data_1D3D # _model_server_result.job_id ecDjFwF07MwX2-5tDWC1eQ _model_server_result.datetime_utc '2024-11-21 17:20:50' _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 1d3d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 1D3D # _exptl.entry_id 1D3D _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-glucopyranose _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 100.6 _cell.angle_gamma 90 _cell.entry_id 1D3D _cell.length_a 71.11 _cell.length_b 71.888 _cell.length_c 73.321 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D3D _symmetry.cell_setting monoclinic _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 ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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 # _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 # 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 disulf ? disulf1 A SG CYS 4 A CYS 9 1_555 B SG CYS 119 B CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf2 B SG CYS 28 B CYS 64 1_555 B SG CYS 44 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 B SG CYS 173 B CYS 209 1_555 B SG CYS 187 B CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 B SG CYS 201 B CYS 237 1_555 B SG CYS 231 B CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 B ND2 ASN 53 B ASN 89 1_555 D C1 NAG . B NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale2 C C GLU 9 H GLU 308 1_555 C N TYS 10 H TYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 C C TYS 10 H TYS 309 1_555 C N LEU 11 H LEU 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? metalc ? metalc1 B O LYS 174 B LYS 210 1_555 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc2 B O THR 177 B THR 213 1_555 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc3 B O PHE 215 B PHE 251 4_446 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc4 B O ARG 233 B ARG 269 1_555 F NA NA . B NA 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc5 B O LYS 236 B LYS 272 1_555 F NA NA . B NA 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc6 E NA NA . B NA 398 1_555 I O HOH . B HOH 547 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc7 E NA NA . B NA 398 1_555 I O HOH . B HOH 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc8 E NA NA . B NA 398 1_555 I O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.858 ? metalc ? metalc9 F NA NA . B NA 399 1_555 I O HOH . B HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc10 F NA NA . B NA 399 1_555 I O HOH . B HOH 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc11 F NA NA . B NA 399 1_555 I O HOH . B HOH 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 NAG sing 315 n n C1 O1 NAG sing 316 n n C1 O5 NAG sing 317 n n C1 H1 NAG sing 318 n n C2 C3 NAG sing 319 n n C2 N2 NAG sing 320 n n C2 H2 NAG sing 321 n n C3 C4 NAG sing 322 n n C3 O3 NAG sing 323 n n C3 H3 NAG sing 324 n n C4 C5 NAG sing 325 n n C4 O4 NAG sing 326 n n C4 H4 NAG sing 327 n n C5 C6 NAG sing 328 n n C5 O5 NAG sing 329 n n C5 H5 NAG sing 330 n n C6 O6 NAG sing 331 n n C6 H61 NAG sing 332 n n C6 H62 NAG sing 333 n n C7 C8 NAG sing 334 n n C7 N2 NAG sing 335 n n C7 O7 NAG doub 336 n n C8 H81 NAG sing 337 n n C8 H82 NAG sing 338 n n C8 H83 NAG sing 339 n n N2 HN2 NAG sing 340 n n O1 HO1 NAG sing 341 n n O3 HO3 NAG sing 342 n n O4 HO4 NAG sing 343 n n O6 HO6 NAG sing 344 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 NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 1D3D _atom_sites.fract_transf_matrix[1][1] 0.014063 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002632 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013911 _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] 0.013875 _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 D 4 NAG B 1 500 500 NAG NAG . E 5 NA B 1 398 398 NA NA . F 5 NA B 1 399 399 NA NA . G 6 BZT B 1 400 400 BZT BZT . H 7 HOH A 1 34 26 HOH TIP . H 7 HOH A 2 35 31 HOH TIP . H 7 HOH A 3 36 52 HOH TIP . H 7 HOH A 4 37 57 HOH TIP . H 7 HOH A 5 38 58 HOH TIP . H 7 HOH A 6 39 60 HOH TIP . H 7 HOH A 7 40 86 HOH TIP . H 7 HOH A 8 41 89 HOH TIP . H 7 HOH A 9 42 92 HOH TIP . H 7 HOH A 10 43 94 HOH TIP . H 7 HOH A 11 44 102 HOH TIP . H 7 HOH A 12 45 110 HOH TIP . I 7 HOH B 1 501 1 HOH TIP . I 7 HOH B 2 502 2 HOH TIP . I 7 HOH B 3 503 3 HOH TIP . I 7 HOH B 4 504 4 HOH TIP . I 7 HOH B 5 505 5 HOH TIP . I 7 HOH B 6 506 6 HOH TIP . I 7 HOH B 7 507 7 HOH TIP . I 7 HOH B 8 508 8 HOH TIP . I 7 HOH B 9 509 9 HOH TIP . I 7 HOH B 10 510 10 HOH TIP . I 7 HOH B 11 511 11 HOH TIP . I 7 HOH B 12 512 12 HOH TIP . I 7 HOH B 13 513 13 HOH TIP . I 7 HOH B 14 514 14 HOH TIP . I 7 HOH B 15 515 15 HOH TIP . I 7 HOH B 16 516 16 HOH TIP . I 7 HOH B 17 517 17 HOH TIP . I 7 HOH B 18 518 18 HOH TIP . I 7 HOH B 19 519 19 HOH TIP . I 7 HOH B 20 520 20 HOH TIP . I 7 HOH B 21 521 21 HOH TIP . I 7 HOH B 22 522 22 HOH TIP . I 7 HOH B 23 523 23 HOH TIP . I 7 HOH B 24 524 24 HOH TIP . I 7 HOH B 25 525 25 HOH TIP . I 7 HOH B 26 526 27 HOH TIP . I 7 HOH B 27 527 28 HOH TIP . I 7 HOH B 28 528 29 HOH TIP . I 7 HOH B 29 529 30 HOH TIP . I 7 HOH B 30 530 32 HOH TIP . I 7 HOH B 31 531 33 HOH TIP . I 7 HOH B 32 532 34 HOH TIP . I 7 HOH B 33 533 35 HOH TIP . I 7 HOH B 34 534 36 HOH TIP . I 7 HOH B 35 535 37 HOH TIP . I 7 HOH B 36 536 38 HOH TIP . I 7 HOH B 37 537 39 HOH TIP . I 7 HOH B 38 538 40 HOH TIP . I 7 HOH B 39 539 41 HOH TIP . I 7 HOH B 40 540 42 HOH TIP . I 7 HOH B 41 541 43 HOH TIP . I 7 HOH B 42 542 44 HOH TIP . I 7 HOH B 43 543 45 HOH TIP . I 7 HOH B 44 544 46 HOH TIP . I 7 HOH B 45 545 47 HOH TIP . I 7 HOH B 46 546 48 HOH TIP . I 7 HOH B 47 547 49 HOH TIP . I 7 HOH B 48 548 50 HOH TIP . I 7 HOH B 49 549 51 HOH TIP . I 7 HOH B 50 550 53 HOH TIP . I 7 HOH B 51 551 54 HOH TIP . I 7 HOH B 52 552 55 HOH TIP . I 7 HOH B 53 553 56 HOH TIP . I 7 HOH B 54 554 59 HOH TIP . I 7 HOH B 55 555 61 HOH TIP . I 7 HOH B 56 556 62 HOH TIP . I 7 HOH B 57 557 63 HOH TIP . I 7 HOH B 58 558 64 HOH TIP . I 7 HOH B 59 559 65 HOH TIP . I 7 HOH B 60 560 66 HOH TIP . I 7 HOH B 61 561 67 HOH TIP . I 7 HOH B 62 562 68 HOH TIP . I 7 HOH B 63 563 69 HOH TIP . I 7 HOH B 64 564 70 HOH TIP . I 7 HOH B 65 565 71 HOH TIP . I 7 HOH B 66 566 72 HOH TIP . I 7 HOH B 67 567 73 HOH TIP . I 7 HOH B 68 568 74 HOH TIP . I 7 HOH B 69 569 75 HOH TIP . I 7 HOH B 70 570 76 HOH TIP . I 7 HOH B 71 571 77 HOH TIP . I 7 HOH B 72 572 78 HOH TIP . I 7 HOH B 73 573 79 HOH TIP . I 7 HOH B 74 574 80 HOH TIP . I 7 HOH B 75 575 81 HOH TIP . I 7 HOH B 76 576 82 HOH TIP . I 7 HOH B 77 577 83 HOH TIP . I 7 HOH B 78 578 84 HOH TIP . I 7 HOH B 79 579 85 HOH TIP . I 7 HOH B 80 580 87 HOH TIP . I 7 HOH B 81 581 88 HOH TIP . I 7 HOH B 82 582 91 HOH TIP . I 7 HOH B 83 583 93 HOH TIP . I 7 HOH B 84 584 95 HOH TIP . I 7 HOH B 85 585 96 HOH TIP . I 7 HOH B 86 586 97 HOH TIP . I 7 HOH B 87 587 98 HOH TIP . I 7 HOH B 88 588 99 HOH TIP . I 7 HOH B 89 589 100 HOH TIP . I 7 HOH B 90 590 101 HOH TIP . I 7 HOH B 91 591 103 HOH TIP . I 7 HOH B 92 592 104 HOH TIP . I 7 HOH B 93 593 105 HOH TIP . I 7 HOH B 94 594 108 HOH TIP . I 7 HOH B 95 595 109 HOH TIP . I 7 HOH B 96 596 111 HOH TIP . I 7 HOH B 97 597 112 HOH TIP . I 7 HOH B 98 598 113 HOH TIP . I 7 HOH B 99 599 114 HOH TIP . I 7 HOH B 100 600 115 HOH TIP . I 7 HOH B 101 601 116 HOH TIP . I 7 HOH B 102 602 117 HOH TIP . I 7 HOH B 103 603 118 HOH TIP . I 7 HOH B 104 604 119 HOH TIP . I 7 HOH B 105 605 120 HOH TIP . I 7 HOH B 106 606 121 HOH TIP . I 7 HOH B 107 607 122 HOH TIP . # 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 NAG . . . D 4 -3.443 -28.892 10.976 1 50.4 ? C1 NAG 500 B 1 HETATM 2 C C2 NAG . . . D 4 -2.109 -29.637 11.187 1 52.49 ? C2 NAG 500 B 1 HETATM 3 C C3 NAG . . . D 4 -0.853 -28.731 11.261 1 54.25 ? C3 NAG 500 B 1 HETATM 4 C C4 NAG . . . D 4 -0.924 -27.759 10.061 1 54.5 ? C4 NAG 500 B 1 HETATM 5 C C5 NAG . . . D 4 -2.329 -27.118 9.932 1 53.61 ? C5 NAG 500 B 1 HETATM 6 C C6 NAG . . . D 4 -2.375 -26.169 8.729 1 54.22 ? C6 NAG 500 B 1 HETATM 7 C C7 NAG . . . D 4 -2.339 -30.055 13.567 1 51.53 ? C7 NAG 500 B 1 HETATM 8 C C8 NAG . . . D 4 -2.501 -31.131 14.623 1 48.27 ? C8 NAG 500 B 1 HETATM 9 N N2 NAG . . . D 4 -2.195 -30.528 12.334 1 52.24 ? N2 NAG 500 B 1 HETATM 10 O O3 NAG . . . D 4 0.352 -29.488 11.131 1 57.14 ? O3 NAG 500 B 1 HETATM 11 O O4 NAG . . . D 4 0.073 -26.744 10.267 1 56.53 ? O4 NAG 500 B 1 HETATM 12 O O5 NAG . . . D 4 -3.35 -28.112 9.786 1 52.63 ? O5 NAG 500 B 1 HETATM 13 O O6 NAG . . . D 4 -2.525 -26.874 7.49 1 54.18 ? O6 NAG 500 B 1 HETATM 14 O O7 NAG . . . D 4 -2.339 -28.85 13.821 1 52.94 ? O7 NAG 500 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #