data_1M54
#
_model_server_result.job_id            uSj3riF81R9Lb-wY3E_Gyw 
_model_server_result.datetime_utc      '2024-11-24 04:55:23' 
_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          1m54 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":1420}' 
#
_entry.id    1M54 
#
_exptl.entry_id    1M54 
_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    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         102.01 
_cell.angle_beta          101.53 
_cell.angle_gamma         112.6 
_cell.entry_id            1M54 
_cell.length_a            85.74 
_cell.length_b            85.626 
_cell.length_c            97.082 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1M54 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 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,B,G,H,I,J,S,T 1 1 
C,D,K,L,M,N,U,V 2 1 
E,F,O,P,Q,R,W,X 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 H N N 
? 3 J N N 
? 3 L N N 
? 3 N N N 
? 3 P N N 
? 3 R 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 A NZ LYS 76 A LYS 119 1_555 G C4A PLP . A PLP 1110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? 
covale ? covale2 B NZ LYS 76 B LYS 119 1_555 I C4A PLP . B PLP 1210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.025 ? 
covale ? covale3 C NZ LYS 76 C LYS 119 1_555 K C4A PLP . C PLP 1310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.05 ? 
covale ? covale4 D NZ LYS 76 D LYS 119 1_555 M C4A PLP . D PLP 1410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? 
covale ? covale5 E NZ LYS 76 E LYS 119 1_555 O C4A PLP . E PLP 1510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? 
covale ? covale6 F NZ LYS 76 F LYS 119 1_555 Q C4A PLP . F PLP 1610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? 
metalc ? metalc1 A SG CYS 9 A CYS 52 1_555 H FE HEM . A HEM 1120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? 
metalc ? metalc2 A NE2 HIS 22 A HIS 65 1_555 H FE HEM . A HEM 1120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc3 B SG CYS 9 B CYS 52 1_555 J FE HEM . B HEM 1220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc4 B NE2 HIS 22 B HIS 65 1_555 J FE HEM . B HEM 1220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
metalc ? metalc5 C SG CYS 9 C CYS 52 1_555 L FE HEM . C HEM 1320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc6 C NE2 HIS 22 C HIS 65 1_555 L FE HEM . C HEM 1320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc7 D SG CYS 9 D CYS 52 1_555 N FE HEM . D HEM 1420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc8 D NE2 HIS 22 D HIS 65 1_555 N FE HEM . D HEM 1420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? 
metalc ? metalc9 E SG CYS 9 E CYS 52 1_555 P FE HEM . E HEM 1520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? 
metalc ? metalc10 E NE2 HIS 22 E HIS 65 1_555 P FE HEM . E HEM 1520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? 
metalc ? metalc11 F SG CYS 9 F CYS 52 1_555 R FE HEM . F HEM 1620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? 
metalc ? metalc12 F NE2 HIS 22 F HIS 65 1_555 R FE HEM . F HEM 1620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
#
_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 
#
_atom_sites.entry_id                     1M54 
_atom_sites.fract_transf_matrix[1][1]    0.011663 
_atom_sites.fract_transf_matrix[1][2]    0.004854 
_atom_sites.fract_transf_matrix[1][3]    0.004117 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01265 
_atom_sites.fract_transf_matrix[2][3]    0.004197 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.011076 
_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
G 2 PLP A 1 1110 1110 PLP PLP . 
H 3 HEM A 1 1120 1120 HEM HEM . 
I 2 PLP B 1 1210 1210 PLP PLP . 
J 3 HEM B 1 1220 1220 HEM HEM . 
K 2 PLP C 1 1310 1310 PLP PLP . 
L 3 HEM C 1 1320 1320 HEM HEM . 
M 2 PLP D 1 1410 1410 PLP PLP . 
N 3 HEM D 1 1420 1420 HEM HEM . 
O 2 PLP E 1 1510 1510 PLP PLP . 
P 3 HEM E 1 1520 1520 HEM HEM . 
Q 2 PLP F 1 1610 1610 PLP PLP . 
R 3 HEM F 1 1620 1620 HEM HEM . 
S 4 HOH A 1 1121 4 HOH HOH . 
S 4 HOH A 2 1122 10 HOH HOH . 
S 4 HOH A 3 1123 25 HOH HOH . 
S 4 HOH A 4 1124 28 HOH HOH . 
S 4 HOH A 5 1125 31 HOH HOH . 
S 4 HOH A 6 1126 38 HOH HOH . 
S 4 HOH A 7 1127 42 HOH HOH . 
S 4 HOH A 8 1128 52 HOH HOH . 
S 4 HOH A 9 1129 53 HOH HOH . 
S 4 HOH A 10 1130 62 HOH HOH . 
S 4 HOH A 11 1131 76 HOH HOH . 
S 4 HOH A 12 1132 87 HOH HOH . 
T 4 HOH B 1 1221 1 HOH HOH . 
T 4 HOH B 2 1222 6 HOH HOH . 
T 4 HOH B 3 1223 7 HOH HOH . 
T 4 HOH B 4 1224 11 HOH HOH . 
T 4 HOH B 5 1225 13 HOH HOH . 
T 4 HOH B 6 1226 30 HOH HOH . 
T 4 HOH B 7 1227 34 HOH HOH . 
T 4 HOH B 8 1228 60 HOH HOH . 
T 4 HOH B 9 1229 66 HOH HOH . 
T 4 HOH B 10 1230 70 HOH HOH . 
T 4 HOH B 11 1231 78 HOH HOH . 
T 4 HOH B 12 1232 89 HOH HOH . 
U 4 HOH C 1 1321 17 HOH HOH . 
U 4 HOH C 2 1322 22 HOH HOH . 
U 4 HOH C 3 1323 27 HOH HOH . 
U 4 HOH C 4 1324 29 HOH HOH . 
U 4 HOH C 5 1325 35 HOH HOH . 
U 4 HOH C 6 1326 37 HOH HOH . 
U 4 HOH C 7 1327 46 HOH HOH . 
U 4 HOH C 8 1328 51 HOH HOH . 
U 4 HOH C 9 1329 63 HOH HOH . 
U 4 HOH C 10 1330 72 HOH HOH . 
U 4 HOH C 11 1331 81 HOH HOH . 
U 4 HOH C 12 1332 91 HOH HOH . 
U 4 HOH C 13 1333 99 HOH HOH . 
U 4 HOH C 14 1334 100 HOH HOH . 
V 4 HOH D 1 1421 2 HOH HOH . 
V 4 HOH D 2 1422 5 HOH HOH . 
V 4 HOH D 3 1423 16 HOH HOH . 
V 4 HOH D 4 1424 21 HOH HOH . 
V 4 HOH D 5 1425 32 HOH HOH . 
V 4 HOH D 6 1426 36 HOH HOH . 
V 4 HOH D 7 1427 43 HOH HOH . 
V 4 HOH D 8 1428 44 HOH HOH . 
V 4 HOH D 9 1429 45 HOH HOH . 
V 4 HOH D 10 1430 50 HOH HOH . 
V 4 HOH D 11 1431 54 HOH HOH . 
V 4 HOH D 12 1432 58 HOH HOH . 
V 4 HOH D 13 1433 59 HOH HOH . 
V 4 HOH D 14 1434 67 HOH HOH . 
V 4 HOH D 15 1435 71 HOH HOH . 
V 4 HOH D 16 1436 74 HOH HOH . 
V 4 HOH D 17 1437 79 HOH HOH . 
V 4 HOH D 18 1438 80 HOH HOH . 
V 4 HOH D 19 1439 82 HOH HOH . 
V 4 HOH D 20 1440 83 HOH HOH . 
V 4 HOH D 21 1441 85 HOH HOH . 
V 4 HOH D 22 1442 90 HOH HOH . 
V 4 HOH D 23 1443 94 HOH HOH . 
V 4 HOH D 24 1444 97 HOH HOH . 
V 4 HOH D 25 1445 98 HOH HOH . 
V 4 HOH D 26 1446 102 HOH HOH . 
W 4 HOH E 1 1521 3 HOH HOH . 
W 4 HOH E 2 1522 8 HOH HOH . 
W 4 HOH E 3 1523 9 HOH HOH . 
