data_1APZ # _model_server_result.job_id gSSynJNK873Tnfe1L3yFrw _model_server_result.datetime_utc '2025-03-06 01:12:24' _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 1apz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 1APZ # _exptl.entry_id 1APZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details 'COMPLEX WITH REACTION PRODUCT' _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 3 _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 120 _cell.entry_id 1APZ _cell.length_a 98.4 _cell.length_b 98.4 _cell.length_c 134.2 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1APZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,J,K,L,M,N _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 G N N ? 4 I N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n E NAG 1 E 1 NAG ? 531 NAG 3 n E NAG 2 E 2 NAG ? 532 NAG 3 n E BMA 3 E 3 BMA ? 533 MAN # 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 41 A CYS 41 1_555 A SG CYS 46 A CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf2 A SG CYS 140 A CYS 140 1_555 A SG CYS 156 A CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf3 B SG CYS 81 B CYS 263 1_555 B SG CYS 101 B CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 B SG CYS 112 B CYS 294 1_555 B SG CYS 140 B CYS 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 C SG CYS 41 C CYS 41 1_555 C SG CYS 46 C CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf6 C SG CYS 140 C CYS 140 1_555 C SG CYS 156 C CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf7 D SG CYS 81 D CYS 263 1_555 D SG CYS 101 D CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf8 D SG CYS 112 D CYS 294 1_555 D SG CYS 140 D CYS 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 A ND2 ASN 15 A ASN 15 1_555 F C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 B ND2 ASN 103 B ASN 285 1_555 G C1 NAG . B NAG 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.482 ? covale ? covale3 C ND2 ASN 15 C ASN 15 1_555 I C1 NAG . C NAG 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.498 ? covale ? covale4 D ND2 ASN 103 D ASN 285 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale5 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale6 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 1APZ _atom_sites.fract_transf_matrix[1][1] 0.010163 _atom_sites.fract_transf_matrix[1][2] 0.005867 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011735 _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] 0.007452 _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 F 4 NAG A 1 501 501 NAG NAG . G 4 NAG B 1 511 511 NAG NAG . H 5 ASP B 1 551 551 ASP ASP . I 4 NAG C 1 521 521 NAG NAG . J 5 ASP D 1 552 552 ASP ASP . K 6 HOH A 