data_8PD1
#
_model_server_result.job_id            90p_JERAQIkNMidpR4E5CA 
_model_server_result.datetime_utc      '2024-11-29 17:57:14' 
_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          8pd1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":507}' 
#
_entry.id    8PD1 
#
_exptl.entry_id    8PD1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              78.133 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'DIMETHYL SULFOXIDE' 
_entity.pdbx_number_of_molecules    8 
_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            8PD1 
_cell.length_a            100.99 
_cell.length_b            103.76 
_cell.length_c            141.61 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8PD1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 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,D,E,F,G,H,I,J,K,L,M,N,O,CA 1 1,3 
B,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,DA 2 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' 3_454 -x-1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 -100.99 0 -70.805 
3 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 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 D N N 
? 2 F N N 
? 2 H N N 
? 2 I N N 
? 2 P N N 
? 2 V N N 
? 2 W N N 
#
_chem_comp.formula           'C2 H6 O S' 
_chem_comp.formula_weight    78.133 
_chem_comp.id                DMS 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'DIMETHYL SULFOXIDE' 
_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
S O DMS doub 83 n n 
S C1 DMS sing 84 n n 
S C2 DMS sing 85 n n 
C1 H11 DMS sing 86 n n 
C1 H12 DMS sing 87 n n 
C1 H13 DMS sing 88 n n 
C2 H21 DMS sing 89 n n 
C2 H22 DMS sing 90 n n 
C2 H23 DMS sing 91 n n 
#
_atom_sites.entry_id                     8PD1 
_atom_sites.fract_transf_matrix[1][1]    0.009902 
_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]    0.009638 
_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]    0.007062 
_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 DMS A 1 501 501 DMS DMS . 
D 2 DMS A 1 502 503 DMS DMS . 
E 3 PO4 A 1 503 504 PO4 PO4 . 
F 2 DMS A 1 504 505 DMS DMS . 
G 4 FMT A 1 505 507 FMT FMT . 
H 2 DMS A 1 506 509 DMS DMS . 
I 2 DMS A 1 507 510 DMS DMS . 
J 4 FMT A 1 508 511 FMT FMT . 
K 3 PO4 A 1 509 513 PO4 PO4 . 
L 4 FMT A 1 510 515 FMT FMT . 
M 4 FMT A 1 511 517 FMT FMT . 
N 4 FMT A 1 512 519 FMT FMT . 
O 5 YHU A 1 513 520 YHU In8 . 
P 2 DMS B 1 501 501 DMS DMS . 
Q 4 FMT B 1 502 503 FMT FMT . 
R 4 FMT B 1 503 504 FMT FMT . 
S 4 FMT B 1 504 505 FMT FMT . 
T 4 FMT B 1 505 506 FMT FMT . 
U 4 FMT B 1 506 507 FMT FMT . 
V 2 DMS B 1 507 508 DMS DMS . 
W 2 DMS B 1 508 509 DMS DMS . 
X 4 FMT B 1 509 512 FMT FMT . 
Y 4 FMT B 1 510 515 FMT FMT . 
Z 4 FMT B 1 511 519 FMT FMT . 
AA 5 YHU B 1 512 524 YHU In8 . 
BA 6 CL B 1 513 1 CL CL . 
CA 7 HOH A 1 601 293 HOH HOH . 
CA 7 HOH A 2 602 115 HOH HOH . 
CA 7 HOH A 3 603 26 HOH HOH . 
CA 7 HOH A 4 604 287 HOH HOH . 
CA 7 HOH A 5 605 164 HOH HOH . 
CA 7 HOH A 6 606 270 HOH HOH . 
CA 7 HOH A 7 607 105 HOH HOH . 
CA 7 HOH A 8 608 63 HOH HOH . 
CA 7 HOH A 9 609 104 HOH HOH . 
CA 7 HOH A 10 610 204 HOH HOH . 
CA 7 HOH A 11 611 123 HOH HOH . 
CA 7 HOH A 12 612 218 HOH HOH . 
