data_1D3P # _model_server_result.job_id y1jnxswQcZ3mfseQEuaPCQ _model_server_result.datetime_utc '2024-11-21 17:19:14' _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 1d3p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 1D3P # _exptl.entry_id 1D3P _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 100.36 _cell.angle_gamma 90 _cell.entry_id 1D3P _cell.length_a 71.37 _cell.length_b 72.01 _cell.length_c 73.44 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D3P _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 ? _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 9 A CYS 9 1_555 B SG CYS 119 B CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf4 B SG CYS 201 B CYS 237 1_555 B SG CYS 231 B CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 B ND2 ASN 53 B ASN 89 1_555 D C1 NAG . B NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale2 C C GLU 9 H GLU 308 1_555 C N TYS 10 H TYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 C C TYS 10 H TYS 309 1_555 C N LEU 11 H LEU 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 B O LYS 174 B LYS 210 1_555 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc2 B O THR 177 B THR 213 1_555 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc3 B O PHE 215 B PHE 251 4_446 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc4 B O ARG 233 B ARG 269 1_555 F NA NA . B NA 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc5 B O LYS 236 B LYS 272 1_555 F NA NA . B NA 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc6 E NA NA . B NA 398 1_555 I O HOH . B HOH 547 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc7 E NA NA . B NA 398 1_555 I O HOH . B HOH 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc8 F NA NA . B NA 399 1_555 I O HOH . B HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc9 F NA NA . B NA 399 1_555 I O HOH . B HOH 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc10 F NA NA . B NA 399 1_555 I O HOH . B HOH 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? # _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 318 n n C1 O1 NAG sing 319 n n C1 O5 NAG sing 320 n n C1 H1 NAG sing 321 n n C2 C3 NAG sing 322 n n C2 N2 NAG sing 323 n n C2 H2 NAG sing 324 n n C3 C4 NAG sing 325 n n C3 O3 NAG sing 326 n n C3 H3 NAG sing 327 n n C4 C5 NAG sing 328 n n C4 O4 NAG sing 329 n n C4 H4 NAG sing 330 n n C5 C6 NAG sing 331 n n C5 O5 NAG sing 332 n n C5 H5 NAG sing 333 n n C6 O6 NAG sing 334 n n C6 H61 NAG sing 335 n n C6 H62 NAG sing 336 n n C7 C8 NAG sing 337 n n C7 N2 NAG sing 338 n n C7 O7 NAG doub 339 n n C8 H81 NAG sing 340 n n C8 H82 NAG sing 341 n n C8 H83 NAG sing 342 n n N2 HN2 NAG sing 343 n n O1 HO1 NAG sing 344 n n O3 HO3 NAG sing 345 n n O4 HO4 NAG sing 346 n n O6 HO6 NAG sing 347 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 1D3P _atom_sites.fract_transf_matrix[1][1] 0.014006 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002571 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013889 _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] 0.013852 _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 BT3 B 1 400 400 BT3 BT3 . H 7 HOH A 1 37 26 HOH HOH . H 7 HOH A 2 38 31 HOH HOH . H 7 HOH A 3 39 52 HOH HOH . H 7 HOH A 4 40 57 HOH HOH . H 7 HOH A 5 41 58 HOH HOH . H 7 HOH A 6 42 86 HOH HOH . H 7 HOH A 7 43 89 HOH HOH . H 7 HOH A 8 44 92 HOH HOH . H 7 HOH A 9 45 94 HOH HOH . H 7 HOH A 10 46 102 HOH HOH . H 7 HOH A 11 47 106 HOH HOH . H 7 HOH A 12 48 107 HOH HOH . H 7 HOH A 13 49 110 HOH HOH . H 7 HOH A 14 50 116 HOH HOH . I 7 HOH B 1 501 1 HOH HOH . I 7 HOH B 2 502 2 HOH HOH . I 7 HOH B 3 503 3 HOH HOH . I 7 HOH B 4 504 4 HOH HOH . I 7 HOH B 5 505 5 HOH HOH . I 7 HOH B 6 506 6 HOH HOH . I 7 HOH B 7 507 7 HOH HOH . I 7 HOH B 8 508 8 HOH HOH . I 7 HOH B 9 509 9 HOH HOH . I 7 HOH B 10 510 10 HOH HOH . I 