data_5M7F
#
_model_server_result.job_id            c-TJY6mWI9uc9zexY1Gw4g 
_model_server_result.datetime_utc      '2024-12-02 02:23:07' 
_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":"G","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 . . . G 2 -15.103 10.746 0.058 1 51.57 ? C1A DPM 401 B 1 
HETATM 2 C C2A DPM . . . G 2 -14.296 9.985 -0.773 1 53.19 ? C2A DPM 401 B 1 
HETATM 3 C C3A DPM . . . G 2 -13.308 10.84 -1.313 1 54.58 ? C3A DPM 401 B 1 
HETATM 4 C C4A DPM . . . G 2 -13.528 12.094 -0.761 1 51.39 ? C4A DPM 401 B 1 
HETATM 5 C C5A DPM . . . G 2 -14.434 8.518 -1.084 1 56.05 ? C5A DPM 401 B 1 
HETATM 6 C C6A DPM . . . G 2 -15.463 8.241 -2.148 1 56.76 ? C6A DPM 401 B 1 
HETATM 7 C C7A DPM . . . G 2 -12.377 10.489 -2.443 1 56.87 ? C7A DPM 401 B 1 
HETATM 8 C C8A DPM . . . G 2 -11.034 9.875 -2.062 1 59.26 ? C8A DPM 401 B 1 
HETATM 9 C C9A DPM . . . G 2 -10.181 9.528 -3.255 1 61.72 ? C9A DPM 401 B 1 
HETATM 10 C CHA DPM . . . G 2 -16.353 10.394 0.806 1 55.28 ? CHA DPM 401 B 1 
HETATM 11 N NA DPM . . . G 2 -14.614 12.008 0.076 1 48.9 ? NA DPM 401 B 1 
HETATM 12 O O1A DPM . . . G 2 -15.93 7.133 -2.334 1 57.51 ? O1A DPM 401 B 1 
HETATM 13 O O2A DPM . . . G 2 -15.802 9.304 -2.838 1 55.53 ? O2A DPM 401 B 1 
HETATM 14 O O3A DPM . . . G 2 -9.582 8.485 -3.365 1 64.46 ? O3A DPM 401 B 1 
HETATM 15 O O4A DPM . . . G 2 -10.149 10.44 -4.188 1 61.22 ? O4A DPM 401 B 1 
HETATM 16 C C1B DPM . . . G 2 -13.653 14.464 -1.653 1 47.04 ? C1B DPM 401 B 1 
HETATM 17 C C2B DPM . . . G 2 -13.512 15.077 -2.87 1 47.37 ? C2B DPM 401 B 1 
HETATM 18 C C3B DPM . . . G 2 -14.53 16.106 -2.95 1 48.78 ? C3B DPM 401 B 1 
HETATM 19 C C4B DPM . . . G 2 -15.227 16.038 -1.758 1 45.92 ? C4B DPM 401 B 1 
HETATM 20 C C5B DPM . . . G 2 -12.417 14.808 -3.869 1 46.73 ? C5B DPM 401 B 1 
HETATM 21 C C6B DPM . . . G 2 -12.608 13.627 -4.783 1 45.28 ? C6B DPM 401 B 1 
HETATM 22 C C7B DPM . . . G 2 -14.73 17.107 -4.064 1 49.23 ? C7B DPM 401 B 1 
HETATM 23 C C8B DPM . . . G 2 -15.935 16.837 -4.962 1 48.37 ? C8B DPM 401 B 1 
HETATM 24 C C9B DPM . . . G 2 -17.251 16.73 -4.241 1 46.83 ? C9B DPM 401 B 1 
HETATM 25 C CHB DPM . . . G 2 -12.822 13.393 -1.009 1 49.53 ? CHB DPM 401 B 1 
HETATM 26 N NB DPM . . . G 2 -14.697 15.048 -0.981 1 46.2 ? NB DPM 401 B 1 
HETATM 27 O O1B DPM . . . G 2 -13.434 12.77 -4.63 1 43.89 ? O1B DPM 401 B 1 
HETATM 28 O O2B DPM . . . G 2 -11.783 13.628 -5.761 1 47.8 ? O2B DPM 401 B 1 
HETATM 29 O O3B DPM . . . G 2 -17.979 15.798 -4.403 1 42.09 ? O3B DPM 401 B 1 
HETATM 30 O O4B DPM . . . G 2 -17.579 17.74 -3.474 1 51.29 ? O4B DPM 401 B 1 
HETATM 31 H H5A1 DPM . . . G 2 -14.722 8.002 -0.169 1 56.59 ? H5A1 DPM 401 B 1 
HETATM 32 H H5A2 DPM . . . G 2 -13.479 8.085 -1.377 1 57.03 ? H5A2 DPM 401 B 1 
HETATM 33 H H7A1 DPM . . . G 2 -12.188 11.38 -3.037 1 56.71 ? H7A1 DPM 401 B 1 
HETATM 34 H H7A2 DPM . . . G 2 -12.91 9.824 -3.121 1 56.24 ? H7A2 DPM 401 B 1 
HETATM 35 H H8A1 DPM . . . G 2 -10.471 10.572 -1.443 1 59.67 ? H8A1 DPM 401 B 1 
HETATM 36 H H8A2 DPM . . . G 2 -11.197 9.01 -1.42 1 59.45 ? H8A2 DPM 401 B 1 
HETATM 37 H HCA1 DPM . . . G 2 -16.976 11.28 0.918 1 54.64 ? HCA1 DPM 401 B 1 
HETATM 38 H HCA2 DPM . . . G 2 -16.944 9.649 0.276 1 55.09 ? HCA2 DPM 401 B 1 
HETATM 39 H H10 DPM . . . G 2 -14.99 12.757 0.646 1 48.27 ? H10 DPM 401 B 1 
HETATM 40 H HOA2 DPM . . . G 2 -16.49 9.102 -3.522 1 54.83 ? HOA2 DPM 401 B 1 
HETATM 41 H HOA4 DPM . . . G 2 -9.579 10.168 -4.955 1 61.81 ? HOA4 DPM 401 B 1 
HETATM 42 H H4B1 DPM . . . G 2 -16.069 16.628 -1.404 1 44.72 ? H4B1 DPM 401 B 1 
HETATM 43 H H5B1 DPM . . . G 2 -11.484 14.672 -3.326 1 48.46 ? H5B1 DPM 401 B 1 
HETATM 44 H H5B2 DPM . . . G 2 -12.254 15.682 -4.497 1 46.52 ? H5B2 DPM 401 B 1 
HETATM 45 H H7B1 DPM . . . G 2 -13.833 17.154 -4.679 1 49.76 ? H7B1 DPM 401 B 1 
HETATM 46 H H7B2 DPM . . . G 2 -14.806 18.097 -3.619 1 49 ? H7B2 DPM 401 B 1 
HETATM 47 H H8B1 DPM . . . G 2 -16.014 17.608 -5.728 1 48.08 ? H8B1 DPM 401 B 1 
HETATM 48 H H8B2 DPM . . . G 2 -15.78 15.917 -5.523 1 48.52 ? H8B2 DPM 401 B 1 
HETATM 49 H HCB1 DPM . . . G 2 -11.906 13.236 -1.576 1 50.39 ? HCB1 DPM 401 B 1 
HETATM 50 H HCB2 DPM . . . G 2 -12.486 13.758 -0.039 1 50.25 ? HCB2 DPM 401 B 1 
HETATM 51 H H22 DPM . . . G 2 -15.009 14.79 -0.053 1 46.36 ? H22 DPM 401 B 1 
HETATM 52 H HOB2 DPM . . . G 2 -11.918 12.831 -6.337 1 48.38 ? HOB2 DPM 401 B 1 
HETATM 53 H HOB4 DPM . . . G 2 -16.866 18.129 -2.905 1 52.2 ? HOB4 DPM 401 B 1 
#
_model_server_stats.io_time_ms              32 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           943 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           53 
#