CA 7 HOH A 13 613 122 HOH HOH . 
CA 7 HOH A 14 614 158 HOH HOH . 
CA 7 HOH A 15 615 72 HOH HOH . 
CA 7 HOH A 16 616 91 HOH HOH . 
CA 7 HOH A 17 617 41 HOH HOH . 
CA 7 HOH A 18 618 237 HOH HOH . 
CA 7 HOH A 19 619 170 HOH HOH . 
CA 7 HOH A 20 620 266 HOH HOH . 
CA 7 HOH A 21 621 53 HOH HOH . 
CA 7 HOH A 22 622 148 HOH HOH . 
CA 7 HOH A 23 623 54 HOH HOH . 
CA 7 HOH A 24 624 192 HOH HOH . 
CA 7 HOH A 25 625 9 HOH HOH . 
CA 7 HOH A 26 626 13 HOH HOH . 
CA 7 HOH A 27 627 217 HOH HOH . 
CA 7 HOH A 28 628 126 HOH HOH . 
CA 7 HOH A 29 629 262 HOH HOH . 
CA 7 HOH A 30 630 196 HOH HOH . 
CA 7 HOH A 31 631 24 HOH HOH . 
CA 7 HOH A 32 632 86 HOH HOH . 
CA 7 HOH A 33 633 14 HOH HOH . 
CA 7 HOH A 34 634 3 HOH HOH . 
CA 7 HOH A 35 635 84 HOH HOH . 
CA 7 HOH A 36 636 147 HOH HOH . 
CA 7 HOH A 37 637 211 HOH HOH . 
CA 7 HOH A 38 638 108 HOH HOH . 
CA 7 HOH A 39 639 222 HOH HOH . 
CA 7 HOH A 40 640 125 HOH HOH . 
CA 7 HOH A 41 641 20 HOH HOH . 
CA 7 HOH A 42 642 145 HOH HOH . 
CA 7 HOH A 43 643 31 HOH HOH . 
CA 7 HOH A 44 644 40 HOH HOH . 
CA 7 HOH A 45 645 178 HOH HOH . 
CA 7 HOH A 46 646 37 HOH HOH . 
CA 7 HOH A 47 647 52 HOH HOH . 
CA 7 HOH A 48 648 269 HOH HOH . 
CA 7 HOH A 49 649 144 HOH HOH . 
CA 7 HOH A 50 650 198 HOH HOH . 
CA 7 HOH A 51 651 239 HOH HOH . 
CA 7 HOH A 52 652 213 HOH HOH . 
CA 7 HOH A 53 653 33 HOH HOH . 
CA 7 HOH A 54 654 216 HOH HOH . 
CA 7 HOH A 55 655 234 HOH HOH . 
CA 7 HOH A 56 656 113 HOH HOH . 
CA 7 HOH A 57 657 36 HOH HOH . 
CA 7 HOH A 58 658 133 HOH HOH . 
CA 7 HOH A 59 659 12 HOH HOH . 
CA 7 HOH A 60 660 274 HOH HOH . 
CA 7 HOH A 61 661 169 HOH HOH . 
CA 7 HOH A 62 662 44 HOH HOH . 
CA 7 HOH A 63 663 64 HOH HOH . 
CA 7 HOH A 64 664 251 HOH HOH . 
CA 7 HOH A 65 665 1 HOH HOH . 
CA 7 HOH A 66 666 193 HOH HOH . 
CA 7 HOH A 67 667 111 HOH HOH . 
CA 7 HOH A 68 668 15 HOH HOH . 
CA 7 HOH A 69 669 103 HOH HOH . 
CA 7 HOH A 70 670 224 HOH HOH . 
CA 7 HOH A 71 671 59 HOH HOH . 
CA 7 HOH A 72 672 128 HOH HOH . 
CA 7 HOH A 73 673 85 HOH HOH . 
CA 7 HOH A 74 674 194 HOH HOH . 
CA 7 HOH A 75 675 21 HOH HOH . 
CA 7 HOH A 76 676 78 HOH HOH . 
