29.772 24.173 1 43.06 ? CAB HEM 148 B 1 
HETATM 21 C CBB HEM . . . J 3 8.674 -30.247 25.199 1 43.2 ? CBB HEM 148 B 1 
HETATM 22 C C1C HEM . . . J 3 10.825 -32.042 20.42 1 42.87 ? C1C HEM 148 B 1 
HETATM 23 C C2C HEM . . . J 3 10.015 -32.758 19.425 1 42.5 ? C2C HEM 148 B 1 
HETATM 24 C C3C HEM . . . J 3 10.866 -33.32 18.543 1 42.53 ? C3C HEM 148 B 1 
HETATM 25 C C4C HEM . . . J 3 12.237 -33.013 18.926 1 43.98 ? C4C HEM 148 B 1 
HETATM 26 C CMC HEM . . . J 3 8.466 -32.866 19.363 1 40.59 ? CMC HEM 148 B 1 
HETATM 27 C CAC HEM . . . J 3 10.461 -34.166 17.326 1 40.59 ? CAC HEM 148 B 1 
HETATM 28 C CBC HEM . . . J 3 9.46 -33.772 16.538 1 39.07 ? CBC HEM 148 B 1 
HETATM 29 C C1D HEM . . . J 3 14.727 -33.483 18.714 1 44.98 ? C1D HEM 148 B 1 
HETATM 30 C C2D HEM . . . J 3 15.821 -34.233 18.097 1 45.11 ? C2D HEM 148 B 1 
HETATM 31 C C3D HEM . . . J 3 17.065 -33.933 18.942 1 47.66 ? C3D HEM 148 B 1 
HETATM 32 C C4D HEM . . . J 3 16.605 -33.023 19.986 1 46.79 ? C4D HEM 148 B 1 
HETATM 33 C CMD HEM . . . J 3 15.813 -35.167 16.863 1 42.92 ? CMD HEM 148 B 1 
HETATM 34 C CAD HEM . . . J 3 18.51 -34.474 18.697 1 49.13 ? CAD HEM 148 B 1 
HETATM 35 C CBD HEM . . . J 3 18.664 -35.964 18.97 1 51.51 ? CBD HEM 148 B 1 
HETATM 36 C CGD HEM . . . J 3 20.058 -36.385 18.569 1 52.9 ? CGD HEM 148 B 1 
HETATM 37 O O1D HEM . . . J 3 20.968 -36.403 19.439 1 53.53 ? O1D HEM 148 B 1 
HETATM 38 O O2D HEM . . . J 3 20.27 -36.718 17.377 1 54.01 ? O2D HEM 148 B 1 
HETATM 39 N NA HEM . . . J 3 15.586 -31.663 22.48 1 46.11 ? NA HEM 148 B 1 
HETATM 40 N NB HEM . . . J 3 12.572 -31.284 22.72 1 43.26 ? NB HEM 148 B 1 
HETATM 41 N NC HEM . . . J 3 12.17 -32.242 20.078 1 44.47 ? NC HEM 148 B 1 
HETATM 42 N ND HEM . . . J 3 15.236 -32.799 19.811 1 44.93 ? ND HEM 148 B 1 
HETATM 43 FE FE HEM . . . J 3 13.959 -32.148 21.366 1 44.23 ? FE HEM 148 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    42 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#