7 HOH B 11 511 11 HOH HOH . I 7 HOH B 12 512 12 HOH HOH . I 7 HOH B 13 513 13 HOH HOH . I 7 HOH B 14 514 14 HOH HOH . I 7 HOH B 15 515 15 HOH HOH . I 7 HOH B 16 516 16 HOH HOH . I 7 HOH B 17 517 17 HOH HOH . I 7 HOH B 18 518 18 HOH HOH . I 7 HOH B 19 519 19 HOH HOH . I 7 HOH B 20 520 20 HOH HOH . I 7 HOH B 21 521 21 HOH HOH . I 7 HOH B 22 522 22 HOH HOH . I 7 HOH B 23 523 23 HOH HOH . I 7 HOH B 24 524 24 HOH HOH . I 7 HOH B 25 525 25 HOH HOH . I 7 HOH B 26 526 27 HOH HOH . I 7 HOH B 27 527 28 HOH HOH . I 7 HOH B 28 528 29 HOH HOH . I 7 HOH B 29 529 30 HOH HOH . I 7 HOH B 30 530 32 HOH HOH . I 7 HOH B 31 531 33 HOH HOH . I 7 HOH B 32 532 34 HOH HOH . I 7 HOH B 33 533 35 HOH HOH . I 7 HOH B 34 534 36 HOH HOH . I 7 HOH B 35 535 37 HOH HOH . I 7 HOH B 36 536 38 HOH HOH . I 7 HOH B 37 537 39 HOH HOH . I 7 HOH B 38 538 40 HOH HOH . I 7 HOH B 39 539 41 HOH HOH . I 7 HOH B 40 540 42 HOH HOH . I 7 HOH B 41 541 43 HOH HOH . I 7 HOH B 42 542 44 HOH HOH . I 7 HOH B 43 543 45 HOH HOH . I 7 HOH B 44 544 46 HOH HOH . I 7 HOH B 45 545 47 HOH HOH . I 7 HOH B 46 546 48 HOH HOH . I 7 HOH B 47 547 49 HOH HOH . I 7 HOH B 48 548 50 HOH HOH . I 7 HOH B 49 549 51 HOH HOH . I 7 HOH B 50 550 53 HOH HOH . I 7 HOH B 51 551 54 HOH HOH . I 7 HOH B 52 552 55 HOH HOH . I 7 HOH B 53 553 56 HOH HOH . I 7 HOH B 54 554 59 HOH HOH . I 7 HOH B 55 555 60 HOH HOH . I 7 HOH B 56 556 61 HOH HOH . I 7 HOH B 57 557 62 HOH HOH . I 7 HOH B 58 558 63 HOH HOH . I 7 HOH B 59 559 64 HOH HOH . I 7 HOH B 60 560 65 HOH HOH . I 7 HOH B 61 561 66 HOH HOH . I 7 HOH B 62 562 67 HOH HOH . I 7 HOH B 63 563 68 HOH HOH . I 7 HOH B 64 564 69 HOH HOH . I 7 HOH B 65 565 70 HOH HOH . I 7 HOH B 66 566 71 HOH HOH . I 7 HOH B 67 567 72 HOH HOH . I 7 HOH B 68 568 73 HOH HOH . I 7 HOH B 69 569 74 HOH HOH . I 7 HOH B 70 570 76 HOH HOH . I 7 HOH B 71 571 77 HOH HOH . I 7 HOH B 72 572 78 HOH HOH . I 7 HOH B 73 573 79 HOH HOH . I 7 HOH B 74 574 80 HOH HOH . I 7 HOH B 75 575 81 HOH HOH . I 7 HOH B 76 576 82 HOH HOH . I 7 HOH B 77 577 83 HOH HOH . I 7 HOH B 78 578 84 HOH HOH . I 7 HOH B 79 579 87 HOH HOH . I 7 HOH B 80 580 88 HOH HOH . I 7 HOH B 81 581 90 HOH HOH . I 7 HOH B 82 582 91 HOH HOH . I 7 HOH B 83 583 93 HOH HOH . I 7 HOH B 84 584 97 HOH HOH . I 7 HOH B 85 585 98 HOH HOH . I 7 HOH B 86 586 99 HOH HOH . I 7 HOH B 87 587 100 HOH HOH . I 7 HOH B 88 588 101 HOH HOH . I 7 HOH B 89 589 105 HOH HOH . I 7 HOH B 90 590 108 HOH HOH . I 7 HOH B 91 591 109 HOH HOH . I 7 HOH B 92 592 111 HOH HOH . I 7 HOH B 93 593 112 HOH HOH . I 7 HOH B 94 594 113 HOH HOH . I 7 HOH B 95 595 114 HOH HOH . I 7 HOH B 96 596 115 HOH HOH . I 7 HOH B 97 597 117 HOH HOH . I 7 HOH B 98 598 118 HOH HOH . I 7 HOH B 99 599 119 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 NAG . . . D 4 -3.432 -29.01 10.938 1 55.47 ? C1 NAG 500 B 1 HETATM 2 C C2 NAG . . . D 4 -2.095 -29.737 11.216 1 56.11 ? C2 NAG 500 B 1 HETATM 3 C C3 NAG . . . D 4 -0.864 -28.802 11.335 1 57.73 ? C3 NAG 500 B 1 HETATM 4 C C4 NAG . . . D 4 -0.896 -27.949 10.043 1 58.66 ? C4 NAG 500 B 1 HETATM 5 C C5 NAG . . . D 4 -2.275 -27.253 9.881 1 57.88 ? C5 NAG 500 B 1 HETATM 6 C C6 NAG . . . D 4 -2.265 -26.31 8.671 1 57.96 ? C6 NAG 500 B 1 HETATM 7 C C7 NAG . . . D 4 -2.371 -30.147 13.599 1 54.69 ? C7 NAG 500 B 1 HETATM 8 C C8 NAG . . . D 4 -2.564 -31.233 14.634 1 52.57 ? C8 NAG 500 B 1 HETATM 9 N N2 NAG . . . D 4 -2.212 -30.621 12.369 1 54.96 ? N2 NAG 500 B 1 HETATM 10 O O3 NAG . . . D 4 0.354 -29.559 11.376 1 58.44 ? O3 NAG 500 B 1 HETATM 11 O O4 NAG . . . D 4 0.187 -26.992 10.099 1 62.46 ? O4 NAG 500 B 1 HETATM 12 O O5 NAG . . . D 4 -3.326 -28.23 9.721 1 57.56 ? O5 NAG 500 B 1 HETATM 13 O O6 NAG . . . D 4 -2.379 -26.978 7.41 1 58.94 ? O6 NAG 500 B 1 HETATM 14 O O7 NAG . . . D 4 -2.36 -28.942 13.862 1 54.94 ? O7 NAG 500 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #