data_5KGJ # _model_server_result.job_id 95xas22gu0rGfjxL4cjqQA _model_server_result.datetime_utc '2024-10-12 06:18:16' _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 5kgj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5KGJ # _exptl.entry_id 5KGJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 179.171 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-amino-2-deoxy-alpha-D-galactopyranose _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 120.81 _cell.angle_gamma 90 _cell.entry_id 5KGJ _cell.length_a 119.076 _cell.length_b 43.84 _cell.length_c 74.169 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KGJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _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 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C6 H13 N O5' _chem_comp.formula_weight 179.171 _chem_comp.id X6X _chem_comp.mon_nstd_flag . _chem_comp.name 2-amino-2-deoxy-alpha-D-galactopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms alpha-D-galactosamine;2-amino-2-deoxy-alpha-D-galactose;2-amino-2-deoxy-D-galactose;2-amino-2-deoxy-galactose # 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 O3 C3 X6X sing 598 n n C3 C4 X6X sing 599 n n C3 C2 X6X sing 600 n n C4 O4 X6X sing 601 n n C4 C5 X6X sing 602 n n N2 C2 X6X sing 603 n n O6 C6 X6X sing 604 n n C5 C6 X6X sing 605 n n C5 O5 X6X sing 606 n n C2 C1 X6X sing 607 n n O1 C1 X6X sing 608 n n C1 O5 X6X sing 609 n n O4 HO4 X6X sing 610 n n C4 H4 X6X sing 611 n n C3 H3 X6X sing 612 n n O3 HO3 X6X sing 613 n n C2 H2 X6X sing 614 n n N2 HN21 X6X sing 615 n n N2 HN22 X6X sing 616 n n C1 H1 X6X sing 617 n n O1 HO1 X6X sing 618 n n C5 H5 X6X sing 619 n n C6 H61 X6X sing 620 n n C6 H62 X6X sing 621 n n O6 HO6 X6X sing 622 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version X6X DGalpNa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 X6X a-D-galactopyranosamine 'COMMON NAME' GMML 1 X6X a-D-GalpN 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 X6X GalN 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5KGJ _atom_sites.fract_transf_matrix[1][1] 0.008398 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005009 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02281 _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] 0.015699 _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 B 2 COA A 1 401 1 COA C0F . C 3 X6X A 1 402 401 X6X X6X . D 4 ACO A 1 403 2 ACO ACO . E 5 EDO A 1 404 1 EDO EDO . F 5 EDO A 1 405 2 EDO EDO . G 5 EDO A 1 406 1 EDO EDO . H 6 EP1 A 1 407 1 EP1 EP1 . I 7 HOH A 1 501 249 HOH HOH . I 7 HOH A 2 502 176 HOH HOH . I 7 HOH A 3 503 267 HOH HOH . I 7 HOH A 4 504 48 HOH HOH . I 7 HOH A 5 505 244 HOH HOH . I 7 HOH A 6 506 10 HOH HOH . I 7 HOH A 7 507 125 HOH HOH . I 7 HOH A 8 508 165 HOH HOH . I 7 HOH A 9 509 270 HOH HOH . I 7 HOH A 10 510 217 HOH HOH . I 7 HOH A 11 511 78 HOH HOH . I 7 HOH A 12 512 260 HOH HOH . I 7 HOH A 13 513 122 HOH HOH . I 7 HOH A 14 514 179 HOH HOH . I 7 HOH A 15 515 221 HOH HOH . I 7 HOH A 16 516 74 HOH HOH . I 7 HOH A 17 517 210 HOH HOH . I 7 HOH A 18 518 139 HOH HOH . I 7 HOH A 19 519 268 HOH HOH . I 7 HOH A 20 520 252 HOH HOH . I 7 HOH A 21 521 238 HOH HOH . I 7 HOH A 22 522 119 HOH HOH . I 7 HOH A 23 523 52 HOH HOH . I 7 HOH A 24 524 83 HOH HOH . I 7 HOH A 25 525 27 HOH HOH . I 7 HOH A 26 526 124 HOH HOH . I 7 HOH A 27 527 22 HOH HOH . I 7 HOH A 28 528 231 HOH HOH . I 7 HOH A 29 529 55 HOH HOH . I 7 HOH A 30 530 273 HOH HOH . I 7 HOH A 31 531 262 HOH HOH . I 7 HOH A 32 532 91 HOH HOH . I 7 HOH A 33 533 96 HOH HOH . I 7 HOH A 34 534 24 HOH HOH . I 7 HOH A 35 535 127 HOH HOH . I 7 HOH A 36 536 132 HOH HOH . I 7 HOH A 37 537 50 HOH HOH . I 7 HOH A 38 538 72 HOH HOH . I 7 HOH A 39 539 56 HOH HOH . I 7 HOH A 40 540 81 HOH HOH . I 7 HOH A 41 541 114 HOH HOH . I 7 HOH A 42 542 251 HOH HOH . I 7 HOH A 43 543 253 HOH HOH . I 7 HOH A 44 544 58 HOH HOH . I 7 HOH A 45 545 241 HOH HOH . I 7 HOH A 46 546 126 HOH HOH . I 7 HOH A 47 547 53 HOH HOH . I 7 HOH A 48 548 7 HOH HOH . I 7 HOH A 49 549 255 HOH HOH . I 7 HOH A 50 550 269 HOH HOH . I 7 HOH A 51 551 14 HOH HOH . I 7 HOH A 52 552 108 HOH HOH . I 7 HOH A 53 553 19 HOH HOH . I 7 HOH A 54 554 28 HOH HOH . I 7 HOH A 55 555 43 HOH HOH . I 7 HOH A 56 556 8 HOH HOH . I 7 HOH A 57 557 23 HOH HOH . I 7 HOH A 58 558 63 HOH HOH . I 7 HOH A 59 559 21 HOH HOH . I 7 HOH A 60 560 45 HOH HOH . I 7 HOH A 61 561 129 HOH HOH . I 7 HOH A 62 562 261 HOH HOH . I 7 HOH A 63 563 109 HOH HOH . I 7 HOH A 64 564 161 HOH HOH . I 7 HOH A 65 565 242 HOH HOH . I 7 HOH A 66 566 6 HOH HOH . I 7 HOH A 67 567 16 HOH HOH . I 7 HOH A 68 568 75 HOH HOH . I 7 HOH A 69 569 59 HOH HOH . I 7 HOH A 70 570 86 HOH HOH . I 7 HOH A 71 571 248 HOH HOH . I 7 HOH A 72 572 265 HOH HOH . I 7 HOH A 73 573 258 HOH HOH . I 7 HOH A 74 574 36 HOH HOH . I 7 HOH A 75 575 30 HOH HOH . I 7 HOH A 76 576 12 HOH HOH . I 7 HOH A 77 577 5 HOH HOH . I 7 HOH A 78 578 256 HOH HOH . I 7 HOH A 79 579 229 HOH HOH . I 7 HOH A 80 580 236 HOH HOH . I 7 HOH A 81 581 134 HOH HOH . I 7 HOH A 82 582 92 HOH HOH . I 7 HOH A 83 583 240 HOH HOH . I 7 HOH A 84 584 232 HOH HOH . I 7 HOH A 85 585 1 HOH HOH . I 7 HOH A 86 586 185 HOH HOH . I 7 HOH A 87 587 4 HOH HOH . I 7 HOH A 88 588 9 HOH HOH . I 7 HOH A 89 589 90 HOH HOH . I 7 HOH A 90 590 191 HOH HOH . I 7 HOH A 91 591 29 HOH HOH . I 7 HOH A 92 592 17 HOH HOH . I 7 HOH A 93 593 95 HOH HOH . I 7 HOH A 94 594 271 HOH HOH . I 7 HOH A 95 595 47 HOH HOH . I 7 HOH A 96 596 84 HOH HOH . I 7 HOH A 97 597 243 HOH HOH . I 7 HOH A 98 598 60 HOH HOH . I 7 HOH A 99 599 39 HOH HOH . I 7 HOH A 100 600 31 HOH HOH . I 7 HOH A 101 601 259 HOH HOH . I 7 HOH A 102 602 38 HOH HOH . I 7 HOH A 103 603 33 HOH HOH . I 7 HOH A 104 604 35 HOH HOH . I 7 HOH A 105 605 140 HOH HOH . I 7 HOH A 106 606 207 HOH HOH . I 7 HOH A 107 607 199 HOH HOH . I 7 HOH A 108 608 136 HOH HOH . I 7 HOH A 109 609 98 HOH HOH . I 7 HOH A 110 610 70 HOH HOH . I 7 HOH A 111 611 235 HOH HOH . I 7 HOH A 112 612 62 HOH HOH . I 7 HOH A 113 613 73 HOH HOH . I 7 HOH A 114 614 116 HOH HOH . I 7 HOH A 115 615 64 HOH HOH . I 7 HOH A 116 616 152 HOH HOH . I 7 HOH A 117 617 151 HOH HOH . I 7 HOH A 118 618 160 HOH HOH . I 7 HOH A 119 619 208 HOH HOH . I 7 HOH A 120 620 87 HOH HOH . I 7 HOH A 121 621 212 HOH HOH . I 7 HOH A 122 622 263 HOH HOH . I 7 HOH A 123 623 215 HOH HOH . I 7 HOH A 124 624 18 HOH HOH . I 7 HOH A 125 625 11 HOH HOH . I 7 HOH A 126 626 211 HOH HOH . I 7 HOH A 127 627 219 HOH HOH . I 7 HOH A 128 628 77 HOH HOH . I 7 HOH A 129 629 13 HOH HOH . I 7 HOH A 130 630 94 HOH HOH . I 7 HOH A 131 631 237 HOH HOH . I 7 HOH A 132 632 220 HOH HOH . I 7 HOH A 133 633 34 HOH HOH . I 7 HOH A 134 634 130 HOH HOH . I 7 HOH A 135 635 57 HOH HOH . I 7 HOH A 136 636 46 HOH HOH . I 7 HOH A 137 637 227 HOH HOH . I 7 HOH A 138 638 69 HOH HOH . I 7 HOH A 139 639 245 HOH HOH . I 7 HOH A 140 640 264 HOH HOH . I 7 HOH A 141 641 233 HOH HOH . I 7 HOH A 142 642 51 HOH HOH . I 7 HOH A 143 643 32 HOH HOH . I 7 HOH A 144 644 213 HOH HOH . I 7 HOH A 145 645 224 HOH HOH . I 7 HOH A 146 646 226 HOH HOH . I 7 HOH A 147 647 230 HOH HOH . I 7 HOH A 148 648 225 HOH HOH . I 7 HOH A 149 649 54 HOH HOH . I 7 HOH A 150 650 153 HOH HOH . I 7 HOH A 151 651 218 HOH HOH . I 7 HOH A 152 652 222 HOH HOH . I 7 HOH A 153 653 228 HOH HOH . I 7 HOH A 154 654 104 HOH HOH . I 7 HOH A 155 655 183 HOH HOH . I 7 HOH A 156 656 209 HOH HOH . I 7 HOH A 157 657 189 HOH HOH . I 7 HOH A 158 658 272 HOH HOH . I 7 HOH A 159 659 254 HOH HOH . I 7 HOH A 160 660 26 HOH HOH . I 7 HOH A 161 661 246 HOH HOH . I 7 HOH A 162 662 239 HOH HOH . I 7 HOH A 163 663 234 HOH HOH . I 7 HOH A 164 664 79 HOH HOH . I 7 HOH A 165 665 68 HOH HOH . I 7 HOH A 166 666 247 HOH HOH . I 7 HOH A 167 667 115 HOH HOH . I 7 HOH A 168 668 203 HOH HOH . I 7 HOH A 169 669 206 HOH HOH . I 7 HOH A 170 670 144 HOH HOH . I 7 HOH A 171 671 223 HOH HOH . I 7 HOH A 172 672 175 HOH HOH . I 7 HOH A 173 673 214 HOH HOH . I 7 HOH A 174 674 105 HOH HOH . I 7 HOH A 175 675 266 HOH HOH . I 7 HOH A 176 676 188 HOH HOH . I 7 HOH A 177 677 157 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 O O4 X6X . . . C 3 11.688 11.766 16.598 1 34.32 ? O4 X6X 402 A 1 HETATM 2 C C4 X6X . . . C 3 10.712 12.312 15.69 1 38.03 ? C4 X6X 402 A 1 HETATM 3 C C3 X6X . . . C 3 10.946 11.811 14.256 1 33.68 ? C3 X6X 402 A 1 HETATM 4 O O3 X6X . . . C 3 11.028 10.39 14.331 1 32.6 ? O3 X6X 402 A 1 HETATM 5 C C2 X6X . . . C 3 12.226 12.375 13.648 1 31.06 ? C2 X6X 402 A 1 HETATM 6 N N2 X6X . . . C 3 12.33 12.161 12.193 1 31.2 ? N2 X6X 402 A 1 HETATM 7 C C1 X6X . . . C 3 12.467 13.846 14.024 1 34.41 ? C1 X6X 402 A 1 HETATM 8 O O1 X6X . . . C 3 13.024 14.625 12.929 1 28.36 ? O1 X6X 402 A 1 HETATM 9 O O5 X6X . . . C 3 11.41 14.524 14.727 1 36.64 ? O5 X6X 402 A 1 HETATM 10 C C5 X6X . . . C 3 10.583 13.846 15.703 1 33.82 ? C5 X6X 402 A 1 HETATM 11 C C6 X6X . . . C 3 10.735 14.477 17.087 1 35.93 ? C6 X6X 402 A 1 HETATM 12 O O6 X6X . . . C 3 10.57 15.886 16.912 1 31.48 ? O6 X6X 402 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 12 #