data_4Y8W
#
_model_server_result.job_id            Xs9smAcUIH-t4RqonX546Q 
_model_server_result.datetime_utc      '2024-11-14 04:28:18' 
_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          4y8w 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":602}' 
#
_entry.id    4Y8W 
#
_exptl.entry_id    4Y8W 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          102.11 
_cell.angle_gamma         90 
_cell.entry_id            4Y8W 
_cell.length_a            150.383 
_cell.length_b            86.86 
_cell.length_c            108.923 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4Y8W 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G,N 1 1 
B,H,I,J,O 2 1 
C,K,L,M,P 3 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 F N N 
? 3 I N N 
? 3 L 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
covale ? covale1 D S SO4 . A SO4 601 1_555 E O2 SO4 . A SO4 602 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? 
covale ? covale2 D S SO4 . A SO4 601 1_555 E O4 SO4 . A SO4 602 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.568 ? 
covale ? covale3 D S SO4 . A SO4 601 1_555 E O3 SO4 . A SO4 602 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.66 ? 
covale ? covale4 D O2 SO4 . A SO4 601 1_555 E S SO4 . A SO4 602 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? 
covale ? covale5 D O3 SO4 . A SO4 601 1_555 E S SO4 . A SO4 602 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.668 ? 
covale ? covale6 D O4 SO4 . A SO4 601 1_555 E S SO4 . A SO4 602 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.578 ? 
metalc ? metalc1 A SG CYS 410 A CYS 429 1_555 F FE HEM . A HEM 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? 
metalc ? metalc2 B SG CYS 410 B CYS 429 1_555 I FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? 
metalc ? metalc3 C SG CYS 410 C CYS 429 1_555 L FE HEM . C HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? 
#
_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                     4Y8W 
_atom_sites.fract_transf_matrix[1][1]    0.00665 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001427 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011513 
_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]    0.00939 
_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
D 2 SO4 A 1 601 3 SO4 SO4 . 
E 2 SO4 A 1 602 4 SO4 SO4 . 
F 3 HEM A 1 603 500 HEM HEM . 
G 4 STR A 1 604 501 STR STR . 
H 2 SO4 B 1 601 2 SO4 SO4 . 
I 3 HEM B 1 602 500 HEM HEM . 
J 4 STR B 1 603 501 STR STR . 
K 2 SO4 C 1 601 1 SO4 SO4 . 
L 3 HEM C 1 602 500 HEM HEM . 
M 4 STR C 1 603 501 STR STR . 
N 5 HOH A 1 701 39 HOH HOH . 
N 5 HOH A 2 702 56 HOH HOH . 
N 5 HOH A 3 703 73 HOH HOH . 
N 5 HOH A 4 704 69 HOH HOH . 
N 5 HOH A 5 705 70 HOH HOH . 
N 5 HOH A 6 706 29 HOH HOH . 
N 5 HOH A 7 707 45 HOH HOH . 
N 5 HOH A 8 708 32 HOH HOH . 
N 5 HOH A 9 709 55 HOH HOH . 
N 5 HOH A 10 710 21 HOH HOH . 
N 5 HOH A 11 711 2 HOH HOH . 
N 5 HOH A 12 712 42 HOH HOH . 
N 5 HOH A 13 713 72 HOH HOH . 
N 5 HOH A 14 714 68 HOH HOH . 
N 5 HOH A 15 715 4 HOH HOH . 
N 5 HOH A 16 716 1 HOH HOH . 
N 5 HOH A 17 717 81 HOH HOH . 
N 5 HOH A 18 718 51 HOH HOH . 
N 5 HOH A 19 719 71 HOH HOH . 
N 5 HOH A 20 720 3 HOH HOH . 
N 5 HOH A 21 721 40 HOH HOH . 
N 5 HOH A 22 722 54 HOH HOH . 
O 5 HOH B 1 701 37 HOH HOH . 
O 5 HOH B 2 702 64 HOH HOH . 
O 5 HOH B 3 703 67 HOH HOH . 
O 5 HOH B 4 704 47 HOH HOH . 
O 5 HOH B 5 705 65 HOH HOH . 
O 5 HOH B 6 706 49 HOH HOH . 
O 5 HOH B 7 707 36 HOH HOH . 
O 5 HOH B 8 708 80 HOH HOH . 
O 5 HOH B 9 709 50 HOH HOH . 
