data_8DGQ
#
_model_server_result.job_id            R-VyYooHCf5vJEvNOAkXTA 
_model_server_result.datetime_utc      '2024-11-25 18:33:06' 
_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          8dgq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":501}' 
#
_entry.id    8DGQ 
#
_exptl.entry_id    8DGQ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              102.046 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MALONATE ION' 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            8DGQ 
_cell.length_a            55.21 
_cell.length_b            113.5 
_cell.length_c            119.07 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DGQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,F,H,J 1 1 
B,D,G,I,K 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
? 3 E N N 
? 3 F N N 
? 3 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 C C ASP 4 U ASP 1086 1_555 C N PTR 5 U PTR 1087 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale2 C C PTR 5 U PTR 1087 1_555 C N ALA 6 U ALA 1088 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale3 C C ILE 22 U ILE 1104 1_555 C N PTR 23 U PTR 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 C C PTR 23 U PTR 1105 1_555 C N SER 24 U SER 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale5 D C ASP 4 V ASP 1086 1_555 D N PTR 5 V PTR 1087 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale6 D C PTR 5 V PTR 1087 1_555 D N ALA 6 V ALA 1088 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale7 D C ILE 22 V ILE 1104 1_555 D N PTR 23 V PTR 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale8 D C PTR 23 V PTR 1105 1_555 D N SER 24 V SER 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
#
_chem_comp.formula           'C3 H2 O4 -2' 
_chem_comp.formula_weight    102.046 
_chem_comp.id                MLI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'MALONATE ION' 
_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
C1 C2 MLI sing 237 n n 
C1 C3 MLI sing 238 n n 
C1 H11 MLI sing 239 n n 
C1 H12 MLI sing 240 n n 
C2 O6 MLI doub 241 n n 
C2 O7 MLI sing 242 n n 
C3 O8 MLI doub 243 n n 
C3 O9 MLI sing 244 n n 
#
_atom_sites.entry_id                     8DGQ 
_atom_sites.fract_transf_matrix[1][1]    0.018113 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008811 
_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]    0.008398 
_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
E 3 MLI A 1 501 234 MLI MLI . 
F 3 MLI A 1 502 235 MLI MLI . 
G 3 MLI B 1 501 236 MLI MLI . 
H 4 HOH A 1 601 15 HOH HOH . 
H 4 HOH A 2 602 117 HOH HOH . 
H 4 HOH A 3 603 40 HOH HOH . 
H 4 HOH A 4 604 92 HOH HOH . 
H 4 HOH A 5 605 48 HOH HOH . 
H 4 HOH A 6 606 26 HOH HOH . 
H 4 HOH A 7 607 63 HOH HOH . 
H 4 HOH A 8 608 34 HOH HOH . 
H 4 HOH A 9 609 31 HOH HOH . 
H 4 HOH A 10 610 83 HOH HOH . 
H 4 HOH A 11 611 5 HOH HOH . 
H 4 HOH A 12 612 19 HOH HOH . 
H 4 HOH A 13 613 95 HOH HOH . 
H 4 HOH A 14 614 97 HOH HOH . 
H 4 HOH A 15 615 105 HOH HOH . 
H 4 HOH A 16 616 107 HOH HOH . 
H 4 HOH A 17 617 65 HOH HOH . 
H 4 HOH A 18 618 172 HOH HOH . 
H 4 HOH A 19 619 17 HOH HOH . 
H 4 HOH A 20 620 4 HOH HOH . 
H 4 HOH A 21 621 14 HOH HOH . 
H 4 HOH A 22 622 84 HOH HOH . 
H 4 HOH A 23 623 41 HOH HOH . 
H 4 HOH A 24 624 57 HOH HOH . 
H 4 HOH A 25 625 11 HOH HOH . 
H 4 HOH A 26 626 67 HOH HOH . 
H 4 HOH A 27 627 93 HOH HOH . 
H 4 HOH A 28 628 115 HOH HOH . 
H 4 HOH A 29 629 32 HOH HOH . 
H 4 HOH A 30 630 49 HOH HOH . 
H 4 HOH A 31 631 36 HOH HOH . 
H 4 HOH A 32 632 189 HOH HOH . 
H 4 HOH A 33 633 24 HOH HOH . 
H 4 HOH A 34 634 163 HOH HOH . 
H 4 HOH A 35 635 90 HOH HOH . 
H 4 HOH A 36 636 187 HOH HOH . 
H 4 HOH A 37 637 191 HOH HOH . 
H 4 HOH A 38 638 75 HOH HOH . 
H 4 HOH A 39 639 80 HOH HOH . 
H 4 HOH A 40 640 25 HOH HOH . 
H 4 HOH A 41 641 111 HOH HOH . 
H 4 HOH A 42 642 85 HOH HOH . 
H 4 HOH A 43 643 30 HOH HOH . 
H 4 HOH A 44 644 193 HOH HOH . 
H 4 HOH A 45 645 53 HOH HOH . 
H 4 HOH A 46 646 145 HOH HOH . 
H 4 HOH A 47 647 8 HOH HOH . 
H 4 HOH A 48 648 72 HOH HOH . 
H 4 HOH A 49 649 213 HOH HOH . 
H 4 HOH A 50 650 192 HOH HOH . 
H 4 HOH A 51 651 29 HOH HOH . 
H 4 HOH A 52 652 78 HOH HOH . 
H 4 HOH A 53 653 13 HOH HOH . 
H 4 HOH A 54 654 62 HOH HOH . 
H 4 HOH A 55 655 28 HOH HOH . 
H 4 HOH A 56 656 42 HOH HOH . 
H 4 HOH A 57 657 44 HOH HOH . 
H 4 HOH A 58 658 56 HOH HOH . 
H 4 HOH A 59 659 98 HOH HOH . 
H 4 HOH A 60 660 94 HOH HOH . 
H 4 HOH A 61 661 50 HOH HOH . 
H 4 HOH A 62 662 222 HOH HOH . 
H 4 HOH A 63 663 150 HOH HOH . 
H 4 HOH A 64 664 159 HOH HOH . 
H 4 HOH A 65 665 155 HOH HOH . 
H 4 HOH A 66 666 143 HOH HOH . 
H 4 HOH A 67 667 43 HOH HOH . 
H 4 HOH A 68 668 140 HOH HOH . 
H 4 HOH A 69 669 197 HOH HOH . 
H 4 HOH A 70 670 23 HOH HOH . 
H 4 HOH A 71 671 188 HOH HOH . 
H 4 HOH A 72 672 179 HOH HOH . 
H 4 HOH A 73 673 128 HOH HOH . 
H 4 HOH A 74 674 58 HOH HOH . 
H 4 HOH A 75 675 3 HOH HOH . 
H 4 HOH A 76 676 212 HOH HOH . 
H 4 HOH A 77 677 223 HOH HOH . 
H 4 HOH A 78 678 152 HOH HOH . 
H 4 HOH A 79 679 164 HOH HOH . 
H 4 HOH A 80 680 166 HOH HOH . 
H 4 HOH A 81 681 106 HOH HOH . 
H 4 HOH A 82 682 232 HOH HOH . 
H 4 HOH A 83 683 218 HOH HOH . 
H 4 HOH A 84 684 167 HOH HOH . 
H 4 HOH A 85 685 89 HOH HOH . 
H 4 HOH A 86 686 123 HOH HOH . 
H 4 HOH A 87 687 224 HOH HOH . 
H 4 HOH A 88 688 220 HOH HOH . 
H 4 HOH A 89 689 190 HOH HOH . 
H 4 HOH A 90 690 86 HOH HOH . 
H 4 HOH A 91 691 146 HOH HOH . 
H 4 HOH A 92 692 154 HOH HOH . 
H 4 HOH A 93 693 38 HOH HOH . 
H 4 HOH A 94 694 165 HOH HOH . 
H 4 HOH A 95 695 200 HOH HOH . 
H 4 HOH A 96 696 228 HOH HOH . 
H 4 HOH A 97 697 119 HOH HOH . 
H 4 HOH A 98 698 231 HOH HOH . 
H 4 HOH A 99 699 214 HOH HOH . 
H 4 HOH A 100 700 126 HOH HOH . 
H 4 HOH A 101 701 186 HOH HOH . 
I 4 HOH B 1 601 39 HOH HOH . 
I 4 HOH B 2 602 161 HOH HOH . 
I 4 HOH B 3 603 147 HOH HOH . 
I 4 HOH B 4 604 76 HOH HOH . 
I 4 HOH B 5 605 227 HOH HOH . 
I 4 HOH B 6 606 20 HOH HOH . 
I 4 HOH B 7 607 51 HOH HOH . 
I 4 HOH B 8 608 35 HOH HOH . 
I 4 HOH B 9 609 7 HOH HOH . 
I 4 HOH B 10 610 112 HOH HOH . 
I 4 HOH B 11 611 137 HOH HOH . 
I 4 HOH B 12 612 217 HOH HOH . 
I 4 HOH B 13 613 183 HOH HOH . 
I 4 HOH B 14 614 160 HOH HOH . 
I 4 HOH B 15 615 59 HOH HOH . 
I 4 HOH B 16 616 81 HOH HOH . 
I 4 HOH B 17 617 60 HOH HOH . 
I 4 HOH B 18 618 21 HOH HOH . 
I 4 HOH B 19 619 104 HOH HOH . 
I 4 HOH B 20 620 182 HOH HOH . 
I 4 HOH B 21 621 47 HOH HOH . 
I 4 HOH B 22 622 125 HOH HOH . 
I 4 HOH B 23 623 6 HOH HOH . 
I 4 HOH B 24 624 101 HOH HOH . 
I 4 HOH B 25 625 77 HOH HOH . 
I 4 HOH B 26 626 68 HOH HOH . 
I 4 HOH B 27 627 52 HOH HOH . 
I 4 HOH B 28 628 135 HOH HOH . 
I 4 HOH B 29 629 141 HOH HOH . 
I 4 HOH B 30 630 133 HOH HOH . 
I 4 HOH B 31 631 55 HOH HOH . 
I 4 HOH B 32 632 209 HOH HOH . 
I 4 HOH B 33 633 87 HOH HOH . 
I 4 HOH B 34 634 10 HOH HOH . 
I 4 HOH B 35 635 16 HOH HOH . 
I 4 HOH B 36 636 37 HOH HOH . 
I 4 HOH B 37 637 221 HOH HOH . 
I 4 HOH B 38 638 69 HOH HOH . 
I 4 HOH B 39 639 27 HOH HOH . 
I 4 HOH B 40 640 118 HOH HOH . 
I 4 HOH B 41 641 226 HOH HOH . 
I 4 HOH B 42 642 12 HOH HOH . 
I 4 HOH B 43 643 18 HOH HOH . 
I 4 HOH B 44 644 139 HOH HOH . 
I 4 HOH B 45 645 2 HOH HOH . 
I 4 HOH B 46 646 196 HOH HOH . 
I 4 HOH B 47 647 73 HOH HOH . 
I 4 HOH B 48 648 148 HOH HOH . 
I 4 HOH B 49 649 170 HOH HOH . 
I 4 HOH B 50 650 61 HOH HOH . 
I 4 HOH B 51 651 131 HOH HOH . 
I 4 HOH B 52 652 46 HOH HOH . 
I 4 HOH B 53 653 91 HOH HOH . 
I 4 HOH B 54 654 219 HOH HOH . 
I 4 HOH B 55 655 103 HOH HOH . 
I 4 HOH B 56 656 113 HOH HOH . 
I 4 HOH B 57 657 233 HOH HOH . 
I 4 HOH B 58 658 157 HOH HOH . 
I 4 HOH B 59 659 124 HOH HOH . 
I 4 HOH B 60 660 127 HOH HOH . 
I 4 HOH B 61 661 88 HOH HOH . 
I 4 HOH B 62 662 132 HOH HOH . 
I 4 HOH B 63 663 144 HOH HOH . 
I 4 HOH B 64 664 79 HOH HOH . 
I 4 HOH B 65 665 45 HOH HOH . 
I 4 HOH B 66 666 33 HOH HOH . 
I 4 HOH B 67 667 210 HOH HOH . 
I 4 HOH B 68 668 230 HOH HOH . 
I 4 HOH B 69 669 185 HOH HOH . 
I 4 HOH B 70 670 70 HOH HOH . 
I 4 HOH B 71 671 66 HOH HOH . 
I 4 HOH B 72 672 158 HOH HOH . 
I 4 HOH B 73 673 99 HOH HOH . 
I 4 HOH B 74 674 108 HOH HOH . 
I 4 HOH B 75 675 64 HOH HOH . 
I 4 HOH B 76 676 175 HOH HOH . 
I 4 HOH B 77 677 151 HOH HOH . 
I 4 HOH B 78 678 207 HOH HOH . 
I 4 HOH B 79 679 100 HOH HOH . 
I 4 HOH B 80 680 129 HOH HOH . 
I 4 HOH B 81 681 153 HOH HOH . 
I 4 HOH B 82 682 138 HOH HOH . 
I 4 HOH B 83 683 102 HOH HOH . 
I 4 HOH B 84 684 204 HOH HOH . 
I 4 HOH B 85 685 198 HOH HOH . 
I 4 HOH B 86 686 180 HOH HOH . 
I 4 HOH B 87 687 1 HOH HOH . 
I 4 HOH B 88 688 122 HOH HOH . 
I 4 HOH B 89 689 168 HOH HOH . 
I 4 HOH B 90 690 195 HOH HOH . 
I 4 HOH B 91 691 130 HOH HOH . 
I 4 HOH B 92 692 203 HOH HOH . 
I 4 HOH B 93 693 211 HOH HOH . 
I 4 HOH B 94 694 215 HOH HOH . 
I 4 HOH B 95 695 202 HOH HOH . 
I 4 HOH B 96 696 178 HOH HOH . 
I 4 HOH B 97 697 116 HOH HOH . 
I 4 HOH B 98 698 173 HOH HOH . 
I 4 HOH B 99 699 229 HOH HOH . 
I 4 HOH B 100 700 162 HOH HOH . 
I 4 HOH B 101 701 216 HOH HOH . 
I 4 HOH B 102 702 149 HOH HOH . 
I 4 HOH B 103 703 169 HOH HOH . 
I 4 HOH B 104 704 181 HOH HOH . 
I 4 HOH B 105 705 96 HOH HOH . 
I 4 HOH B 106 706 134 HOH HOH . 
I 4 HOH B 107 707 71 HOH HOH . 
I 4 HOH B 108 708 174 HOH HOH . 
I 4 HOH B 109 709 114 HOH HOH . 
I 4 HOH B 110 710 201 HOH HOH . 
J 4 HOH U 1 1201 82 HOH HOH . 
J 4 HOH U 2 1202 208 HOH HOH . 
J 4 HOH U 3 1203 194 HOH HOH . 
J 4 HOH U 4 1204 142 HOH HOH . 
J 4 HOH U 5 1205 156 HOH HOH . 
J 4 HOH U 6 1206 199 HOH HOH . 
J 4 HOH U 7 1207 136 HOH HOH . 
J 4 HOH U 8 1208 54 HOH HOH . 
J 4 HOH U 9 1209 121 HOH HOH . 
J 4 HOH U 10 1210 225 HOH HOH . 
J 4 HOH U 11 1211 206 HOH HOH . 
K 4 HOH V 1 1201 176 HOH HOH . 
K 4 HOH V 2 1202 171 HOH HOH . 
K 4 HOH V 3 1203 110 HOH HOH . 
K 4 HOH V 4 1204 22 HOH HOH . 
K 4 HOH V 5 1205 74 HOH HOH . 
K 4 HOH V 6 1206 184 HOH HOH . 
K 4 HOH V 7 1207 177 HOH HOH . 
K 4 HOH V 8 1208 120 HOH HOH . 
K 4 HOH V 9 1209 9 HOH HOH . 
K 4 HOH V 10 1210 205 HOH HOH . 
K 4 HOH V 11 1211 109 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 C1 MLI . . . G 3 50.954 48.65 86.059 1 65.12 ? C1 MLI 501 B 1 
HETATM 2 C C2 MLI . . . G 3 49.936 48.916 87.178 1 65.96 ? C2 MLI 501 B 1 
HETATM 3 C C3 MLI . . . G 3 50.356 47.912 84.852 1 56.26 ? C3 MLI 501 B 1 
HETATM 4 O O6 MLI . . . G 3 48.699 48.994 86.935 1 50.72 ? O6 MLI 501 B 1 
HETATM 5 O O7 MLI . . . G 3 50.341 49.067 88.363 1 65.24 ? O7 MLI 501 B 1 
HETATM 6 O O8 MLI . . . G 3 49.836 48.574 83.912 1 46.99 ? O8 MLI 501 B 1 
HETATM 7 O O9 MLI . . . G 3 50.399 46.649 84.786 1 51.42 ? O9 MLI 501 B 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           7 
#