CA 7 HOH A 77 677 281 HOH HOH . 
CA 7 HOH A 78 678 28 HOH HOH . 
CA 7 HOH A 79 679 174 HOH HOH . 
CA 7 HOH A 80 680 106 HOH HOH . 
CA 7 HOH A 81 681 151 HOH HOH . 
CA 7 HOH A 82 682 283 HOH HOH . 
CA 7 HOH A 83 683 49 HOH HOH . 
CA 7 HOH A 84 684 200 HOH HOH . 
CA 7 HOH A 85 685 2 HOH HOH . 
CA 7 HOH A 86 686 22 HOH HOH . 
CA 7 HOH A 87 687 87 HOH HOH . 
CA 7 HOH A 88 688 238 HOH HOH . 
CA 7 HOH A 89 689 257 HOH HOH . 
CA 7 HOH A 90 690 62 HOH HOH . 
CA 7 HOH A 91 691 99 HOH HOH . 
CA 7 HOH A 92 692 30 HOH HOH . 
CA 7 HOH A 93 693 27 HOH HOH . 
CA 7 HOH A 94 694 205 HOH HOH . 
CA 7 HOH A 95 695 100 HOH HOH . 
CA 7 HOH A 96 696 80 HOH HOH . 
CA 7 HOH A 97 697 98 HOH HOH . 
CA 7 HOH A 98 698 284 HOH HOH . 
CA 7 HOH A 99 699 221 HOH HOH . 
CA 7 HOH A 100 700 207 HOH HOH . 
CA 7 HOH A 101 701 181 HOH HOH . 
CA 7 HOH A 102 702 236 HOH HOH . 
CA 7 HOH A 103 703 232 HOH HOH . 
CA 7 HOH A 104 704 140 HOH HOH . 
CA 7 HOH A 105 705 278 HOH HOH . 
CA 7 HOH A 106 706 233 HOH HOH . 
CA 7 HOH A 107 707 117 HOH HOH . 
CA 7 HOH A 108 708 210 HOH HOH . 
CA 7 HOH A 109 709 93 HOH HOH . 
CA 7 HOH A 110 710 166 HOH HOH . 
CA 7 HOH A 111 711 139 HOH HOH . 
CA 7 HOH A 112 712 175 HOH HOH . 
CA 7 HOH A 113 713 225 HOH HOH . 
CA 7 HOH A 114 714 290 HOH HOH . 
CA 7 HOH A 115 715 167 HOH HOH . 
CA 7 HOH A 116 716 138 HOH HOH . 
CA 7 HOH A 117 717 179 HOH HOH . 
CA 7 HOH A 118 718 180 HOH HOH . 
CA 7 HOH A 119 719 245 HOH HOH . 
CA 7 HOH A 120 720 162 HOH HOH . 
CA 7 HOH A 121 721 230 HOH HOH . 
CA 7 HOH A 122 722 214 HOH HOH . 
CA 7 HOH A 123 723 132 HOH HOH . 
CA 7 HOH A 124 724 275 HOH HOH . 
CA 7 HOH A 125 725 244 HOH HOH . 
CA 7 HOH A 126 726 134 HOH HOH . 
CA 7 HOH A 127 727 265 HOH HOH . 
CA 7 HOH A 128 728 202 HOH HOH . 
CA 7 HOH A 129 729 229 HOH HOH . 
CA 7 HOH A 130 730 203 HOH HOH . 
CA 7 HOH A 131 731 131 HOH HOH . 
CA 7 HOH A 132 732 142 HOH HOH . 
CA 7 HOH A 133 733 223 HOH HOH . 
CA 7 HOH A 134 734 152 HOH HOH . 
CA 7 HOH A 135 735 231 HOH HOH . 
CA 7 HOH A 136 736 209 HOH HOH . 
CA 7 HOH A 137 737 206 HOH HOH . 
DA 7 HOH B 1 601 70 HOH HOH . 
DA 7 HOH B 2 602 120 HOH HOH . 
DA 7 HOH B 3 603 118 HOH HOH . 
DA 7 HOH B 4 604 119 HOH HOH . 
DA 7 HOH B 5 605 66 HOH HOH . 
DA 7 HOH B 6 606 248 HOH HOH . 
DA 7 HOH B 7 607 285 HOH HOH . 
DA 7 HOH B 8 608 43 HOH HOH . 
DA 7 HOH B 9 609 46 HOH HOH . 
DA 7 HOH B 10 610 161 HOH HOH . 
DA 7 HOH B 11 611 94 HOH HOH . 
DA 7 HOH B 12 612 83 HOH HOH . 
DA 7 HOH B 13 613 254 HOH HOH . 
DA 7 HOH B 14 614 272 HOH HOH . 
DA 7 HOH B 15 615 79 HOH HOH . 
DA 7 HOH B 16 616 263 HOH HOH . 
DA 7 HOH B 17 617 252 HOH HOH . 
DA 7 HOH B 18 618 114 HOH HOH . 
DA 7 HOH B 19 619 172 HOH HOH . 
DA 7 HOH B 20 620 73 HOH HOH . 
DA 7 HOH B 21 621 89 HOH HOH . 
DA 7 HOH B 22 622 10 HOH HOH . 
DA 7 HOH B 23 623 176 HOH HOH . 
DA 7 HOH B 24 624 76 HOH HOH . 
DA 7 HOH B 25 625 8 HOH HOH . 
DA 7 HOH B 26 626 149 HOH HOH . 
DA 7 HOH B 27 627 136 HOH HOH . 
DA 7 HOH B 28 628 197 HOH HOH . 
DA 7 HOH B 29 629 68 HOH HOH . 
DA 7 HOH B 30 630 255 HOH HOH . 
DA 7 HOH B 31 631 171 HOH HOH . 
DA 7 HOH B 32 632 159 HOH HOH . 
DA 7 HOH B 33 633 294 HOH HOH . 
DA 7 HOH B 34 634 71 HOH HOH . 
DA 7 HOH B 35 635 17 HOH HOH . 
DA 7 HOH B 36 636 92 HOH HOH . 
DA 7 HOH B 37 637 16 HOH HOH . 
DA 7 HOH B 38 638 48 HOH HOH . 
DA 7 HOH B 39 639 177 HOH HOH . 
DA 7 HOH B 40 640 90 HOH HOH . 
DA 7 HOH B 41 641 25 HOH HOH . 
DA 7 HOH B 42 642 183 HOH HOH . 
DA 7 HOH B 43 643 75 HOH HOH . 
DA 7 HOH B 44 644 34 HOH HOH . 
DA 7 HOH B 45 645 38 HOH HOH . 
DA 7 HOH B 46 646 185 HOH HOH . 
DA 7 HOH B 47 647 11 HOH HOH . 
DA 7 HOH B 48 648 60 HOH HOH . 
DA 7 HOH B 49 649 219 HOH HOH . 
DA 7 HOH B 50 650 155 HOH HOH . 
DA 7 HOH B 51 651 212 HOH HOH . 
DA 7 HOH B 52 652 4 HOH HOH . 
DA 7 HOH B 53 653 65 HOH HOH . 
DA 7 HOH B 54 654 97 HOH HOH . 
DA 7 HOH B 55 655 45 HOH HOH . 
DA 7 HOH B 56 656 186 HOH HOH . 
DA 7 HOH B 57 657 215 HOH HOH . 
DA 7 HOH B 58 658 227 HOH HOH . 
DA 7 HOH B 59 659 6 HOH HOH . 
DA 7 HOH B 60 660 264 HOH HOH . 
DA 7 HOH B 61 661 110 HOH HOH . 
DA 7 HOH B 62 662 253 HOH HOH . 
DA 7 HOH B 63 663 220 HOH HOH . 
DA 7 HOH B 64 664 18 HOH HOH . 
DA 7 HOH B 65 665 82 HOH HOH . 
DA 7 HOH B 66 666 19 HOH HOH . 
DA 7 HOH B 67 667 228 HOH HOH . 
DA 7 HOH B 68 668 107 HOH HOH . 
DA 7 HOH B 69 669 35 HOH HOH . 
DA 7 HOH B 70 670 121 HOH HOH . 
DA 7 HOH B 71 671 102 HOH HOH . 
DA 7 HOH B 72 672 116 HOH HOH . 
DA 7 HOH B 73 673 39 HOH HOH . 
DA 7 HOH B 74 674 141 HOH HOH . 
DA 7 HOH B 75 675 157 HOH HOH . 
DA 7 HOH B 76 676 163 HOH HOH . 
DA 7 HOH B 77 677 74 HOH HOH . 
DA 7 HOH B 78 678 260 HOH HOH . 
DA 7 HOH B 79 679 124 HOH HOH . 
DA 7 HOH B 80 680 81 HOH HOH . 
DA 7 HOH B 81 681 295 HOH HOH . 
DA 7 HOH B 82 682 42 HOH HOH . 
DA 7 HOH B 83 683 109 HOH HOH . 
DA 7 HOH B 84 684 153 HOH HOH . 
DA 7 HOH B 85 685 32 HOH HOH . 
DA 7 HOH B 86 686 7 HOH HOH . 
DA 7 HOH B 87 687 182 HOH HOH . 
DA 7 HOH B 88 688 61 HOH HOH . 
DA 7 HOH B 89 689 23 HOH HOH . 
DA 7 HOH B 90 690 129 HOH HOH . 
DA 7 HOH B 91 691 288 HOH HOH . 
DA 7 HOH B 92 692 250 HOH HOH . 
DA 7 HOH B 93 693 95 HOH HOH . 
DA 7 HOH B 94 694 208 HOH HOH . 
DA 7 HOH B 95 695 135 HOH HOH . 
DA 7 HOH B 96 696 5 HOH HOH . 
DA 7 HOH B 97 697 292 HOH HOH . 
DA 7 HOH B 98 698 271 HOH HOH . 
DA 7 HOH B 99 699 241 HOH HOH . 
DA 7 HOH B 100 700 240 HOH HOH . 
DA 7 HOH B 101 701 188 HOH HOH . 
DA 7 HOH B 102 702 127 HOH HOH . 
DA 7 HOH B 103 703 201 HOH HOH . 
DA 7 HOH B 104 704 165 HOH HOH . 
DA 7 HOH B 105 705 291 HOH HOH . 
DA 7 HOH B 106 706 259 HOH HOH . 
DA 7 HOH B 107 707 242 HOH HOH . 
DA 7 HOH B 108 708 277 HOH HOH . 
DA 7 HOH B 109 709 289 HOH HOH . 
DA 7 HOH B 110 710 96 HOH HOH . 
DA 7 HOH B 111 711 143 HOH HOH . 
DA 7 HOH B 112 712 256 HOH HOH . 
DA 7 HOH B 113 713 146 HOH HOH . 
DA 7 HOH B 114 714 156 HOH HOH . 
DA 7 HOH B 115 715 101 HOH HOH . 
DA 7 HOH B 116 716 160 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 S S DMS . . . V 2 -34.565 -0.344 -63.46 1 86.13 ? S DMS 507 B 1 
HETATM 2 O O DMS . . . V 2 -33.522 0.51 -64.148 1 72.35 ? O DMS 507 B 1 
HETATM 3 C C1 DMS . . . V 2 -34.11 -2.029 -63.79 1 90.53 ? C1 DMS 507 B 1 
HETATM 4 C C2 DMS . . . V 2 -36.009 -0.293 -64.496 1 87.05 ? C2 DMS 507 B 1 
#
_model_server_stats.io_time_ms              30 
_model_server_stats.parse_time_ms           46 
_model_server_stats.create_model_time_ms    120 
_model_server_stats.query_time_ms           1305 
_model_server_stats.encode_time_ms          25 
_model_server_stats.element_count           4 
#