O 5 HOH B 10 710 22 HOH HOH . 
O 5 HOH B 11 711 44 HOH HOH . 
O 5 HOH B 12 712 43 HOH HOH . 
O 5 HOH B 13 713 62 HOH HOH . 
O 5 HOH B 14 714 79 HOH HOH . 
O 5 HOH B 15 715 31 HOH HOH . 
O 5 HOH B 16 716 66 HOH HOH . 
O 5 HOH B 17 717 20 HOH HOH . 
O 5 HOH B 18 718 24 HOH HOH . 
O 5 HOH B 19 719 25 HOH HOH . 
O 5 HOH B 20 720 19 HOH HOH . 
O 5 HOH B 21 721 61 HOH HOH . 
O 5 HOH B 22 722 26 HOH HOH . 
O 5 HOH B 23 723 38 HOH HOH . 
O 5 HOH B 24 724 63 HOH HOH . 
O 5 HOH B 25 725 30 HOH HOH . 
P 5 HOH C 1 701 60 HOH HOH . 
P 5 HOH C 2 702 52 HOH HOH . 
P 5 HOH C 3 703 11 HOH HOH . 
P 5 HOH C 4 704 59 HOH HOH . 
P 5 HOH C 5 705 7 HOH HOH . 
P 5 HOH C 6 706 77 HOH HOH . 
P 5 HOH C 7 707 34 HOH HOH . 
P 5 HOH C 8 708 41 HOH HOH . 
P 5 HOH C 9 709 5 HOH HOH . 
P 5 HOH C 10 710 74 HOH HOH . 
P 5 HOH C 11 711 6 HOH HOH . 
P 5 HOH C 12 712 9 HOH HOH . 
P 5 HOH C 13 713 14 HOH HOH . 
P 5 HOH C 14 714 28 HOH HOH . 
P 5 HOH C 15 715 8 HOH HOH . 
P 5 HOH C 16 716 78 HOH HOH . 
P 5 HOH C 17 717 15 HOH HOH . 
P 5 HOH C 18 718 53 HOH HOH . 
P 5 HOH C 19 719 13 HOH HOH . 
P 5 HOH C 20 720 12 HOH HOH . 
P 5 HOH C 21 721 27 HOH HOH . 
P 5 HOH C 22 722 75 HOH HOH . 
P 5 HOH C 23 723 17 HOH HOH . 
P 5 HOH C 24 724 18 HOH HOH . 
P 5 HOH C 25 725 58 HOH HOH . 
P 5 HOH C 26 726 16 HOH HOH . 
P 5 HOH C 27 727 57 HOH HOH . 
P 5 HOH C 28 728 46 HOH HOH . 
P 5 HOH C 29 729 76 HOH HOH . 
P 5 HOH C 30 730 48 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 . . . L 3 -57.597 14.827 30.761 1 25.66 ? CHA HEM 602 C 1 
HETATM 2 C CHB HEM . . . L 3 -57.478 19.029 28.368 1 25.84 ? CHB HEM 602 C 1 
HETATM 3 C CHC HEM . . . L 3 -58.288 16.645 24.192 1 25.5 ? CHC HEM 602 C 1 
HETATM 4 C CHD HEM . . . L 3 -58.609 12.493 26.635 1 25.7 ? CHD HEM 602 C 1 
HETATM 5 C C1A HEM . . . L 3 -57.488 16.156 30.463 1 25.73 ? C1A HEM 602 C 1 
HETATM 6 C C2A HEM . . . L 3 -57.25 17.165 31.426 1 26.26 ? C2A HEM 602 C 1 
HETATM 7 C C3A HEM . . . L 3 -57.223 18.354 30.747 1 26.14 ? C3A HEM 602 C 1 
HETATM 8 C C4A HEM . . . L 3 -57.429 18.078 29.375 1 26.02 ? C4A HEM 602 C 1 
HETATM 9 C CMA HEM . . . L 3 -57.001 19.727 31.332 1 26.18 ? CMA HEM 602 C 1 
HETATM 10 C CAA HEM . . . L 3 -57.096 16.937 32.926 1 26.24 ? CAA HEM 602 C 1 
HETATM 11 C CBA HEM . . . L 3 -55.719 17.252 33.524 1 26.26 ? CBA HEM 602 C 1 
HETATM 12 C CGA HEM . . . L 3 -55.676 16.916 35.004 1 26.72 ? CGA HEM 602 C 1 
HETATM 13 O O1A HEM . . . L 3 -56.451 16.074 35.523 1 26.63 ? O1A HEM 602 C 1 
