data_6YDM
#
_model_server_result.job_id            qCbMPOAmaJ_9IsxlpPKw-g 
_model_server_result.datetime_utc      '2024-12-01 00:36:06' 
_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          6ydm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    6YDM 
#
_exptl.entry_id    6YDM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              192.124 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'CITRIC ACID' 
_entity.pdbx_number_of_molecules    1 
_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            6YDM 
_cell.length_a            53.13 
_cell.length_b            76.64 
_cell.length_c            117.26 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YDM 
_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
? 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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 OD2 ASP 8 A ASP 8 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc2 A O ASP 10 A ASP 10 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc3 A OE1 GLU 169 A GLU 169 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? 
metalc ? metalc4 A OD1 ASP 170 A ASP 170 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc5 D MG MG . A MG 302 1_555 K O HOH . A HOH 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc6 B OD2 ASP 8 B ASP 8 1_555 G MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc7 B O ASP 10 B ASP 10 1_555 G MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? 
metalc ? metalc8 B OE1 GLU 169 B GLU 169 1_555 G MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? 
metalc ? metalc9 B OD1 ASP 170 B ASP 170 1_555 G MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc10 G MG MG . B MG 301 1_555 L O HOH . B HOH 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
#
_chem_comp.formula           'C6 H8 O7' 
_chem_comp.formula_weight    192.124 
_chem_comp.id                CIT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'CITRIC ACID' 
_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 O1 CIT doub 76 n n 
C1 O2 CIT sing 77 n n 
C1 C2 CIT sing 78 n n 
O2 HO2 CIT sing 79 n n 
C2 C3 CIT sing 80 n n 
C2 H21 CIT sing 81 n n 
C2 H22 CIT sing 82 n n 
C3 O7 CIT sing 83 n n 
C3 C4 CIT sing 84 n n 
C3 C6 CIT sing 85 n n 
O7 HO7 CIT sing 86 n n 
C4 C5 CIT sing 87 n n 
C4 H41 CIT sing 88 n n 
C4 H42 CIT sing 89 n n 
C5 O3 CIT doub 90 n n 
C5 O4 CIT sing 91 n n 
O4 HO4 CIT sing 92 n n 
C6 O5 CIT doub 93 n n 
C6 O6 CIT sing 94 n n 
O6 HO6 CIT sing 95 n n 
#
_atom_sites.entry_id                     6YDM 
_atom_sites.fract_transf_matrix[1][1]    0.018822 
_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]    0.013048 
_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]    0.008528 
_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 CIT A 1 301 1 CIT CIT . 
D 3 MG A 1 302 2 MG MG . 
E 4 ACT A 1 303 1 ACT ACT . 
F 5 PDO A 1 304 1 PDO PDO . 
G 3 MG B 1 301 1 MG MG . 
H 4 ACT B 1 302 2 ACT ACT . 
I 6 TRS B 1 303 1 TRS TRS . 
J 7 EDO B 1 304 2 EDO EDO . 
K 8 HOH A 1 401 236 HOH HOH . 
K 8 HOH A 2 402 231 HOH HOH . 
K 8 HOH A 3 403 227 HOH HOH . 
K 8 HOH A 4 404 234 HOH HOH . 
K 8 HOH A 5 405 115 HOH HOH . 
K 8 HOH A 6 406 147 HOH HOH . 
K 8 HOH A 7 407 88 HOH HOH . 
K 8 HOH A 8 408 235 HOH HOH . 
K 8 HOH A 9 409 197 HOH HOH . 
K 8 HOH A 10 410 203 HOH HOH . 
K 8 HOH A 11 411 110 HOH HOH . 
K 8 HOH A 12 412 215 HOH HOH . 
K 8 HOH A 13 413 71 HOH HOH . 
K 8 HOH A 14 414 199 HOH HOH . 
K 8 HOH A 15 415 65 HOH HOH . 
K 8 HOH A 16 416 33 HOH HOH . 
K 8 HOH A 17 417 15 HOH HOH . 
K 8 HOH A 18 418 76 HOH HOH . 
K 8 HOH A 19 419 82 HOH HOH . 
K 8 HOH A 20 420 35 HOH HOH . 
K 8 HOH A 21 421 48 HOH HOH . 
K 8 HOH A 22 422 209 HOH HOH . 
K 8 HOH A 23 423 18 HOH HOH . 
K 8 HOH A 24 424 205 HOH HOH . 
K 8 HOH A 25 425 54 HOH HOH . 
K 8 HOH A 26 426 17 HOH HOH . 
K 8 HOH A 27 427 68 HOH HOH . 
K 8 HOH A 28 428 67 HOH HOH . 
K 8 HOH A 29 429 94 HOH HOH . 
K 8 HOH A 30 430 200 HOH HOH . 
K 8 HOH A 31 431 83 HOH HOH . 
K 8 HOH A 32 432 161 HOH HOH . 
K 8 HOH A 33 433 39 HOH HOH . 
K 8 HOH A 34 434 41 HOH HOH . 
K 8 HOH A 35 435 14 HOH HOH . 
K 8 HOH A 36 436 10 HOH HOH . 
K 8 HOH A 37 437 204 HOH HOH . 
K 8 HOH A 38 438 77 HOH HOH . 
K 8 HOH A 39 439 113 HOH HOH . 
K 8 HOH A 40 440 73 HOH HOH . 
K 8 HOH A 41 441 112 HOH HOH . 
K 8 HOH A 42 442 191 HOH HOH . 
K 8 HOH A 43 443 153 HOH HOH . 
K 8 HOH A 44 444 61 HOH HOH . 
K 8 HOH A 45 445 2 HOH HOH . 
K 8 HOH A 46 446 32 HOH HOH . 
K 8 HOH A 47 447 150 HOH HOH . 
K 8 HOH A 48 448 233 HOH HOH . 
K 8 HOH A 49 449 116 HOH HOH . 
K 8 HOH A 50 450 19 HOH HOH . 
K 8 HOH A 51 451 58 HOH HOH . 
K 8 HOH A 52 452 109 HOH HOH . 
K 8 HOH A 53 453 51 HOH HOH . 
K 8 HOH A 54 454 146 HOH HOH . 
K 8 HOH A 55 455 53 HOH HOH . 
K 8 HOH A 56 456 56 HOH HOH . 
K 8 HOH A 57 457 40 HOH HOH . 
K 8 HOH A 58 458 16 HOH HOH . 
K 8 HOH A 59 459 26 HOH HOH . 
K 8 HOH A 60 460 49 HOH HOH . 
K 8 HOH A 61 461 81 HOH HOH . 
K 8 HOH A 62 462 221 HOH HOH . 
K 8 HOH A 63 463 5 HOH HOH . 
K 8 HOH A 64 464 31 HOH HOH . 
K 8 HOH A 65 465 123 HOH HOH . 
K 8 HOH A 66 466 202 HOH HOH . 
K 8 HOH A 67 467 105 HOH HOH . 
K 8 HOH A 68 468 232 HOH HOH . 
K 8 HOH A 69 469 100 HOH HOH . 
K 8 HOH A 70 470 98 HOH HOH . 
K 8 HOH A 71 471 130 HOH HOH . 
K 8 HOH A 72 472 1 HOH HOH . 
K 8 HOH A 73 473 212 HOH HOH . 
K 8 HOH A 74 474 151 HOH HOH . 
K 8 HOH A 75 475 198 HOH HOH . 
K 8 HOH A 76 476 148 HOH HOH . 
K 8 HOH A 77 477 128 HOH HOH . 
K 8 HOH A 78 478 124 HOH HOH . 
K 8 HOH A 79 479 143 HOH HOH . 
K 8 HOH A 80 480 222 HOH HOH . 
K 8 HOH A 81 481 139 HOH HOH . 
K 8 HOH A 82 482 119 HOH HOH . 
K 8 HOH A 83 483 101 HOH HOH . 
K 8 HOH A 84 484 210 HOH HOH . 
K 8 HOH A 85 485 133 HOH HOH . 
K 8 HOH A 86 486 121 HOH HOH . 
K 8 HOH A 87 487 188 HOH HOH . 
K 8 HOH A 88 488 55 HOH HOH . 
K 8 HOH A 89 489 131 HOH HOH . 
K 8 HOH A 90 490 93 HOH HOH . 
K 8 HOH A 91 491 129 HOH HOH . 
K 8 HOH A 92 492 190 HOH HOH . 
K 8 HOH A 93 493 127 HOH HOH . 
L 8 HOH B 1 401 160 HOH HOH . 
L 8 HOH B 2 402 193 HOH HOH . 
L 8 HOH B 3 403 103 HOH HOH . 
L 8 HOH B 4 404 106 HOH HOH . 
L 8 HOH B 5 405 108 HOH HOH . 
L 8 HOH B 6 406 111 HOH HOH . 
L 8 HOH B 7 407 30 HOH HOH . 
L 8 HOH B 8 408 145 HOH HOH . 
L 8 HOH B 9 409 37 HOH HOH . 
L 8 HOH B 10 410 219 HOH HOH . 
L 8 HOH B 11 411 201 HOH HOH . 
L 8 HOH B 12 412 208 HOH HOH . 
L 8 HOH B 13 413 25 HOH HOH . 
L 8 HOH B 14 414 27 HOH HOH . 
L 8 HOH B 15 415 114 HOH HOH . 
L 8 HOH B 16 416 64 HOH HOH . 
L 8 HOH B 17 417 99 HOH HOH . 
L 8 HOH B 18 418 12 HOH HOH . 
L 8 HOH B 19 419 87 HOH HOH . 
L 8 HOH B 20 420 20 HOH HOH . 
L 8 HOH B 21 421 43 HOH HOH . 
L 8 HOH B 22 422 213 HOH HOH . 
L 8 HOH B 23 423 85 HOH HOH . 
L 8 HOH B 24 424 89 HOH HOH . 
L 8 HOH B 25 425 50 HOH HOH . 
L 8 HOH B 26 426 8 HOH HOH . 
L 8 HOH B 27 427 59 HOH HOH . 
L 8 HOH B 28 428 47 HOH HOH . 
L 8 HOH B 29 429 22 HOH HOH . 
L 8 HOH B 30 430 46 HOH HOH . 
L 8 HOH B 31 431 107 HOH HOH . 
L 8 HOH B 32 432 186 HOH HOH . 
L 8 HOH B 33 433 104 HOH HOH . 
L 8 HOH B 34 434 13 HOH HOH . 
L 8 HOH B 35 435 158 HOH HOH . 
L 8 HOH B 36 436 42 HOH HOH . 
L 8 HOH B 37 437 21 HOH HOH . 
L 8 HOH B 38 438 163 HOH HOH . 
L 8 HOH B 39 439 95 HOH HOH . 
L 8 HOH B 40 440 29 HOH HOH . 
L 8 HOH B 41 441 36 HOH HOH . 
L 8 HOH B 42 442 206 HOH HOH . 
L 8 HOH B 43 443 80 HOH HOH . 
L 8 HOH B 44 444 52 HOH HOH . 
L 8 HOH B 45 445 84 HOH HOH . 
L 8 HOH B 46 446 187 HOH HOH . 
L 8 HOH B 47 447 69 HOH HOH . 
L 8 HOH B 48 448 3 HOH HOH . 
L 8 HOH B 49 449 152 HOH HOH . 
L 8 HOH B 50 450 138 HOH HOH . 
L 8 HOH B 51 451 211 HOH HOH . 
L 8 HOH B 52 452 171 HOH HOH . 
L 8 HOH B 53 453 34 HOH HOH . 
L 8 HOH B 54 454 11 HOH HOH . 
L 8 HOH B 55 455 45 HOH HOH . 
L 8 HOH B 56 456 216 HOH HOH . 
L 8 HOH B 57 457 75 HOH HOH . 
L 8 HOH B 58 458 9 HOH HOH . 
L 8 HOH B 59 459 97 HOH HOH . 
L 8 HOH B 60 460 117 HOH HOH . 
L 8 HOH B 61 461 196 HOH HOH . 
L 8 HOH B 62 462 24 HOH HOH . 
L 8 HOH B 63 463 4 HOH HOH . 
L 8 HOH B 64 464 149 HOH HOH . 
L 8 HOH B 65 465 23 HOH HOH . 
L 8 HOH B 66 466 224 HOH HOH . 
L 8 HOH B 67 467 96 HOH HOH . 
L 8 HOH B 68 468 207 HOH HOH . 
L 8 HOH B 69 469 79 HOH HOH . 
L 8 HOH B 70 470 195 HOH HOH . 
L 8 HOH B 71 471 159 HOH HOH . 
L 8 HOH B 72 472 90 HOH HOH . 
L 8 HOH B 73 473 62 HOH HOH . 
L 8 HOH B 74 474 70 HOH HOH . 
L 8 HOH B 75 475 220 HOH HOH . 
L 8 HOH B 76 476 228 HOH HOH . 
L 8 HOH B 77 477 218 HOH HOH . 
L 8 HOH B 78 478 144 HOH HOH . 
L 8 HOH B 79 479 122 HOH HOH . 
L 8 HOH B 80 480 229 HOH HOH . 
L 8 HOH B 81 481 134 HOH HOH . 
L 8 HOH B 82 482 120 HOH HOH . 
L 8 HOH B 83 483 142 HOH HOH . 
L 8 HOH B 84 484 126 HOH HOH . 
L 8 HOH B 85 485 78 HOH HOH . 
L 8 HOH B 86 486 125 HOH HOH . 
L 8 HOH B 87 487 223 HOH HOH . 
L 8 HOH B 88 488 91 HOH HOH . 
L 8 HOH B 89 489 57 HOH HOH . 
L 8 HOH B 90 490 72 HOH HOH . 
L 8 HOH B 91 491 137 HOH HOH . 
L 8 HOH B 92 492 135 HOH HOH . 
L 8 HOH B 93 493 230 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 CIT . . . C 2 10.973 -29.517 -11.326 1 61.66 ? C1 CIT 301 A 1 
HETATM 2 O O1 CIT . . . C 2 10.696 -29.788 -12.525 1 61.76 ? O1 CIT 301 A 1 
HETATM 3 O O2 CIT . . . C 2 11.075 -28.337 -10.878 1 58.21 ? O2 CIT 301 A 1 
HETATM 4 C C2 CIT . . . C 2 11.172 -30.674 -10.354 1 47.99 ? C2 CIT 301 A 1 
HETATM 5 C C3 CIT . . . C 2 12.323 -30.487 -9.353 1 54.98 ? C3 CIT 301 A 1 
HETATM 6 O O7 CIT . . . C 2 12.071 -29.375 -8.504 1 55.48 ? O7 CIT 301 A 1 
HETATM 7 C C4 CIT . . . C 2 12.542 -31.741 -8.486 1 52.26 ? C4 CIT 301 A 1 
HETATM 8 C C5 CIT . . . C 2 11.385 -32.708 -8.298 1 57.38 ? C5 CIT 301 A 1 
HETATM 9 O O3 CIT . . . C 2 11.22 -33.581 -9.157 1 59.17 ? O3 CIT 301 A 1 
HETATM 10 O O4 CIT . . . C 2 10.689 -32.624 -7.26 1 72.15 ? O4 CIT 301 A 1 
HETATM 11 C C6 CIT . . . C 2 13.614 -30.192 -10.149 1 48.27 ? C6 CIT 301 A 1 
HETATM 12 O O5 CIT . . . C 2 13.961 -31.012 -11.023 1 46.63 ? O5 CIT 301 A 1 
HETATM 13 O O6 CIT . . . C 2 14.212 -29.146 -9.864 1 55.16 ? O6 CIT 301 A 1 
HETATM 14 H H21 CIT . . . C 2 11.335 -31.488 -10.873 1 53.51 ? H21 CIT 301 A 1 
HETATM 15 H H22 CIT . . . C 2 10.339 -30.8 -9.856 1 52.43 ? H22 CIT 301 A 1 
HETATM 16 H HO7 CIT . . . C 2 12.723 -28.801 -8.63 0 30 ? HO7 CIT 301 A 1 
HETATM 17 H H41 CIT . . . C 2 12.825 -31.445 -7.602 1 53.88 ? H41 CIT 301 A 1 
HETATM 18 H H42 CIT . . . C 2 13.285 -32.245 -8.863 1 54.63 ? H42 CIT 301 A 1 
#
_model_server_stats.io_time_ms              70 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    38 
_model_server_stats.query_time_ms           398 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           18 
#