data_1D4P # _model_server_result.job_id '_Bgh-jZiSSybg0eA32nK1A' _model_server_result.datetime_utc '2024-10-24 04:20:28' _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 1d4p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 1D4P # _exptl.entry_id 1D4P _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 101.2 _cell.angle_gamma 90 _cell.entry_id 1D4P _cell.length_a 71.56 _cell.length_b 72.06 _cell.length_c 73.22 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D4P _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf2 B SG CYS 28 B CYS 64 1_555 B SG CYS 44 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 B SG CYS 173 B CYS 209 1_555 B SG CYS 187 B CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 B SG CYS 201 B CYS 237 1_555 B SG CYS 231 B CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc2 B O THR 177 B THR 213 1_555 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc3 B O PHE 215 B PHE 251 4_446 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc4 B O ARG 233 B ARG 269 1_555 F NA NA . B NA 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc5 B O LYS 236 B LYS 272 1_555 F NA NA . B NA 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc6 E NA NA . B NA 398 1_555 I O HOH . B HOH 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc7 E NA NA . B NA 398 1_555 I O HOH . B HOH 553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc8 E NA NA . B NA 398 1_555 I O HOH . B HOH 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc9 F NA NA . B NA 399 1_555 I O HOH . B HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc10 F NA NA . B NA 399 1_555 I O HOH . B HOH 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc11 F NA NA . B NA 399 1_555 I O HOH . B HOH 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? # _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_ _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 1D4P _atom_sites.fract_transf_matrix[1][1] 0.013974 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002767 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013877 _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] 0.013923 _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 BPP B 1 400 400 BPP BPP . H 7 HOH A 1 526 526 HOH HOH . H 7 HOH A 2 531 531 HOH HOH . H 7 HOH A 3 552 552 HOH HOH . H 7 HOH A 4 557 557 HOH HOH . H 7 HOH A 5 558 558 HOH HOH . H 7 HOH A 6 560 560 HOH HOH . H 7 HOH A 7 586 586 HOH HOH . H 7 HOH A 8 589 589 HOH HOH . H 7 HOH A 9 592 592 HOH HOH . H 7 HOH A 10 594 594 HOH HOH . H 7 HOH A 11 610 610 HOH HOH . H 7 HOH A 12 621 621 HOH HOH . H 7 HOH A 13 624 624 HOH HOH . H 7 HOH A 14 625 625 HOH HOH . I 7 HOH B 1 501 501 HOH HOH . I 7 HOH B 2 502 502 HOH HOH . I 7 HOH B 3 503 503 HOH HOH . I 7 HOH B 4 504 504 HOH HOH . I 7 HOH B 5 505 505 HOH HOH . I 7 HOH B 6 506 506 HOH HOH . I 7 HOH B 7 507 507 HOH HOH . I 7 HOH B 8 508 508 HOH HOH . I 7 HOH B 9 509 509 HOH HOH . I 7 HOH B 10 510 510 HOH HOH . I 7 HOH B 11 511 511 HOH HOH . I 7 HOH B 12 512 512 HOH HOH . I 7 HOH B 13 513 513 HOH HOH . I 7 HOH B 14 514 514 HOH HOH . I 7 HOH B 15 515 515 HOH HOH . I 7 HOH B 16 516 516 HOH HOH . I 7 HOH B 17 517 517 HOH HOH . I 7 HOH B 18 518 518 HOH HOH . I 7 HOH B 19 519 519 HOH HOH . I 7 HOH B 20 520 520 HOH HOH . I 7 HOH B 21 521 521 HOH HOH . I 7 HOH B 22 522 522 HOH HOH . I 7 HOH B 23 523 523 HOH HOH . I 7 HOH B 24 524 524 HOH HOH . I 7 HOH B 25 525 525 HOH HOH . I 7 HOH B 26 527 527 HOH HOH . I 7 HOH B 27 528 528 HOH HOH . I 7 HOH B 28 529 529 HOH HOH . I 7 HOH B 29 530 530 HOH HOH . I 7 HOH B 30 532 532 HOH HOH . I 7 HOH B 31 533 533 HOH HOH . I 7 HOH B 32 534 534 HOH HOH . I 7 HOH B 33 535 535 HOH HOH . I 7 HOH B 34 536 536 HOH HOH . I 7 HOH B 35 537 537 HOH HOH . I 7 HOH B 36 538 538 HOH HOH . I 7 HOH B 37 539 539 HOH HOH . I 7 HOH B 38 540 540 HOH HOH . I 7 HOH B 39 541 541 HOH HOH . I 7 HOH B 40 542 542 HOH HOH . I 7 HOH B 41 543 543 HOH HOH . I 7 HOH B 42 544 544 HOH HOH . I 7 HOH B 43 545 545 HOH HOH . I 7 HOH B 44 546 546 HOH HOH . I 7 HOH B 45 547 547 HOH HOH . I 7 HOH B 46 548 548 HOH HOH . I 7 HOH B 47 549 549 HOH HOH . I 7 HOH B 48 550 550 HOH HOH . I 7 HOH B 49 551 551 HOH HOH . I 7 HOH B 50 553 553 HOH HOH . I 7 HOH B 51 554 554 HOH HOH . I 7 HOH B 52 555 555 HOH HOH . I 7 HOH B 53 556 556 HOH HOH . I 7 HOH B 54 559 559 HOH HOH . I 7 HOH B 55 561 561 HOH HOH . I 7 HOH B 56 562 562 HOH HOH . I 7 HOH B 57 563 563 HOH HOH . I 7 HOH B 58 564 564 HOH HOH . I 7 HOH B 59 565 565 HOH HOH . I 7 HOH B 60 566 566 HOH HOH . I 7 HOH B 61 567 567 HOH HOH . I 7 HOH B 62 568 568 HOH HOH . I 7 HOH B 63 569 569 HOH HOH . I 7 HOH B 64 570 570 HOH HOH . I 7 HOH B 65 571 571 HOH HOH . I 7 HOH B 66 572 572 HOH HOH . I 7 HOH B 67 573 573 HOH HOH . I 7 HOH B 68 575 575 HOH HOH . I 7 HOH B 69 576 576 HOH HOH . I 7 HOH B 70 577 577 HOH HOH . I 7 HOH B 71 578 578 HOH HOH . I 7 HOH B 72 579 579 HOH HOH . I 7 HOH B 73 581 581 HOH HOH . I 7 HOH B 74 582 582 HOH HOH . I 7 HOH B 75 583 583 HOH HOH . I 7 HOH B 76 584 584 HOH HOH . I 7 HOH B 77 588 588 HOH HOH . I 7 HOH B 78 590 590 HOH HOH . I 7 HOH B 79 591 591 HOH HOH . I 7 HOH B 80 593 593 HOH HOH . I 7 HOH B 81 595 595 HOH HOH . I 7 HOH B 82 596 596 HOH HOH . I 7 HOH B 83 599 599 HOH HOH . I 7 HOH B 84 600 600 HOH HOH . I 7 HOH B 85 601 601 HOH HOH . I 7 HOH B 86 603 603 HOH HOH . I 7 HOH B 87 604 604 HOH HOH . I 7 HOH B 88 605 605 HOH HOH . I 7 HOH B 89 609 609 HOH HOH . I 7 HOH B 90 612 612 HOH HOH . I 7 HOH B 91 613 613 HOH HOH . I 7 HOH B 92 614 614 HOH HOH . I 7 HOH B 93 615 615 HOH HOH . I 7 HOH B 94 616 616 HOH HOH . I 7 HOH B 95 617 617 HOH HOH . I 7 HOH B 96 618 618 HOH HOH . I 7 HOH B 97 619 619 HOH HOH . I 7 HOH B 98 620 620 HOH HOH . I 7 HOH B 99 622 622 HOH HOH . I 7 HOH B 100 623 623 HOH HOH . I 7 HOH B 101 626 626 HOH HOH . I 7 HOH B 102 627 627 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 -3.686 -28.828 10.868 1 48.69 ? C1 NAG 500 B 1 HETATM 2 C C2 NAG . . . D 4 -2.357 -29.545 11.204 1 50.97 ? C2 NAG 500 B 1 HETATM 3 C C3 NAG . . . D 4 -1.132 -28.596 11.214 1 53.21 ? C3 NAG 500 B 1 HETATM 4 C C4 NAG . . . D 4 -1.162 -27.858 9.851 1 53.33 ? C4 NAG 500 B 1 HETATM 5 C C5 NAG . . . D 4 -2.552 -27.231 9.566 1 52.43 ? C5 NAG 500 B 1 HETATM 6 C C6 NAG . . . D 4 -2.571 -26.553 8.211 1 53.1 ? C6 NAG 500 B 1 HETATM 7 C C7 NAG . . . D 4 -2.703 -29.67 13.602 1 50.63 ? C7 NAG 500 B 1 HETATM 8 C C8 NAG . . . D 4 -2.885 -30.601 14.778 1 49.62 ? C8 NAG 500 B 1 HETATM 9 N N2 NAG . . . D 4 -2.464 -30.29 12.452 1 50.18 ? N2 NAG 500 B 1 HETATM 10 O O3 NAG . . . D 4 0.083 -29.372 11.335 1 55.33 ? O3 NAG 500 B 1 HETATM 11 O O4 NAG . . . D 4 -0.148 -26.83 9.833 1 55.74 ? O4 NAG 500 B 1 HETATM 12 O O5 NAG . . . D 4 -3.613 -28.164 9.598 1 49.82 ? O5 NAG 500 B 1 HETATM 13 O O6 NAG . . . D 4 -2.646 -25.174 8.536 1 57.75 ? O6 NAG 500 B 1 HETATM 14 O O7 NAG . . . D 4 -2.772 -28.44 13.7 1 51.64 ? O7 NAG 500 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #