data_7RB7
#
_model_server_result.job_id            D3mwlWVuWR1kLPrtR978fA 
_model_server_result.datetime_utc      '2024-11-22 19:55:36' 
_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          7rb7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":602}' 
#
_entry.id    7RB7 
#
_exptl.entry_id    7RB7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              258.276 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "1,1'-methylenebis{4-[(E)-(hydroxyimino)methyl]pyridin-1-ium}" 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            7RB7 
_cell.length_a            125.462 
_cell.length_b            125.462 
_cell.length_c            130.948 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7RB7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        144 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 1 2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_655 -y+1,x-y,z+1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 125.462 0 43.649333 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F 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
disulf ? disulf1 A SG CYS 72 A CYS 69 1_555 A SG CYS 99 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 A SG CYS 260 A CYS 257 1_555 A SG CYS 275 A CYS 272 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 A SG CYS 412 A CYS 409 1_555 A SG CYS 532 A CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 B SG CYS 72 B CYS 69 1_555 B SG CYS 99 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 B SG CYS 260 B CYS 257 1_555 B SG CYS 275 B CYS 272 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf6 B SG CYS 412 B CYS 409 1_555 B SG CYS 532 B CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
covale ? covale1 A OG SER 206 A SER 203 1_555 C C5 NWA . A NWA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? 
covale ? covale2 B OG SER 206 B SER 203 1_555 E C5 NWA . B NWA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? 
#
_chem_comp.formula           'C13 H14 N4 O2 2' 
_chem_comp.formula_weight    258.276 
_chem_comp.id                3VI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "1,1'-methylenebis{4-[(E)-(hydroxyimino)methyl]pyridin-1-ium}" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
OAA NAN 3VI sing 1 n n 
NAN CAC 3VI doub 2 e n 
CAC CAP 3VI sing 3 n n 
CAP CAE 3VI doub 4 n y 
CAP CAF 3VI sing 5 n y 
CAE CAI 3VI sing 6 n y 
CAF CAJ 3VI doub 7 n y 
CAI NAR 3VI doub 8 n y 
CAJ NAR 3VI sing 9 n y 
NAR CAM 3VI sing 10 n n 
CAM NAS 3VI sing 11 n n 
NAS CAK 3VI doub 12 n y 
NAS CAL 3VI sing 13 n y 
CAK CAG 3VI sing 14 n y 
CAL CAH 3VI doub 15 n y 
CAG CAQ 3VI doub 16 n y 
CAH CAQ 3VI sing 17 n y 
CAQ CAD 3VI sing 18 n n 
CAD NAO 3VI doub 19 e n 
NAO OAB 3VI sing 20 n n 
CAC H1 3VI sing 21 n n 
CAD H2 3VI sing 22 n n 
CAE H3 3VI sing 23 n n 
CAF H4 3VI sing 24 n n 
CAG H5 3VI sing 25 n n 
CAH H6 3VI sing 26 n n 
CAI H7 3VI sing 27 n n 
CAJ H8 3VI sing 28 n n 
CAK H9 3VI sing 29 n n 
CAL H10 3VI sing 30 n n 
CAM H11 3VI sing 31 n n 
CAM H12 3VI sing 32 n n 
OAA H13 3VI sing 33 n n 
OAB H14 3VI sing 34 n n 
#
_atom_sites.entry_id                     7RB7 
_atom_sites.fract_transf_matrix[1][1]    0.007971 
_atom_sites.fract_transf_matrix[1][2]    0.004602 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009204 
_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]    0.007637 
_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 NWA A 1 601 601 NWA NWA . 
D 3 3VI A 1 602 2 3VI MMB . 
E 2 NWA B 1 601 601 NWA NWA . 
F 3 3VI B 1 602 1 3VI MMB . 
G 4 HOH A 1 701 96 HOH HOH . 
G 4 HOH A 2 702 77 HOH HOH . 
G 4 HOH A 3 703 90 HOH HOH . 
G 4 HOH A 4 704 32 HOH HOH . 
G 4 HOH A 5 705 69 HOH HOH . 
G 4 HOH A 6 706 51 HOH HOH . 
G 4 HOH A 7 707 163 HOH HOH . 
G 4 HOH A 8 708 141 HOH HOH . 
G 4 HOH A 9 709 15 HOH HOH . 
G 4 HOH A 10 710 2 HOH HOH . 
G 4 HOH A 11 711 61 HOH HOH . 
G 4 HOH A 12 712 19 HOH HOH . 
G 4 HOH A 13 713 54 HOH HOH . 
G 4 HOH A 14 714 83 HOH HOH . 
G 4 HOH A 15 715 13 HOH HOH . 
G 4 HOH A 16 716 65 HOH HOH . 
G 4 HOH A 17 717 3 HOH HOH . 
G 4 HOH A 18 718 72 HOH HOH . 
G 4 HOH A 19 719 131 HOH HOH . 
G 4 HOH A 20 720 24 HOH HOH . 
G 4 HOH A 21 721 44 HOH HOH . 
G 4 HOH A 22 722 161 HOH HOH . 
G 4 HOH A 23 723 20 HOH HOH . 
G 4 HOH A 24 724 84 HOH HOH . 
G 4 HOH A 25 725 27 HOH HOH . 
G 4 HOH A 26 726 164 HOH HOH . 
G 4 HOH A 27 727 17 HOH HOH . 
G 4 HOH A 28 728 11 HOH HOH . 
G 4 HOH A 29 729 26 HOH HOH . 
G 4 HOH A 30 730 56 HOH HOH . 
G 4 HOH A 31 731 7 HOH HOH . 
G 4 HOH A 32 732 43 HOH HOH . 
G 4 HOH A 33 733 162 HOH HOH . 
G 4 HOH A 34 734 129 HOH HOH . 
G 4 HOH A 35 735 40 HOH HOH . 
G 4 HOH A 36 736 80 HOH HOH . 
G 4 HOH A 37 737 64 HOH HOH . 
G 4 HOH A 38 738 100 HOH HOH . 
G 4 HOH A 39 739 71 HOH HOH . 
G 4 HOH A 40 740 60 HOH HOH . 
G 4 HOH A 41 741 47 HOH HOH . 
G 4 HOH A 42 742 82 HOH HOH . 
G 4 HOH A 43 743 28 HOH HOH . 
G 4 HOH A 44 744 91 HOH HOH . 
G 4 HOH A 45 745 102 HOH HOH . 
G 4 HOH A 46 746 21 HOH HOH . 
G 4 HOH A 47 747 52 HOH HOH . 
G 4 HOH A 48 748 87 HOH HOH . 
G 4 HOH A 49 749 62 HOH HOH . 
G 4 HOH A 50 750 36 HOH HOH . 
G 4 HOH A 51 751 78 HOH HOH . 
G 4 HOH A 52 752 55 HOH HOH . 
G 4 HOH A 53 753 127 HOH HOH . 
G 4 HOH A 54 754 6 HOH HOH . 
G 4 HOH A 55 755 22 HOH HOH . 
G 4 HOH A 56 756 124 HOH HOH . 
G 4 HOH A 57 757 159 HOH HOH . 
G 4 HOH A 58 758 59 HOH HOH . 
G 4 HOH A 59 759 88 HOH HOH . 
G 4 HOH A 60 760 138 HOH HOH . 
G 4 HOH A 61 761 79 HOH HOH . 
G 4 HOH A 62 762 140 HOH HOH . 
G 4 HOH A 63 763 109 HOH HOH . 
G 4 HOH A 64 764 137 HOH HOH . 
G 4 HOH A 65 765 110 HOH HOH . 
G 4 HOH A 66 766 81 HOH HOH . 
G 4 HOH A 67 767 104 HOH HOH . 
G 4 HOH A 68 768 42 HOH HOH . 
G 4 HOH A 69 769 125 HOH HOH . 
G 4 HOH A 70 770 143 HOH HOH . 
G 4 HOH A 71 771 49 HOH HOH . 
G 4 HOH A 72 772 160 HOH HOH . 
G 4 HOH A 73 773 142 HOH HOH . 
G 4 HOH A 74 774 95 HOH HOH . 
G 4 HOH A 75 775 114 HOH HOH . 
G 4 HOH A 76 776 73 HOH HOH . 
G 4 HOH A 77 777 98 HOH HOH . 
G 4 HOH A 78 778 134 HOH HOH . 
G 4 HOH A 79 779 139 HOH HOH . 
G 4 HOH A 80 780 106 HOH HOH . 
H 4 HOH B 1 701 70 HOH HOH . 
H 4 HOH B 2 702 29 HOH HOH . 
H 4 HOH B 3 703 154 HOH HOH . 
H 4 HOH B 4 704 5 HOH HOH . 
H 4 HOH B 5 705 156 HOH HOH . 
H 4 HOH B 6 706 46 HOH HOH . 
H 4 HOH B 7 707 92 HOH HOH . 
H 4 HOH B 8 708 148 HOH HOH . 
H 4 HOH B 9 709 48 HOH HOH . 
H 4 HOH B 10 710 35 HOH HOH . 
H 4 HOH B 11 711 158 HOH HOH . 
H 4 HOH B 12 712 50 HOH HOH . 
H 4 HOH B 13 713 101 HOH HOH . 
H 4 HOH B 14 714 23 HOH HOH . 
H 4 HOH B 15 715 12 HOH HOH . 
H 4 HOH B 16 716 99 HOH HOH . 
H 4 HOH B 17 717 33 HOH HOH . 
H 4 HOH B 18 718 38 HOH HOH . 
H 4 HOH B 19 719 157 HOH HOH . 
H 4 HOH B 20 720 30 HOH HOH . 
H 4 HOH B 21 721 8 HOH HOH . 
H 4 HOH B 22 722 85 HOH HOH . 
H 4 HOH B 23 723 4 HOH HOH . 
H 4 HOH B 24 724 58 HOH HOH . 
H 4 HOH B 25 725 37 HOH HOH . 
H 4 HOH B 26 726 34 HOH HOH . 
H 4 HOH B 27 727 57 HOH HOH . 
H 4 HOH B 28 728 41 HOH HOH . 
H 4 HOH B 29 729 1 HOH HOH . 
H 4 HOH B 30 730 93 HOH HOH . 
H 4 HOH B 31 731 16 HOH HOH . 
H 4 HOH B 32 732 86 HOH HOH . 
H 4 HOH B 33 733 66 HOH HOH . 
H 4 HOH B 34 734 123 HOH HOH . 
H 4 HOH B 35 735 75 HOH HOH . 
H 4 HOH B 36 736 31 HOH HOH . 
H 4 HOH B 37 737 153 HOH HOH . 
H 4 HOH B 38 738 9 HOH HOH . 
H 4 HOH B 39 739 76 HOH HOH . 
H 4 HOH B 40 740 89 HOH HOH . 
H 4 HOH B 41 741 155 HOH HOH . 
H 4 HOH B 42 742 18 HOH HOH . 
H 4 HOH B 43 743 119 HOH HOH . 
H 4 HOH B 44 744 150 HOH HOH . 
H 4 HOH B 45 745 10 HOH HOH . 
H 4 HOH B 46 746 25 HOH HOH . 
H 4 HOH B 47 747 146 HOH HOH . 
H 4 HOH B 48 748 39 HOH HOH . 
H 4 HOH B 49 749 132 HOH HOH . 
H 4 HOH B 50 750 14 HOH HOH . 
H 4 HOH B 51 751 53 HOH HOH . 
H 4 HOH B 52 752 117 HOH HOH . 
H 4 HOH B 53 753 74 HOH HOH . 
H 4 HOH B 54 754 103 HOH HOH . 
H 4 HOH B 55 755 130 HOH HOH . 
H 4 HOH B 56 756 111 HOH HOH . 
H 4 HOH B 57 757 151 HOH HOH . 
H 4 HOH B 58 758 136 HOH HOH . 
H 4 HOH B 59 759 105 HOH HOH . 
H 4 HOH B 60 760 147 HOH HOH . 
H 4 HOH B 61 761 45 HOH HOH . 
H 4 HOH B 62 762 144 HOH HOH . 
H 4 HOH B 63 763 133 HOH HOH . 
H 4 HOH B 64 764 94 HOH HOH . 
H 4 HOH B 65 765 121 HOH HOH . 
H 4 HOH B 66 766 165 HOH HOH . 
H 4 HOH B 67 767 97 HOH HOH . 
H 4 HOH B 68 768 122 HOH HOH . 
H 4 HOH B 69 769 118 HOH HOH . 
H 4 HOH B 70 770 68 HOH HOH . 
H 4 HOH B 71 771 126 HOH HOH . 
H 4 HOH B 72 772 152 HOH HOH . 
H 4 HOH B 73 773 67 HOH HOH . 
H 4 HOH B 74 774 107 HOH HOH . 
H 4 HOH B 75 775 145 HOH HOH . 
H 4 HOH B 76 776 113 HOH HOH . 
H 4 HOH B 77 777 112 HOH HOH . 
H 4 HOH B 78 778 115 HOH HOH . 
H 4 HOH B 79 779 116 HOH HOH . 
H 4 HOH B 80 780 128 HOH HOH . 
H 4 HOH B 81 781 63 HOH HOH . 
H 4 HOH B 82 782 120 HOH HOH . 
H 4 HOH B 83 783 149 HOH HOH . 
H 4 HOH B 84 784 108 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 CAD 3VI . . . D 3 89.57 54.946 6.429 1 62.1 ? CAD 3VI 602 A 1 
HETATM 2 C CAG 3VI . . . D 3 89.384 53.113 4.877 1 67.75 ? CAG 3VI 602 A 1 
HETATM 3 C CAH 3VI . . . D 3 91.428 54.384 5.003 1 61.78 ? CAH 3VI 602 A 1 
HETATM 4 C CAK 3VI . . . D 3 89.936 52.31 3.884 1 71.48 ? CAK 3VI 602 A 1 
HETATM 5 C CAL 3VI . . . D 3 91.988 53.587 4.01 1 68.81 ? CAL 3VI 602 A 1 
HETATM 6 C CAM 3VI . . . D 3 91.841 51.694 2.388 1 46.81 ? CAM 3VI 602 A 1 
HETATM 7 C CAQ 3VI . . . D 3 90.127 54.148 5.435 1 67.22 ? CAQ 3VI 602 A 1 
HETATM 8 N NAO 3VI . . . D 3 90.436 55.754 7.061 1 61.26 ? NAO 3VI 602 A 1 
HETATM 9 N NAS 3VI . . . D 3 91.245 52.544 3.445 1 65.53 ? NAS 3VI 602 A 1 
HETATM 10 O OAB 3VI . . . D 3 89.894 56.613 8.126 1 54.95 ? OAB 3VI 602 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           10 
#