HETATM 14 O O2A HEM . . . L 3 -54.839 17.487 35.737 1 26.52 ? O2A HEM 602 C 1 
HETATM 15 C C1B HEM . . . L 3 -57.685 18.731 27.01 1 26.05 ? C1B HEM 602 C 1 
HETATM 16 C C2B HEM . . . L 3 -57.68 19.733 25.978 1 25.99 ? C2B HEM 602 C 1 
HETATM 17 C C3B HEM . . . L 3 -57.913 19.077 24.786 1 25.73 ? C3B HEM 602 C 1 
HETATM 18 C C4B HEM . . . L 3 -58.053 17.64 25.146 1 25.76 ? C4B HEM 602 C 1 
HETATM 19 C CMB HEM . . . L 3 -57.453 21.22 26.193 1 25.59 ? CMB HEM 602 C 1 
HETATM 20 C CAB HEM . . . L 3 -58.013 19.585 23.391 1 25.8 ? CAB HEM 602 C 1 
HETATM 21 C CBB HEM . . . L 3 -57.72 20.822 22.992 1 25.96 ? CBB HEM 602 C 1 
HETATM 22 C C1C HEM . . . L 3 -58.373 15.282 24.468 1 25.51 ? C1C HEM 602 C 1 
HETATM 23 C C2C HEM . . . L 3 -58.4 14.249 23.507 1 25.3 ? C2C HEM 602 C 1 
HETATM 24 C C3C HEM . . . L 3 -58.501 13.045 24.216 1 25.56 ? C3C HEM 602 C 1 
HETATM 25 C C4C HEM . . . L 3 -58.521 13.387 25.604 1 25.72 ? C4C HEM 602 C 1 
HETATM 26 C CMC HEM . . . L 3 -58.334 14.462 22.005 1 24.89 ? CMC HEM 602 C 1 
HETATM 27 C CAC HEM . . . L 3 -58.559 11.644 23.72 1 25.68 ? CAC HEM 602 C 1 
HETATM 28 C CBC HEM . . . L 3 -58.761 11.29 22.455 1 25.74 ? CBC HEM 602 C 1 
HETATM 29 C C1D HEM . . . L 3 -58.334 12.841 27.957 1 25.75 ? C1D HEM 602 C 1 
HETATM 30 C C2D HEM . . . L 3 -58.294 11.808 29.004 1 25.9 ? C2D HEM 602 C 1 
HETATM 31 C C3D HEM . . . L 3 -58.007 12.454 30.153 1 25.76 ? C3D HEM 602 C 1 
HETATM 32 C C4D HEM . . . L 3 -57.882 13.877 29.793 1 25.76 ? C4D HEM 602 C 1 
HETATM 33 C CMD HEM . . . L 3 -58.529 10.323 28.817 1 26.4 ? CMD HEM 602 C 1 
HETATM 34 C CAD HEM . . . L 3 -57.85 11.853 31.535 1 25.53 ? CAD HEM 602 C 1 
HETATM 35 C CBD HEM . . . L 3 -56.38 11.534 31.838 1 25.7 ? CBD HEM 602 C 1 
HETATM 36 C CGD HEM . . . L 3 -56.136 11.26 33.313 1 25.96 ? CGD HEM 602 C 1 
HETATM 37 O O1D HEM . . . L 3 -57.063 11.326 34.154 1 25.68 ? O1D HEM 602 C 1 
HETATM 38 O O2D HEM . . . L 3 -54.984 10.958 33.716 1 26.1 ? O2D HEM 602 C 1 
HETATM 39 N NA HEM . . . L 3 -57.636 16.729 29.223 1 26.01 ? NA HEM 602 C 1 
HETATM 40 N NB HEM . . . L 3 -57.907 17.519 26.478 1 25.95 ? NB HEM 602 C 1 
HETATM 41 N NC HEM . . . L 3 -58.433 14.744 25.728 1 25.91 ? NC HEM 602 C 1 
HETATM 42 N ND HEM . . . L 3 -58.081 14.062 28.473 1 25.76 ? ND HEM 602 C 1 
HETATM 43 FE FE HEM . . . L 3 -58.018 15.706 27.549 1 25.62 ? FE HEM 602 C 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#