data_5M7F
#
_model_server_result.job_id            NnJRgXIyQMpq2XB6SqYHtA 
_model_server_result.datetime_utc      '2024-12-02 02:17:52' 
_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          5m7f 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    5M7F 
#
_exptl.entry_id    5M7F 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              420.413 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid' 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          95.7 
_cell.angle_gamma         90 
_cell.entry_id            5M7F 
_cell.length_a            70.42 
_cell.length_b            80.95 
_cell.length_c            76.22 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5M7F 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,K 1 1 
B,G,H,I,J,L 2 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
? 2 C N N 
? 2 G 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 SG CYS 265 A CYS 261 1_555 C CHA DPM . A DPM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.776 ? 
covale ? covale2 B SG CYS 265 B CYS 261 1_555 G CHA DPM . B DPM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.805 ? 
#
_chem_comp.formula           'C20 H24 N2 O8' 
_chem_comp.formula_weight    420.413 
_chem_comp.id                DPM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'DIPYRROMETHANE COFACTOR' 
#
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
C1A C2A DPM doub 83 n y 
C1A CHA DPM sing 84 n n 
C1A NA DPM sing 85 n y 
C2A C3A DPM sing 86 n y 
C2A C5A DPM sing 87 n n 
C3A C4A DPM doub 88 n y 
C3A C7A DPM sing 89 n n 
C4A NA DPM sing 90 n y 
C4A CHB DPM sing 91 n n 
C5A C6A DPM sing 92 n n 
C6A O1A DPM doub 93 n n 
C6A O2A DPM sing 94 n n 
C7A C8A DPM sing 95 n n 
C8A C9A DPM sing 96 n n 
C9A O3A DPM doub 97 n n 
C9A O4A DPM sing 98 n n 
C1B C2B DPM doub 99 n y 
C1B CHB DPM sing 100 n n 
C1B NB DPM sing 101 n y 
C2B C3B DPM sing 102 n y 
C2B C5B DPM sing 103 n n 
C3B C4B DPM doub 104 n y 
C3B C7B DPM sing 105 n n 
C4B NB DPM sing 106 n y 
C5B C6B DPM sing 107 n n 
C6B O1B DPM doub 108 n n 
C6B O2B DPM sing 109 n n 
C7B C8B DPM sing 110 n n 
C8B C9B DPM sing 111 n n 
C9B O3B DPM doub 112 n n 
C9B O4B DPM sing 113 n n 
C5A H5A1 DPM sing 114 n n 
C5A H5A2 DPM sing 115 n n 
C7A H7A1 DPM sing 116 n n 
C7A H7A2 DPM sing 117 n n 
C8A H8A1 DPM sing 118 n n 
C8A H8A2 DPM sing 119 n n 
CHA HCA1 DPM sing 120 n n 
CHA HCA2 DPM sing 121 n n 
CHA HCA3 DPM sing 122 n n 
NA H10 DPM sing 123 n n 
O2A HOA2 DPM sing 124 n n 
O4A HOA4 DPM sing 125 n n 
C4B H4B1 DPM sing 126 n n 
C5B H5B1 DPM sing 127 n n 
C5B H5B2 DPM sing 128 n n 
C7B H7B1 DPM sing 129 n n 
C7B H7B2 DPM sing 130 n n 
C8B H8B1 DPM sing 131 n n 
C8B H8B2 DPM sing 132 n n 
CHB HCB1 DPM sing 133 n n 
CHB HCB2 DPM sing 134 n n 
NB H22 DPM sing 135 n n 
O2B HOB2 DPM sing 136 n n 
O4B HOB4 DPM sing 137 n n 
#
_atom_sites.entry_id                     5M7F 
_atom_sites.fract_transf_matrix[1][1]    0.014201 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001417 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012353 
_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]    0.013185 
_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
C 2 DPM A 1 401 500 DPM DPM . 
D 3 SO4 A 1 402 511 SO4 SO4 . 
E 3 SO4 A 1 403 512 SO4 SO4 . 
F 3 SO4 A 1 404 514 SO4 SO4 . 
G 2 DPM B 1 401 500 DPM DPM . 
H 3 SO4 B 1 402 511 SO4 SO4 . 
I 3 SO4 B 1 403 512 SO4 SO4 . 
J 3 SO4 B 1 404 514 SO4 SO4 . 
K 4 HOH A 1 501 826 HOH HOH . 
K 4 HOH A 2 502 824 HOH HOH . 
K 4 HOH A 3 503 802 HOH HOH . 
K 4 HOH A 4 504 825 HOH HOH . 
K 4 HOH A 5 505 831 HOH HOH . 
K 4 HOH A 6 506 812 HOH HOH . 
K 4 HOH A 7 507 820 HOH HOH . 
K 4 HOH A 8 508 827 HOH HOH . 
K 4 HOH A 9 509 805 HOH HOH . 
K 4 HOH A 10 510 814 HOH HOH . 
K 4 HOH A 11 511 829 HOH HOH . 
K 4 HOH A 12 512 828 HOH HOH . 
K 4 HOH A 13 513 810 HOH HOH . 
K 4 HOH A 14 514 816 HOH HOH . 
K 4 HOH A 15 515 809 HOH HOH . 
K 4 HOH A 16 516 804 HOH HOH . 
K 4 HOH A 17 517 818 HOH HOH . 
K 4 HOH A 18 518 801 HOH HOH . 
K 4 HOH A 19 519 817 HOH HOH . 
K 4 HOH A 20 520 806 HOH HOH . 
K 4 HOH A 21 521 832 HOH HOH . 
K 4 HOH A 22 522 811 HOH HOH . 
K 4 HOH A 23 523 803 HOH HOH . 
K 4 HOH A 24 524 819 HOH HOH . 
K 4 HOH A 25 525 807 HOH HOH . 
K 4 HOH A 26 526 815 HOH HOH . 
K 4 HOH A 27 527 823 HOH HOH . 
K 4 HOH A 28 528 821 HOH HOH . 
K 4 HOH A 29 529 808 HOH HOH . 
K 4 HOH A 30 530 822 HOH HOH . 
K 4 HOH A 31 531 813 HOH HOH . 
K 4 HOH A 32 532 830 HOH HOH . 
L 4 HOH B 1 501 835 HOH HOH . 
L 4 HOH B 2 502 802 HOH HOH . 
L 4 HOH B 3 503 805 HOH HOH . 
L 4 HOH B 4 504 836 HOH HOH . 
L 4 HOH B 5 505 840 HOH HOH . 
L 4 HOH B 6 506 807 HOH HOH . 
L 4 HOH B 7 507 804 HOH HOH . 
L 4 HOH B 8 508 806 HOH HOH . 
L 4 HOH B 9 509 803 HOH HOH . 
L 4 HOH B 10 510 838 HOH HOH . 
L 4 HOH B 11 511 842 HOH HOH . 
L 4 HOH B 12 512 837 HOH HOH . 
L 4 HOH B 13 513 839 HOH HOH . 
L 4 HOH B 14 514 808 HOH HOH . 
L 4 HOH B 15 515 801 HOH HOH . 
L 4 HOH B 16 516 834 HOH HOH . 
L 4 HOH B 17 517 809 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 C1A DPM . . . C 2 -0.125 2.22 18.277 1 40.71 ? C1A DPM 401 A 1 
HETATM 2 C C2A DPM . . . C 2 0.868 3.002 17.71 1 41.58 ? C2A DPM 401 A 1 
HETATM 3 C C3A DPM . . . C 2 1.593 2.195 16.831 1 40.88 ? C3A DPM 401 A 1 
HETATM 4 C C4A DPM . . . C 2 1.005 0.937 16.869 1 39.41 ? C4A DPM 401 A 1 
HETATM 5 C C5A DPM . . . C 2 1.125 4.469 17.942 1 38.39 ? C5A DPM 401 A 1 
HETATM 6 C C6A DPM . . . C 2 2.295 4.767 18.844 1 33.26 ? C6A DPM 401 A 1 
HETATM 7 C C7A DPM . . . C 2 2.813 2.661 16.091 1 41.67 ? C7A DPM 401 A 1 
HETATM 8 C C8A DPM . . . C 2 2.479 3.26 14.749 1 46.83 ? C8A DPM 401 A 1 
HETATM 9 C C9A DPM . . . C 2 3.182 2.551 13.629 1 51.12 ? C9A DPM 401 A 1 
HETATM 10 C CHA DPM . . . C 2 -1.16 2.544 19.305 1 43.58 ? CHA DPM 401 A 1 
HETATM 11 N NA DPM . . . C 2 -0.036 0.984 17.744 1 38.88 ? NA DPM 401 A 1 
HETATM 12 O O1A DPM . . . C 2 2.666 5.897 19.122 1 35.52 ? O1A DPM 401 A 1 
HETATM 13 O O2A DPM . . . C 2 2.899 3.708 19.255 1 30.45 ? O2A DPM 401 A 1 
HETATM 14 O O3A DPM . . . C 2 4.14 3.015 13.031 1 51.62 ? O3A DPM 401 A 1 
HETATM 15 O O4A DPM . . . C 2 2.676 1.359 13.403 1 51.49 ? O4A DPM 401 A 1 
HETATM 16 C C1B DPM . . . C 2 1.894 -1.413 17.092 1 47.22 ? C1B DPM 401 A 1 
HETATM 17 C C2B DPM . . . C 2 3.182 -1.783 17.404 1 46.58 ? C2B DPM 401 A 1 
HETATM 18 C C3B DPM . . . C 2 3.094 -2.987 18.209 1 44.86 ? C3B DPM 401 A 1 
HETATM 19 C C4B DPM . . . C 2 1.746 -3.222 18.39 1 45.93 ? C4B DPM 401 A 1 
HETATM 20 C C5B DPM . . . C 2 4.408 -0.922 17.227 1 46.24 ? C5B DPM 401 A 1 
HETATM 21 C C6B DPM . . . C 2 5.229 -1.085 15.98 1 49.41 ? C6B DPM 401 A 1 
HETATM 22 C C7B DPM . . . C 2 4.224 -3.855 18.706 1 44.23 ? C7B DPM 401 A 1 
HETATM 23 C C8B DPM . . . C 2 4.675 -3.5 20.115 1 45 ? C8B DPM 401 A 1 
HETATM 24 C C9B DPM . . . C 2 3.64 -3.766 21.175 1 44.97 ? C9B DPM 401 A 1 
HETATM 25 C CHB DPM . . . C 2 1.387 -0.337 16.177 1 44.92 ? CHB DPM 401 A 1 
HETATM 26 N NB DPM . . . C 2 1.025 -2.268 17.72 1 47.31 ? NB DPM 401 A 1 
HETATM 27 O O1B DPM . . . C 2 6.354 -1.556 15.985 1 50.85 ? O1B DPM 401 A 1 
HETATM 28 O O2B DPM . . . C 2 4.64 -0.593 14.928 1 53.07 ? O2B DPM 401 A 1 
HETATM 29 O O3B DPM . . . C 2 3.065 -4.835 21.285 1 46.4 ? O3B DPM 401 A 1 
HETATM 30 O O4B DPM . . . C 2 3.438 -2.759 21.992 1 40.99 ? O4B DPM 401 A 1 
HETATM 31 H H5A1 DPM . . . C 2 0.227 4.916 18.366 1 39.35 ? H5A1 DPM 401 A 1 
HETATM 32 H H5A2 DPM . . . C 2 1.277 4.971 16.988 1 39.64 ? H5A2 DPM 401 A 1 
HETATM 33 H H7A1 DPM . . . C 2 3.518 1.842 15.963 1 40.8 ? H7A1 DPM 401 A 1 
HETATM 34 H H7A2 DPM . . . C 2 3.368 3.379 16.692 1 41.14 ? H7A2 DPM 401 A 1 
HETATM 35 H H8A1 DPM . . . C 2 1.408 3.206 14.562 1 47.16 ? H8A1 DPM 401 A 1 
HETATM 36 H H8A2 DPM . . . C 2 2.691 4.328 14.753 1 47.22 ? H8A2 DPM 401 A 1 
HETATM 37 H HCA1 DPM . . . C 2 -0.743 3.206 20.062 1 42.79 ? HCA1 DPM 401 A 1 
HETATM 38 H HCA2 DPM . . . C 2 -1.511 1.649 19.817 1 42.56 ? HCA2 DPM 401 A 1 
HETATM 39 H H10 DPM . . . C 2 -0.654 0.21 17.96 1 39.94 ? H10 DPM 401 A 1 
HETATM 40 H HOA2 DPM . . . C 2 3.645 3.899 19.876 1 29.93 ? HOA2 DPM 401 A 1 
HETATM 41 H HOA4 DPM . . . C 2 3.137 0.884 12.662 1 52.05 ? HOA4 DPM 401 A 1 
HETATM 42 H H4B1 DPM . . . C 2 1.251 -4.017 18.944 1 46.32 ? H4B1 DPM 401 A 1 
HETATM 43 H H5B1 DPM . . . C 2 5.069 -1.073 18.077 1 45.49 ? H5B1 DPM 401 A 1 
HETATM 44 H H5B2 DPM . . . C 2 4.12 0.126 17.237 1 46.1 ? H5B2 DPM 401 A 1 
HETATM 45 H H7B1 DPM . . . C 2 5.062 -3.788 18.014 1 44.42 ? H7B1 DPM 401 A 1 
HETATM 46 H H7B2 DPM . . . C 2 3.905 -4.896 18.674 1 43.79 ? H7B2 DPM 401 A 1 
HETATM 47 H H8B1 DPM . . . C 2 5.577 -4.061 20.355 1 44.48 ? H8B1 DPM 401 A 1 
HETATM 48 H H8B2 DPM . . . C 2 4.988 -2.458 20.162 1 45.18 ? H8B2 DPM 401 A 1 
HETATM 49 H HCB1 DPM . . . C 2 2.103 -0.17 15.375 1 45.82 ? HCB1 DPM 401 A 1 
HETATM 50 H HCB2 DPM . . . C 2 0.487 -0.699 15.68 1 45.2 ? HCB2 DPM 401 A 1 
HETATM 51 H H22 DPM . . . C 2 0.014 -2.197 17.681 1 47.6 ? H22 DPM 401 A 1 
HETATM 52 H HOB2 DPM . . . C 2 5.174 -0.697 14.097 1 53.77 ? HOB2 DPM 401 A 1 
HETATM 53 H HOB4 DPM . . . C 2 2.659 -2.863 22.598 1 40.78 ? HOB4 DPM 401 A 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           342 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           53 
#