W 4 HOH E 4 1524 15 HOH HOH . 
W 4 HOH E 5 1525 19 HOH HOH . 
W 4 HOH E 6 1526 20 HOH HOH . 
W 4 HOH E 7 1527 23 HOH HOH . 
W 4 HOH E 8 1528 26 HOH HOH . 
W 4 HOH E 9 1529 39 HOH HOH . 
W 4 HOH E 10 1530 40 HOH HOH . 
W 4 HOH E 11 1531 48 HOH HOH . 
W 4 HOH E 12 1532 49 HOH HOH . 
W 4 HOH E 13 1533 55 HOH HOH . 
W 4 HOH E 14 1534 61 HOH HOH . 
W 4 HOH E 15 1535 65 HOH HOH . 
W 4 HOH E 16 1536 68 HOH HOH . 
W 4 HOH E 17 1537 75 HOH HOH . 
W 4 HOH E 18 1538 84 HOH HOH . 
W 4 HOH E 19 1539 88 HOH HOH . 
W 4 HOH E 20 1540 93 HOH HOH . 
W 4 HOH E 21 1541 95 HOH HOH . 
W 4 HOH E 22 1542 96 HOH HOH . 
W 4 HOH E 23 1543 101 HOH HOH . 
W 4 HOH E 24 1544 103 HOH HOH . 
X 4 HOH F 1 1621 12 HOH HOH . 
X 4 HOH F 2 1622 14 HOH HOH . 
X 4 HOH F 3 1623 18 HOH HOH . 
X 4 HOH F 4 1624 24 HOH HOH . 
X 4 HOH F 5 1625 33 HOH HOH . 
X 4 HOH F 6 1626 41 HOH HOH . 
X 4 HOH F 7 1627 47 HOH HOH . 
X 4 HOH F 8 1628 56 HOH HOH . 
X 4 HOH F 9 1629 57 HOH HOH . 
X 4 HOH F 10 1630 64 HOH HOH . 
X 4 HOH F 11 1631 69 HOH HOH . 
X 4 HOH F 12 1632 73 HOH HOH . 
X 4 HOH F 13 1633 77 HOH HOH . 
X 4 HOH F 14 1634 86 HOH HOH . 
X 4 HOH F 15 1635 92 HOH HOH . 
X 4 HOH F 16 1636 104 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 . . . N 3 7.997 46.246 51.756 1 31.14 ? CHA HEM 1420 D 1 
HETATM 2 C CHB HEM . . . N 3 10.727 42.601 53.032 1 34.4 ? CHB HEM 1420 D 1 
HETATM 3 C CHC HEM . . . N 3 10.123 40.54 48.759 1 31.21 ? CHC HEM 1420 D 1 
HETATM 4 C CHD HEM . . . N 3 7.334 44.219 47.425 1 32.25 ? CHD HEM 1420 D 1 
HETATM 5 C C1A HEM . . . N 3 8.791 45.45 52.504 1 31.66 ? C1A HEM 1420 D 1 
HETATM 6 C C2A HEM . . . N 3 9.218 45.714 53.862 1 32.01 ? C2A HEM 1420 D 1 
HETATM 7 C C3A HEM . . . N 3 9.99 44.68 54.229 1 33.35 ? C3A HEM 1420 D 1 
HETATM 8 C C4A HEM . . . N 3 10.053 43.763 53.095 1 34.17 ? C4A HEM 1420 D 1 
HETATM 9 C CMA HEM . . . N 3 10.713 44.448 55.587 1 34.4 ? CMA HEM 1420 D 1 
HETATM 10 C CAA HEM . . . N 3 8.82 46.97 54.663 1 31.6 ? CAA HEM 1420 D 1 
HETATM 11 C CBA HEM . . . N 3 7.697 46.792 55.636 1 33.78 ? CBA HEM 1420 D 1 
HETATM 12 C CGA HEM . . . N 3 7.41 48.098 56.342 1 34.69 ? CGA HEM 1420 D 1 
HETATM 13 O O1A HEM . . . N 3 7.829 48.156 57.58 1 35.51 ? O1A HEM 1420 D 1 
HETATM 14 O O2A HEM . . . N 3 6.81 48.994 55.711 1 34.14 ? O2A HEM 1420 D 1 
HETATM 15 C C1B HEM . . . N 3 10.822 41.719 52.005 1 33.29 ? C1B HEM 1420 D 1 
HETATM 16 C C2B HEM . . . N 3 11.606 40.493 52.052 1 33.03 ? C2B HEM 1420 D 1 
HETATM 17 C C3B HEM . . . N 3 11.453 39.881 50.819 1 32.36 ? C3B HEM 1420 D 1 
HETATM 18 C C4B HEM . . . N 3 10.569 40.75 50.057 1 32.26 ? C4B HEM 1420 D 1 
HETATM 19 C CMB HEM . . . N 3 12.423 40.059 53.29 1 34.39 ? CMB HEM 1420 D 1 
HETATM 20 C CAB HEM . . . N 3 12.041 38.541 50.218 1 30.03 ? CAB HEM 1420 D 1 
HETATM 21 C CBB HEM . . . N 3 13.296 37.919 50.865 1 27.1 ? CBB HEM 1420 D 1 
HETATM 22 C C1C HEM . . . N 3 9.299 41.352 48.016 1 30.36 ? C1C HEM 1420 D 1 
HETATM 23 C C2C HEM . . . N 3 8.883 41.046 46.659 1 29.12 ? C2C HEM 1420 D 1 
HETATM 24 C C3C HEM . . . N 3 8.094 42.07 46.266 1 29.9 ? C3C HEM 1420 D 1 
HETATM 25 C C4C HEM . . . N 3 8.028 43.006 47.379 1 31.2 ? C4C HEM 1420 D 1 
HETATM 26 C CMC HEM . . . N 3 9.325 39.75 45.898 1 28.17 ? CMC HEM 1420 D 1 
HETATM 27 C CAC HEM . . . N 3 7.35 42.314 44.92 1 32.27 ? CAC HEM 1420 D 1 
HETATM 28 C CBC HEM . . . N 3 6.395 41.208 44.445 1 30.69 ? CBC HEM 1420 D 1 
HETATM 29 C C1D HEM . . . N 3 7.253 45.131 48.469 1 31.78 ? C1D HEM 1420 D 1 
HETATM 30 C C2D HEM . . . N 3 6.521 46.406 48.482 1 30.96 ? C2D HEM 1420 D 1 
HETATM 31 C C3D HEM . . . N 3 6.705 46.975 49.717 1 31.34 ? C3D HEM 1420 D 1 
HETATM 32 C C4D HEM . . . N 3 7.558 46.052 50.457 1 32.04 ? C4D HEM 1420 D 1 
HETATM 33 C CMD HEM . . . N 3 5.706 46.967 47.303 1 30.35 ? CMD HEM 1420 D 1 
HETATM 34 C CAD HEM . . . N 3 6.134 48.326 50.257 1 31.26 ? CAD HEM 1420 D 1 
HETATM 35 C CBD HEM . . . N 3 7.228 49.32 50.834 1 31.17 ? CBD HEM 1420 D 1 
HETATM 36 C CGD HEM . . . N 3 6.639 50.597 51.397 1 32.31 ? CGD HEM 1420 D 1 
HETATM 37 O O1D HEM . . . N 3 5.66 50.533 52.169 1 31.05 ? O1D HEM 1420 D 1 
HETATM 38 O O2D HEM . . . N 3 7.202 51.661 51.038 1 32.65 ? O2D HEM 1420 D 1 
HETATM 39 N NA HEM . . . N 3 9.311 44.264 52.076 1 33.62 ? NA HEM 1420 D 1 
HETATM 40 N NB HEM . . . N 3 10.207 41.853 50.788 1 32.78 ? NB HEM 1420 D 1 
HETATM 41 N NC HEM . . . N 3 8.763 42.537 48.435 1 32.08 ? NC HEM 1420 D 1 
HETATM 42 N ND HEM . . . N 3 7.888 44.933 49.694 1 32.26 ? ND HEM 1420 D 1 
HETATM 43 FE FE HEM . . . N 3 9.02 43.4 50.232 1 31.61 ? FE HEM 1420 D 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#