data_5J28
#
_model_server_result.job_id            pUqOvB-aR2aN0ipEe3S7_g 
_model_server_result.datetime_utc      '2025-01-10 22:11:42' 
_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          5j28 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":401}' 
#
_entry.id    5J28 
#
_exptl.entry_id    5J28 
_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    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            5J28 
_cell.length_a            90.832 
_cell.length_b            90.832 
_cell.length_c            206.717 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5J28 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 61' 
#
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 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
metalc ? metalc1 A OE2 GLU 51 A GLU 54 1_555 F NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? 
metalc ? metalc2 A OE1 GLU 164 A GLU 167 1_555 F NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? 
#
_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                     5J28 
_atom_sites.fract_transf_matrix[1][1]    0.011009 
_atom_sites.fract_transf_matrix[1][2]    0.006356 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012712 
_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]    0.004838 
_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 1 401 1 MLI MLI . 
F 4 NA A 1 402 1 NA NA . 
G 3 MLI B 1 401 2 MLI MLI . 
H 5 HOH A 1 501 157 HOH HOH . 
H 5 HOH A 2 502 6 HOH HOH . 
H 5 HOH A 3 503 69 HOH HOH . 
H 5 HOH A 4 504 36 HOH HOH . 
H 5 HOH A 5 505 183 HOH HOH . 
H 5 HOH A 6 506 31 HOH HOH . 
H 5 HOH A 7 507 54 HOH HOH . 
H 5 HOH A 8 508 244 HOH HOH . 
H 5 HOH A 9 509 99 HOH HOH . 
H 5 HOH A 10 510 182 HOH HOH . 
H 5 HOH A 11 511 211 HOH HOH . 
H 5 HOH A 12 512 202 HOH HOH . 
H 5 HOH A 13 513 29 HOH HOH . 
H 5 HOH A 14 514 26 HOH HOH . 
H 5 HOH A 15 515 243 HOH HOH . 
H 5 HOH A 16 516 108 HOH HOH . 
H 5 HOH A 17 517 74 HOH HOH . 
H 5 HOH A 18 518 40 HOH HOH . 
H 5 HOH A 19 519 210 HOH HOH . 
H 5 HOH A 20 520 236 HOH HOH . 
H 5 HOH A 21 521 7 HOH HOH . 
H 5 HOH A 22 522 60 HOH HOH . 
H 5 HOH A 23 523 1 HOH HOH . 
H 5 HOH A 24 524 35 HOH HOH . 
H 5 HOH A 25 525 212 HOH HOH . 
H 5 HOH A 26 526 161 HOH HOH . 
H 5 HOH A 27 527 27 HOH HOH . 
H 5 HOH A 28 528 23 HOH HOH . 
H 5 HOH A 29 529 186 HOH HOH . 
H 5 HOH A 30 530 34 HOH HOH . 
H 5 HOH A 31 531 167 HOH HOH . 
H 5 HOH A 32 532 48 HOH HOH . 
H 5 HOH A 33 533 39 HOH HOH . 
H 5 HOH A 34 534 196 HOH HOH . 
H 5 HOH A 35 535 82 HOH HOH . 
H 5 HOH A 36 536 239 HOH HOH . 
H 5 HOH A 37 537 86 HOH HOH . 
H 5 HOH A 38 538 146 HOH HOH . 
H 5 HOH A 39 539 58 HOH HOH . 
H 5 HOH A 40 540 101 HOH HOH . 
H 5 HOH A 41 541 17 HOH HOH . 
H 5 HOH A 42 542 9 HOH HOH . 
H 5 HOH A 43 543 111 HOH HOH . 
H 5 HOH A 44 544 75 HOH HOH . 
H 5 HOH A 45 545 42 HOH HOH . 
H 5 HOH A 46 546 43 HOH HOH . 
H 5 HOH A 47 547 274 HOH HOH . 
H 5 HOH A 48 548 100 HOH HOH . 
H 5 HOH A 49 549 5 HOH HOH . 
H 5 HOH A 50 550 79 HOH HOH . 
H 5 HOH A 51 551 206 HOH HOH . 
H 5 HOH A 52 552 46 HOH HOH . 
H 5 HOH A 53 553 78 HOH HOH . 
H 5 HOH A 54 554 132 HOH HOH . 
H 5 HOH A 55 555 117 HOH HOH . 
H 5 HOH A 56 556 120 HOH HOH . 
H 5 HOH A 57 557 81 HOH HOH . 
H 5 HOH A 58 558 191 HOH HOH . 
H 5 HOH A 59 559 237 HOH HOH . 
H 5 HOH A 60 560 22 HOH HOH . 
H 5 HOH A 61 561 122 HOH HOH . 
H 5 HOH A 62 562 106 HOH HOH . 
H 5 HOH A 63 563 51 HOH HOH . 
H 5 HOH A 64 564 162 HOH HOH . 
H 5 HOH A 65 565 246 HOH HOH . 
H 5 HOH A 66 566 136 HOH HOH . 
H 5 HOH A 67 567 159 HOH HOH . 
H 5 HOH A 68 568 19 HOH HOH . 
H 5 HOH A 69 569 164 HOH HOH . 
H 5 HOH A 70 570 33 HOH HOH . 
H 5 HOH A 71 571 59 HOH HOH . 
H 5 HOH A 72 572 213 HOH HOH . 
H 5 HOH A 73 573 102 HOH HOH . 
H 5 HOH A 74 574 49 HOH HOH . 
H 5 HOH A 75 575 272 HOH HOH . 
H 5 HOH A 76 576 155 HOH HOH . 
H 5 HOH A 77 577 71 HOH HOH . 
H 5 HOH A 78 578 251 HOH HOH . 
H 5 HOH A 79 579 226 HOH HOH . 
H 5 HOH A 80 580 254 HOH HOH . 
H 5 HOH A 81 581 149 HOH HOH . 
H 5 HOH A 82 582 67 HOH HOH . 
H 5 HOH A 83 583 221 HOH HOH . 
H 5 HOH A 84 584 197 HOH HOH . 
H 5 HOH A 85 585 270 HOH HOH . 
H 5 HOH A 86 586 223 HOH HOH . 
H 5 HOH A 87 587 116 HOH HOH . 
H 5 HOH A 88 588 262 HOH HOH . 
H 5 HOH A 89 589 201 HOH HOH . 
H 5 HOH A 90 590 192 HOH HOH . 
H 5 HOH A 91 591 126 HOH HOH . 
H 5 HOH A 92 592 261 HOH HOH . 
H 5 HOH A 93 593 41 HOH HOH . 
H 5 HOH A 94 594 185 HOH HOH . 
H 5 HOH A 95 595 68 HOH HOH . 
H 5 HOH A 96 596 205 HOH HOH . 
H 5 HOH A 97 597 218 HOH HOH . 
H 5 HOH A 98 598 250 HOH HOH . 
H 5 HOH A 99 599 256 HOH HOH . 
H 5 HOH A 100 600 20 HOH HOH . 
H 5 HOH A 101 601 115 HOH HOH . 
H 5 HOH A 102 602 275 HOH HOH . 
H 5 HOH A 103 603 248 HOH HOH . 
H 5 HOH A 104 604 217 HOH HOH . 
H 5 HOH A 105 605 104 HOH HOH . 
H 5 HOH A 106 606 267 HOH HOH . 
I 5 HOH B 1 501 16 HOH HOH . 
I 5 HOH B 2 502 8 HOH HOH . 
I 5 HOH B 3 503 96 HOH HOH . 
I 5 HOH B 4 504 25 HOH HOH . 
I 5 HOH B 5 505 56 HOH HOH . 
I 5 HOH B 6 506 193 HOH HOH . 
I 5 HOH B 7 507 98 HOH HOH . 
I 5 HOH B 8 508 214 HOH HOH . 
I 5 HOH B 9 509 37 HOH HOH . 
I 5 HOH B 10 510 10 HOH HOH . 
I 5 HOH B 11 511 140 HOH HOH . 
I 5 HOH B 12 512 12 HOH HOH . 
I 5 HOH B 13 513 179 HOH HOH . 
I 5 HOH B 14 514 52 HOH HOH . 
I 5 HOH B 15 515 84 HOH HOH . 
I 5 HOH B 16 516 227 HOH HOH . 
I 5 HOH B 17 517 138 HOH HOH . 
I 5 HOH B 18 518 131 HOH HOH . 
I 5 HOH B 19 519 174 HOH HOH . 
I 5 HOH B 20 520 135 HOH HOH . 
I 5 HOH B 21 521 61 HOH HOH . 
I 5 HOH B 22 522 204 HOH HOH . 
I 5 HOH B 23 523 242 HOH HOH . 
I 5 HOH B 24 524 109 HOH HOH . 
I 5 HOH B 25 525 121 HOH HOH . 
I 5 HOH B 26 526 57 HOH HOH . 
I 5 HOH B 27 527 276 HOH HOH . 
I 5 HOH B 28 528 15 HOH HOH . 
I 5 HOH B 29 529 77 HOH HOH . 
I 5 HOH B 30 530 194 HOH HOH . 
I 5 HOH B 31 531 55 HOH HOH . 
I 5 HOH B 32 532 105 HOH HOH . 
I 5 HOH B 33 533 257 HOH HOH . 
I 5 HOH B 34 534 178 HOH HOH . 
I 5 HOH B 35 535 125 HOH HOH . 
I 5 HOH B 36 536 92 HOH HOH . 
I 5 HOH B 37 537 30 HOH HOH . 
I 5 HOH B 38 538 53 HOH HOH . 
I 5 HOH B 39 539 62 HOH HOH . 
I 5 HOH B 40 540 266 HOH HOH . 
I 5 HOH B 41 541 2 HOH HOH . 
I 5 HOH B 42 542 103 HOH HOH . 
I 5 HOH B 43 543 28 HOH HOH . 
I 5 HOH B 44 544 88 HOH HOH . 
I 5 HOH B 45 545 153 HOH HOH . 
I 5 HOH B 46 546 147 HOH HOH . 
I 5 HOH B 47 547 142 HOH HOH . 
I 5 HOH B 48 548 195 HOH HOH . 
I 5 HOH B 49 549 232 HOH HOH . 
I 5 HOH B 50 550 137 HOH HOH . 
I 5 HOH B 51 551 95 HOH HOH . 
I 5 HOH B 52 552 233 HOH HOH . 
I 5 HOH B 53 553 151 HOH HOH . 
I 5 HOH B 54 554 166 HOH HOH . 
I 5 HOH B 55 555 143 HOH HOH . 
I 5 HOH B 56 556 190 HOH HOH . 
I 5 HOH B 57 557 277 HOH HOH . 
I 5 HOH B 58 558 13 HOH HOH . 
I 5 HOH B 59 559 215 HOH HOH . 
I 5 HOH B 60 560 158 HOH HOH . 
I 5 HOH B 61 561 187 HOH HOH . 
I 5 HOH B 62 562 80 HOH HOH . 
I 5 HOH B 63 563 208 HOH HOH . 
I 5 HOH B 64 564 184 HOH HOH . 
I 5 HOH B 65 565 235 HOH HOH . 
I 5 HOH B 66 566 247 HOH HOH . 
I 5 HOH B 67 567 63 HOH HOH . 
I 5 HOH B 68 568 203 HOH HOH . 
I 5 HOH B 69 569 127 HOH HOH . 
I 5 HOH B 70 570 273 HOH HOH . 
I 5 HOH B 71 571 189 HOH HOH . 
I 5 HOH B 72 572 90 HOH HOH . 
I 5 HOH B 73 573 4 HOH HOH . 
I 5 HOH B 74 574 175 HOH HOH . 
I 5 HOH B 75 575 154 HOH HOH . 
I 5 HOH B 76 576 156 HOH HOH . 
I 5 HOH B 77 577 45 HOH HOH . 
I 5 HOH B 78 578 240 HOH HOH . 
I 5 HOH B 79 579 216 HOH HOH . 
I 5 HOH B 80 580 209 HOH HOH . 
I 5 HOH B 81 581 3 HOH HOH . 
I 5 HOH B 82 582 110 HOH HOH . 
I 5 HOH B 83 583 173 HOH HOH . 
I 5 HOH B 84 584 152 HOH HOH . 
I 5 HOH B 85 585 141 HOH HOH . 
I 5 HOH B 86 586 264 HOH HOH . 
I 5 HOH B 87 587 230 HOH HOH . 
I 5 HOH B 88 588 160 HOH HOH . 
I 5 HOH B 89 589 198 HOH HOH . 
I 5 HOH B 90 590 168 HOH HOH . 
I 5 HOH B 91 591 114 HOH HOH . 
I 5 HOH B 92 592 252 HOH HOH . 
I 5 HOH B 93 593 255 HOH HOH . 
I 5 HOH B 94 594 238 HOH HOH . 
J 5 HOH C 1 601 32 HOH HOH . 
J 5 HOH C 2 602 11 HOH HOH . 
J 5 HOH C 3 603 94 HOH HOH . 
J 5 HOH C 4 604 72 HOH HOH . 
J 5 HOH C 5 605 24 HOH HOH . 
J 5 HOH C 6 606 225 HOH HOH . 
J 5 HOH C 7 607 44 HOH HOH . 
J 5 HOH C 8 608 181 HOH HOH . 
J 5 HOH C 9 609 171 HOH HOH . 
J 5 HOH C 10 610 93 HOH HOH . 
J 5 HOH C 11 611 241 HOH HOH . 
J 5 HOH C 12 612 245 HOH HOH . 
J 5 HOH C 13 613 228 HOH HOH . 
J 5 HOH C 14 614 65 HOH HOH . 
J 5 HOH C 15 615 148 HOH HOH . 
K 5 HOH D 1 601 38 HOH HOH . 
K 5 HOH D 2 602 14 HOH HOH . 
K 5 HOH D 3 603 18 HOH HOH . 
K 5 HOH D 4 604 107 HOH HOH . 
K 5 HOH D 5 605 89 HOH HOH . 
K 5 HOH D 6 606 70 HOH HOH . 
K 5 HOH D 7 607 134 HOH HOH . 
K 5 HOH D 8 608 163 HOH HOH . 
K 5 HOH D 9 609 85 HOH HOH . 
K 5 HOH D 10 610 234 HOH HOH . 
K 5 HOH D 11 611 119 HOH HOH . 
K 5 HOH D 12 612 123 HOH HOH . 
K 5 HOH D 13 613 231 HOH HOH . 
K 5 HOH D 14 614 188 HOH HOH . 
K 5 HOH D 15 615 249 HOH HOH . 
K 5 HOH D 16 616 87 HOH HOH . 
K 5 HOH D 17 617 260 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 -24.246 10.853 15.009 1 24.54 ? C1 MLI 401 B 1 
HETATM 2 C C2 MLI . . . G 3 -23.942 9.369 14.87 1 23.97 ? C2 MLI 401 B 1 
HETATM 3 C C3 MLI . . . G 3 -22.963 11.512 15.496 1 23.83 ? C3 MLI 401 B 1 
HETATM 4 O O6 MLI . . . G 3 -22.817 8.945 15.237 1 24.9 ? O6 MLI 401 B 1 
HETATM 5 O O7 MLI . . . G 3 -24.8 8.579 14.41 1 25.49 ? O7 MLI 401 B 1 
HETATM 6 O O8 MLI . . . G 3 -22.605 11.407 16.702 1 29 ? O8 MLI 401 B 1 
HETATM 7 O O9 MLI . . . G 3 -22.254 12.146 14.678 1 29.33 ? O9 MLI 401 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           7 
#