1 602 602 HOH HOH . K 6 HOH A 2 603 603 HOH HOH . K 6 HOH A 3 604 604 HOH HOH . K 6 HOH A 4 605 605 HOH HOH . K 6 HOH A 5 607 607 HOH HOH . K 6 HOH A 6 608 608 HOH HOH . K 6 HOH A 7 609 609 HOH HOH . K 6 HOH A 8 610 610 HOH HOH . K 6 HOH A 9 611 611 HOH HOH . K 6 HOH A 10 612 612 HOH HOH . K 6 HOH A 11 613 613 HOH HOH . K 6 HOH A 12 615 615 HOH HOH . K 6 HOH A 13 616 616 HOH HOH . K 6 HOH A 14 617 617 HOH HOH . K 6 HOH A 15 618 618 HOH HOH . K 6 HOH A 16 619 619 HOH HOH . K 6 HOH A 17 620 620 HOH HOH . K 6 HOH A 18 622 622 HOH HOH . K 6 HOH A 19 624 624 HOH HOH . K 6 HOH A 20 626 626 HOH HOH . K 6 HOH A 21 627 627 HOH HOH . K 6 HOH A 22 628 628 HOH HOH . K 6 HOH A 23 629 629 HOH HOH . K 6 HOH A 24 630 630 HOH HOH . K 6 HOH A 25 631 631 HOH HOH . K 6 HOH A 26 634 634 HOH HOH . K 6 HOH A 27 675 675 HOH HOH . K 6 HOH A 28 686 686 HOH HOH . K 6 HOH A 29 687 687 HOH HOH . K 6 HOH A 30 688 688 HOH HOH . K 6 HOH A 31 689 689 HOH HOH . K 6 HOH A 32 690 690 HOH HOH . K 6 HOH A 33 691 691 HOH HOH . K 6 HOH A 34 692 692 HOH HOH . K 6 HOH A 35 693 693 HOH HOH . K 6 HOH A 36 694 694 HOH HOH . K 6 HOH A 37 696 696 HOH HOH . K 6 HOH A 38 697 697 HOH HOH . K 6 HOH A 39 698 698 HOH HOH . K 6 HOH A 40 699 699 HOH HOH . K 6 HOH A 41 700 700 HOH HOH . K 6 HOH A 42 701 701 HOH HOH . K 6 HOH A 43 702 702 HOH HOH . K 6 HOH A 44 726 726 HOH HOH . K 6 HOH A 45 727 727 HOH HOH . K 6 HOH A 46 729 729 HOH HOH . K 6 HOH A 47 732 732 HOH HOH . L 6 HOH B 1 600 600 HOH HOH . L 6 HOH B 2 601 601 HOH HOH . L 6 HOH B 3 606 606 HOH HOH . L 6 HOH B 4 621 621 HOH HOH . L 6 HOH B 5 623 623 HOH HOH . L 6 HOH B 6 633 633 HOH HOH . L 6 HOH B 7 635 635 HOH HOH . L 6 HOH B 8 636 636 HOH HOH . L 6 HOH B 9 637 637 HOH HOH . L 6 HOH B 10 638 638 HOH HOH . L 6 HOH B 11 639 639 HOH HOH . L 6 HOH B 12 641 641 HOH HOH . L 6 HOH B 13 642 642 HOH HOH . L 6 HOH B 14 643 643 HOH HOH . L 6 HOH B 15 644 644 HOH HOH . L 6 HOH B 16 645 645 HOH HOH . L 6 HOH B 17 646 646 HOH HOH . L 6 HOH B 18 695 695 HOH HOH . L 6 HOH B 19 704 704 HOH HOH . L 6 HOH B 20 705 705 HOH HOH . L 6 HOH B 21 706 706 HOH HOH . L 6 HOH B 22 707 707 HOH HOH . L 6 HOH B 23 708 708 HOH HOH . L 6 HOH B 24 723 723 HOH HOH . L 6 HOH B 25 728 728 HOH HOH . L 6 HOH B 26 740 740 HOH HOH . M 6 HOH C 1 625 625 HOH HOH . M 6 HOH C 2 640 640 HOH HOH . M 6 HOH C 3 648 648 HOH HOH . M 6 HOH C 4 649 649 HOH HOH . M 6 HOH C 5 650 650 HOH HOH . M 6 HOH C 6 651 651 HOH HOH . M 6 HOH C 7 652 652 HOH HOH . M 6 HOH C 8 653 653 HOH HOH . M 6 HOH C 9 654 654 HOH HOH . M 6 HOH C 10 655 655 HOH HOH . M 6 HOH C 11 657 657 HOH HOH . M 6 HOH C 12 658 658 HOH HOH . M 6 HOH C 13 659 659 HOH HOH . M 6 HOH C 14 660 660 HOH HOH . M 6 HOH C 15 661 661 HOH HOH . M 6 HOH C 16 662 662 HOH HOH . M 6 HOH C 17 663 663 HOH HOH . M 6 HOH C 18 664 664 HOH HOH . M 6 HOH C 19 665 665 HOH HOH . M 6 HOH C 20 682 682 HOH HOH . M 6 HOH C 21 703 703 HOH HOH . M 6 HOH C 22 709 709 HOH HOH . M 6 HOH C 23 710 710 HOH HOH . M 6 HOH C 24 711 711 HOH HOH . M 6 HOH C 25 712 712 HOH HOH . M 6 HOH C 26 713 713 HOH HOH . M 6 HOH C 27 714 714 HOH HOH . M 6 HOH C 28 715 715 HOH HOH . M 6 HOH C 29 716 716 HOH HOH . M 6 HOH C 30 730 730 HOH HOH . M 6 HOH C 31 731 731 HOH HOH . M 6 HOH C 32 733 733 HOH HOH . M 6 HOH C 33 734 734 HOH HOH . M 6 HOH C 34 735 735 HOH HOH . N 6 HOH D 1 614 614 HOH HOH . N 6 HOH D 2 647 647 HOH HOH . N 6 HOH D 3 656 656 HOH HOH . N 6 HOH D 4 666 666 HOH HOH . N 6 HOH D 5 667 667 HOH HOH . N 6 HOH D 6 668 668 HOH HOH . N 6 HOH D 7 669 669 HOH HOH . N 6 HOH D 8 670 670 HOH HOH . N 6 HOH D 9 671 671 HOH HOH . N 6 HOH D 10 672 672 HOH HOH . N 6 HOH D 11 673 673 HOH HOH . N 6 HOH D 12 674 674 HOH HOH . N 6 HOH D 13 676 676 HOH HOH . N 6 HOH D 14 677 677 HOH HOH . N 6 HOH D 15 678 678 HOH HOH . N 6 HOH D 16 679 679 HOH HOH . N 6 HOH D 17 680 680 HOH HOH . N 6 HOH D 18 681 681 HOH HOH . N 6 HOH D 19 683 683 HOH HOH . N 6 HOH D 20 684 684 HOH HOH . N 6 HOH D 21 685 685 HOH HOH . N 6 HOH D 22 717 717 HOH HOH . N 6 HOH D 23 718 718 HOH HOH . N 6 HOH D 24 719 719 HOH HOH . N 6 HOH D 25 720 720 HOH HOH . N 6 HOH D 26 721 721 HOH HOH . N 6 HOH D 27 722 722 HOH HOH . N 6 HOH D 28 724 724 HOH HOH . N 6 HOH D 29 725 725 HOH HOH . N 6 HOH D 30 736 736 HOH HOH . N 6 HOH D 31 737 737 HOH HOH . N 6 HOH D 32 738 738 HOH HOH . N 6 HOH D 33 739 739 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 . . . F 4 -6.189 22.515 1.131 1 20.2 ? C1 NAG 501 A 1 HETATM 2 C C2 NAG . . . F 4 -7.291 21.567 0.668 1 20.2 ? C2 NAG 501 A 1 HETATM 3 C C3 NAG . . . F 4 -8.411 22.219 -0.162 1 20.2 ? C3 NAG 501 A 1 HETATM 4 C C4 NAG . . . F 4 -8.966 23.528 0.499 1 20.2 ? C4 NAG 501 A 1 HETATM 5 C C5 NAG . . . F 4 -7.711 24.473 0.739 1 20.2 ? C5 NAG 501 A 1 HETATM 6 C C6 NAG . . . F 4 -8.04 25.871 1.366 1 20.2 ? C6 NAG 501 A 1 HETATM 7 C C7 NAG . . . F 4 -6.357 19.378 0.131 1 20.2 ? C7 NAG 501 A 1 HETATM 8 C C8 NAG . . . F 4 -5.63 18.409 -0.82 1 20.2 ? C8 NAG 501 A 1 HETATM 9 N N2 NAG . . . F 4 -6.622 20.634 -0.226 1 20.2 ? N2 NAG 501 A 1 HETATM 10 O O3 NAG . . . F 4 -9.424 21.248 -0.186 1 20.2 ? O3 NAG 501 A 1 HETATM 11 O O4 NAG . . . F 4 -10.004 24.164 -0.255 1 20.2 ? O4 NAG 501 A 1 HETATM 12 O O5 NAG . . . F 4 -6.781 23.74 1.631 1 20.2 ? O5 NAG 501 A 1 HETATM 13 O O6 NAG . . . F 4 -9.46 25.953 1.736 1 20.2 ? O6 NAG 501 A 1 HETATM 14 O O7 NAG . . . F 4 -6.706 18.899 1.216 1 20.2 ? O7 NAG 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #