data_5D6T
#
_model_server_result.job_id            6FSOkoXPV-3p-_m8uzInAg 
_model_server_result.datetime_utc      '2025-08-30 23:27:29' 
_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          5d6t 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":403}' 
#
_entry.id    5D6T 
#
_exptl.entry_id    5D6T 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-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          90 
_cell.angle_gamma         90 
_cell.entry_id            5D6T 
_cell.length_a            44.74 
_cell.length_b            58.88 
_cell.length_c            96.79 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5D6T 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C8 H15 N O6' 
_chem_comp.formula_weight    221.208 
_chem_comp.id                NGA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-acetamido-2-deoxy-beta-D-galactopyranose 
_chem_comp.type              'd-saccharide, beta linking' 
_chem_comp.pdbx_synonyms     N-acetyl-beta-D-galactosamine;2-acetamido-2-deoxy-beta-D-galactose;2-acetamido-2-deoxy-D-galactose;2-acetamido-2-deoxy-galactose;N-ACETYL-D-GALACTOSAMINE 
#
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 NGA sing 237 n n 
C1 O1 NGA sing 238 n n 
C1 O5 NGA sing 239 n n 
C1 H1 NGA sing 240 n n 
C2 C3 NGA sing 241 n n 
C2 N2 NGA sing 242 n n 
C2 H2 NGA sing 243 n n 
C3 C4 NGA sing 244 n n 
C3 O3 NGA sing 245 n n 
C3 H3 NGA sing 246 n n 
C4 C5 NGA sing 247 n n 
C4 O4 NGA sing 248 n n 
C4 H4 NGA sing 249 n n 
C5 C6 NGA sing 250 n n 
C5 O5 NGA sing 251 n n 
C5 H5 NGA sing 252 n n 
C6 O6 NGA sing 253 n n 
C6 H61 NGA sing 254 n n 
C6 H62 NGA sing 255 n n 
C7 C8 NGA sing 256 n n 
C7 N2 NGA sing 257 n n 
C7 O7 NGA doub 258 n n 
C8 H81 NGA sing 259 n n 
C8 H82 NGA sing 260 n n 
C8 H83 NGA sing 261 n n 
N2 HN2 NGA sing 262 n n 
O1 HO1 NGA sing 263 n n 
O3 HO3 NGA sing 264 n n 
O4 HO4 NGA sing 265 n n 
O6 HO6 NGA sing 266 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
NGA DGalpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
NGA N-acetyl-b-D-galactopyranosamine 'COMMON NAME' GMML 1 
NGA b-D-GalpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
NGA GalNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 
#
_atom_sites.entry_id                     5D6T 
_atom_sites.fract_transf_matrix[1][1]    0.022351 
_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]    0.016984 
_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]    0.010332 
_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 CL A 1 401 1 CL CL . 
C 3 SO4 A 1 402 1 SO4 SO4 . 
D 4 NGA A 1 403 1 NGA NGA . 
E 5 HOH A 1 501 279 HOH HOH . 
E 5 HOH A 2 502 63 HOH HOH . 
E 5 HOH A 3 503 15 HOH HOH . 
E 5 HOH A 4 504 133 HOH HOH . 
E 5 HOH A 5 505 203 HOH HOH . 
E 5 HOH A 6 506 42 HOH HOH . 
E 5 HOH A 7 507 83 HOH HOH . 
E 5 HOH A 8 508 259 HOH HOH . 
E 5 HOH A 9 509 35 HOH HOH . 
E 5 HOH A 10 510 73 HOH HOH . 
E 5 HOH A 11 511 141 HOH HOH . 
E 5 HOH A 12 512 79 HOH HOH . 
E 5 HOH A 13 513 207 HOH HOH . 
E 5 HOH A 14 514 54 HOH HOH . 
E 5 HOH A 15 515 21 HOH HOH . 
E 5 HOH A 16 516 22 HOH HOH . 
E 5 HOH A 17 517 100 HOH HOH . 
E 5 HOH A 18 518 120 HOH HOH . 
E 5 HOH A 19 519 87 HOH HOH . 
E 5 HOH A 20 520 140 HOH HOH . 
E 5 HOH A 21 521 2 HOH HOH . 
E 5 HOH A 22 522 75 HOH HOH . 
E 5 HOH A 23 523 166 HOH HOH . 
E 5 HOH A 24 524 80 HOH HOH . 
E 5 HOH A 25 525 156 HOH HOH . 
E 5 HOH A 26 526 171 HOH HOH . 
E 5 HOH A 27 527 289 HOH HOH . 
E 5 HOH A 28 528 224 HOH HOH . 
E 5 HOH A 29 529 7 HOH HOH . 
E 5 HOH A 30 530 287 HOH HOH . 
E 5 HOH A 31 531 197 HOH HOH . 
E 5 HOH A 32 532 5 HOH HOH . 
E 5 HOH A 33 533 16 HOH HOH . 
E 5 HOH A 34 534 29 HOH HOH . 
E 5 HOH A 35 535 121 HOH HOH . 
E 5 HOH A 36 536 66 HOH HOH . 
E 5 HOH A 37 537 283 HOH HOH . 
E 5 HOH A 38 538 8 HOH HOH . 
E 5 HOH A 39 539 86 HOH HOH . 
E 5 HOH A 40 540 67 HOH HOH . 
E 5 HOH A 41 541 244 HOH HOH . 
E 5 HOH A 42 542 32 HOH HOH . 
E 5 HOH A 43 543 19 HOH HOH . 
E 5 HOH A 44 544 129 HOH HOH . 
E 5 HOH A 45 545 96 HOH HOH . 
E 5 HOH A 46 546 82 HOH HOH . 
E 5 HOH A 47 547 41 HOH HOH . 
E 5 HOH A 48 548 46 HOH HOH . 
E 5 HOH A 49 549 123 HOH HOH . 
E 5 HOH A 50 550 58 HOH HOH . 
E 5 HOH A 51 551 40 HOH HOH . 
E 5 HOH A 52 552 14 HOH HOH . 
E 5 HOH A 53 553 9 HOH HOH . 
E 5 HOH A 54 554 136 HOH HOH . 
E 5 HOH A 55 555 252 HOH HOH . 
E 5 HOH A 56 556 107 HOH HOH . 
E 5 HOH A 57 557 24 HOH HOH . 
E 5 HOH A 58 558 12 HOH HOH . 
E 5 HOH A 59 559 128 HOH HOH . 
E 5 HOH A 60 560 77 HOH HOH . 
E 5 HOH A 61 561 39 HOH HOH . 
E 5 HOH A 62 562 104 HOH HOH . 
E 5 HOH A 63 563 59 HOH HOH . 
E 5 HOH A 64 564 241 HOH HOH . 
E 5 HOH A 65 565 278 HOH HOH . 
E 5 HOH A 66 566 274 HOH HOH . 
E 5 HOH A 67 567 92 HOH HOH . 
E 5 HOH A 68 568 71 HOH HOH . 
E 5 HOH A 69 569 3 HOH HOH . 
E 5 HOH A 70 570 68 HOH HOH . 
E 5 HOH A 71 571 10 HOH HOH . 
E 5 HOH A 72 572 33 HOH HOH . 
E 5 HOH A 73 573 6 HOH HOH . 
E 5 HOH A 74 574 48 HOH HOH . 
E 5 HOH A 75 575 91 HOH HOH . 
E 5 HOH A 76 576 127 HOH HOH . 
E 5 HOH A 77 577 137 HOH HOH . 
E 5 HOH A 78 578 28 HOH HOH . 
E 5 HOH A 79 579 150 HOH HOH . 
E 5 HOH A 80 580 13 HOH HOH . 
E 5 HOH A 81 581 102 HOH HOH . 
E 5 HOH A 82 582 99 HOH HOH . 
E 5 HOH A 83 583 27 HOH HOH . 
E 5 HOH A 84 584 151 HOH HOH . 
E 5 HOH A 85 585 198 HOH HOH . 
E 5 HOH A 86 586 221 HOH HOH . 
E 5 HOH A 87 587 70 HOH HOH . 
E 5 HOH A 88 588 282 HOH HOH . 
E 5 HOH A 89 589 4 HOH HOH . 
E 5 HOH A 90 590 74 HOH HOH . 
E 5 HOH A 91 591 56 HOH HOH . 
E 5 HOH A 92 592 50 HOH HOH . 
E 5 HOH A 93 593 236 HOH HOH . 
E 5 HOH A 94 594 159 HOH HOH . 
E 5 HOH A 95 595 243 HOH HOH . 
E 5 HOH A 96 596 61 HOH HOH . 
E 5 HOH A 97 597 11 HOH HOH . 
E 5 HOH A 98 598 114 HOH HOH . 
E 5 HOH A 99 599 1 HOH HOH . 
E 5 HOH A 100 600 23 HOH HOH . 
E 5 HOH A 101 601 275 HOH HOH . 
E 5 HOH A 102 602 25 HOH HOH . 
E 5 HOH A 103 603 76 HOH HOH . 
E 5 HOH A 104 604 147 HOH HOH . 
E 5 HOH A 105 605 148 HOH HOH . 
E 5 HOH A 106 606 131 HOH HOH . 
E 5 HOH A 107 607 144 HOH HOH . 
E 5 HOH A 108 608 44 HOH HOH . 
E 5 HOH A 109 609 53 HOH HOH . 
E 5 HOH A 110 610 20 HOH HOH . 
E 5 HOH A 111 611 17 HOH HOH . 
E 5 HOH A 112 612 38 HOH HOH . 
E 5 HOH A 113 613 214 HOH HOH . 
E 5 HOH A 114 614 49 HOH HOH . 
E 5 HOH A 115 615 37 HOH HOH . 
E 5 HOH A 116 616 122 HOH HOH . 
E 5 HOH A 117 617 31 HOH HOH . 
E 5 HOH A 118 618 132 HOH HOH . 
E 5 HOH A 119 619 30 HOH HOH . 
E 5 HOH A 120 620 293 HOH HOH . 
E 5 HOH A 121 621 89 HOH HOH . 
E 5 HOH A 122 622 108 HOH HOH . 
E 5 HOH A 123 623 110 HOH HOH . 
E 5 HOH A 124 624 52 HOH HOH . 
E 5 HOH A 125 625 34 HOH HOH . 
E 5 HOH A 126 626 51 HOH HOH . 
E 5 HOH A 127 627 60 HOH HOH . 
E 5 HOH A 128 628 47 HOH HOH . 
E 5 HOH A 129 629 135 HOH HOH . 
E 5 HOH A 130 630 84 HOH HOH . 
E 5 HOH A 131 631 26 HOH HOH . 
E 5 HOH A 132 632 169 HOH HOH . 
E 5 HOH A 133 633 281 HOH HOH . 
E 5 HOH A 134 634 179 HOH HOH . 
E 5 HOH A 135 635 69 HOH HOH . 
E 5 HOH A 136 636 43 HOH HOH . 
E 5 HOH A 137 637 45 HOH HOH . 
E 5 HOH A 138 638 18 HOH HOH . 
E 5 HOH A 139 639 88 HOH HOH . 
E 5 HOH A 140 640 109 HOH HOH . 
E 5 HOH A 141 641 168 HOH HOH . 
E 5 HOH A 142 642 185 HOH HOH . 
E 5 HOH A 143 643 183 HOH HOH . 
E 5 HOH A 144 644 111 HOH HOH . 
E 5 HOH A 145 645 117 HOH HOH . 
E 5 HOH A 146 646 64 HOH HOH . 
E 5 HOH A 147 647 160 HOH HOH . 
E 5 HOH A 148 648 181 HOH HOH . 
E 5 HOH A 149 649 163 HOH HOH . 
E 5 HOH A 150 650 200 HOH HOH . 
E 5 HOH A 151 651 118 HOH HOH . 
E 5 HOH A 152 652 285 HOH HOH . 
E 5 HOH A 153 653 119 HOH HOH . 
E 5 HOH A 154 654 288 HOH HOH . 
E 5 HOH A 155 655 291 HOH HOH . 
E 5 HOH A 156 656 161 HOH HOH . 
E 5 HOH A 157 657 124 HOH HOH . 
E 5 HOH A 158 658 105 HOH HOH . 
E 5 HOH A 159 659 266 HOH HOH . 
E 5 HOH A 160 660 103 HOH HOH . 
E 5 HOH A 161 661 177 HOH HOH . 
E 5 HOH A 162 662 245 HOH HOH . 
E 5 HOH A 163 663 292 HOH HOH . 
E 5 HOH A 164 664 204 HOH HOH . 
E 5 HOH A 165 665 153 HOH HOH . 
E 5 HOH A 166 666 205 HOH HOH . 
E 5 HOH A 167 667 290 HOH HOH . 
E 5 HOH A 168 668 190 HOH HOH . 
E 5 HOH A 169 669 225 HOH HOH . 
E 5 HOH A 170 670 178 HOH HOH . 
E 5 HOH A 171 671 101 HOH HOH . 
E 5 HOH A 172 672 286 HOH HOH . 
E 5 HOH A 173 673 146 HOH HOH . 
E 5 HOH A 174 674 280 HOH HOH . 
E 5 HOH A 175 675 116 HOH HOH . 
E 5 HOH A 176 676 85 HOH HOH . 
E 5 HOH A 177 677 142 HOH HOH . 
E 5 HOH A 178 678 180 HOH HOH . 
E 5 HOH A 179 679 223 HOH HOH . 
E 5 HOH A 180 680 113 HOH HOH . 
E 5 HOH A 181 681 277 HOH HOH . 
E 5 HOH A 182 682 162 HOH HOH . 
E 5 HOH A 183 683 55 HOH HOH . 
E 5 HOH A 184 684 143 HOH HOH . 
E 5 HOH A 185 685 212 HOH HOH . 
E 5 HOH A 186 686 81 HOH HOH . 
E 5 HOH A 187 687 196 HOH HOH . 
E 5 HOH A 188 688 62 HOH HOH . 
E 5 HOH A 189 689 90 HOH HOH . 
E 5 HOH A 190 690 106 HOH HOH . 
E 5 HOH A 191 691 276 HOH HOH . 
E 5 HOH A 192 692 125 HOH HOH . 
E 5 HOH A 193 693 211 HOH HOH . 
E 5 HOH A 194 694 219 HOH HOH . 
E 5 HOH A 195 695 72 HOH HOH . 
E 5 HOH A 196 696 94 HOH HOH . 
E 5 HOH A 197 697 264 HOH HOH . 
E 5 HOH A 198 698 194 HOH HOH . 
E 5 HOH A 199 699 284 HOH HOH . 
E 5 HOH A 200 700 248 HOH HOH . 
E 5 HOH A 201 701 149 HOH HOH . 
E 5 HOH A 202 702 145 HOH HOH . 
E 5 HOH A 203 703 215 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 NGA . . . D 4 -15.211 13.509 -8.862 1 43.77 ? C1 NGA 403 A 1 
HETATM 2 C C2 NGA . . . D 4 -13.96 12.671 -9.123 1 43.55 ? C2 NGA 403 A 1 
HETATM 3 C C3 NGA . . . D 4 -13.258 12.125 -7.881 1 44.42 ? C3 NGA 403 A 1 
HETATM 4 C C4 NGA . . . D 4 -13.48 12.907 -6.599 1 44.84 ? C4 NGA 403 A 1 
HETATM 5 C C5 NGA . . . D 4 -14.937 13.255 -6.488 1 44.77 ? C5 NGA 403 A 1 
HETATM 6 C C6 NGA . . . D 4 -15.19 13.914 -5.131 1 44.96 ? C6 NGA 403 A 1 
HETATM 7 C C7 NGA . . . D 4 -13.292 10.777 -10.561 1 41.61 ? C7 NGA 403 A 1 
HETATM 8 C C8 NGA . . . D 4 -13.75 9.626 -11.407 1 41.27 ? C8 NGA 403 A 1 
HETATM 9 N N2 NGA . . . D 4 -14.243 11.583 -10.06 1 42.51 ? N2 NGA 403 A 1 
HETATM 10 O O1 NGA . . . D 4 -15.187 14.541 -9.828 1 43.56 ? O1 NGA 403 A 1 
HETATM 11 O O3 NGA . . . D 4 -11.879 12.134 -8.173 1 44.88 ? O3 NGA 403 A 1 
HETATM 12 O O4 NGA . . . D 4 -12.761 14.116 -6.637 1 45.31 ? O4 NGA 403 A 1 
HETATM 13 O O5 NGA . . . D 4 -15.252 14.106 -7.577 1 44.28 ? O5 NGA 403 A 1 
HETATM 14 O O6 NGA . . . D 4 -14.057 14.663 -4.748 1 44.96 ? O6 NGA 403 A 1 
HETATM 15 O O7 NGA . . . D 4 -12.087 10.932 -10.363 1 41.13 ? O7 NGA 403 A 1 
#
_model_server_stats.io_time_ms              59 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           420 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           15 
#