data_7BMD
#
_model_server_result.job_id            zJlvLALDaes7wRWS3EQjog 
_model_server_result.datetime_utc      '2024-11-22 22:25:12' 
_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          7bmd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":616}' 
#
_entry.id    7BMD 
#
_exptl.entry_id    7BMD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          4 
_entity.src_method                  syn 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            7BMD 
_cell.length_a            60.5 
_cell.length_b            73.17 
_cell.length_c            79.38 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7BMD 
_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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 
_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                             Q 
_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 24 A CYS 101 1_555 A SG CYS 106 A CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf2 A SG CYS 53 A CYS 130 1_555 A SG CYS 59 A CYS 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf3 A SG CYS 229 A CYS 306 1_555 A SG CYS 241 A CYS 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
disulf ? disulf4 A SG CYS 309 A CYS 386 1_555 A SG CYS 372 A CYS 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 A SG CYS 336 A CYS 413 1_555 A SG CYS 355 A CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf6 A SG CYS 363 A CYS 440 1_555 A SG CYS 368 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
covale ? covale1 A ND2 ASN 19 A ASN 96 1_555 Q C1 NAG . A NAG 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
#
_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 259 n n 
C1 O1 NAG sing 260 n n 
C1 O5 NAG sing 261 n n 
C1 H1 NAG sing 262 n n 
C2 C3 NAG sing 263 n n 
C2 N2 NAG sing 264 n n 
C2 H2 NAG sing 265 n n 
C3 C4 NAG sing 266 n n 
C3 O3 NAG sing 267 n n 
C3 H3 NAG sing 268 n n 
C4 C5 NAG sing 269 n n 
C4 O4 NAG sing 270 n n 
C4 H4 NAG sing 271 n n 
C5 C6 NAG sing 272 n n 
C5 O5 NAG sing 273 n n 
C5 H5 NAG sing 274 n n 
C6 O6 NAG sing 275 n n 
C6 H61 NAG sing 276 n n 
C6 H62 NAG sing 277 n n 
C7 C8 NAG sing 278 n n 
C7 N2 NAG sing 279 n n 
C7 O7 NAG doub 280 n n 
C8 H81 NAG sing 281 n n 
C8 H82 NAG sing 282 n n 
C8 H83 NAG sing 283 n n 
N2 HN2 NAG sing 284 n n 
O1 HO1 NAG sing 285 n n 
O3 HO3 NAG sing 286 n n 
O4 HO4 NAG sing 287 n n 
O6 HO6 NAG sing 288 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                     7BMD 
_atom_sites.fract_transf_matrix[1][1]    0.016529 
_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]    0.013667 
_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]    0.012598 
_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 SO4 A 1 601 601 SO4 SO4 . 
C 2 SO4 A 1 602 602 SO4 SO4 . 
D 2 SO4 A 1 603 603 SO4 SO4 . 
E 2 SO4 A 1 604 604 SO4 SO4 . 
F 2 SO4 A 1 605 605 SO4 SO4 . 
G 2 SO4 A 1 606 606 SO4 SO4 . 
H 2 SO4 A 1 607 608 SO4 SO4 . 
I 2 SO4 A 1 608 609 SO4 SO4 . 
J 2 SO4 A 1 609 610 SO4 SO4 . 
K 2 SO4 A 1 610 612 SO4 SO4 . 
L 2 SO4 A 1 611 613 SO4 SO4 . 
M 3 GOL A 1 612 704 GOL GOL . 
N 3 GOL A 1 613 709 GOL GOL . 
O 3 GOL A 1 614 711 GOL GOL . 
P 3 GOL A 1 615 713 GOL GOL . 
Q 4 NAG A 1 616 1101 NAG NAG . 
R 5 U3W A 1 617 1201 U3W XXX . 
S 6 DMS A 1 618 1301 DMS DMS . 
T 7 HOH A 1 701 1 HOH HOH . 
T 7 HOH A 2 702 836 HOH HOH . 
T 7 HOH A 3 703 871 HOH HOH . 
T 7 HOH A 4 704 980 HOH HOH . 
T 7 HOH A 5 705 875 HOH HOH . 
T 7 HOH A 6 706 848 HOH HOH . 
T 7 HOH A 7 707 777 HOH HOH . 
T 7 HOH A 8 708 783 HOH HOH . 
T 7 HOH A 9 709 797 HOH HOH . 
T 7 HOH A 10 710 758 HOH HOH . 
T 7 HOH A 11 711 946 HOH HOH . 
T 7 HOH A 12 712 873 HOH HOH . 
T 7 HOH A 13 713 786 HOH HOH . 
T 7 HOH A 14 714 796 HOH HOH . 
T 7 HOH A 15 715 785 HOH HOH . 
T 7 HOH A 16 716 823 HOH HOH . 
T 7 HOH A 17 717 800 HOH HOH . 
T 7 HOH A 18 718 751 HOH HOH . 
T 7 HOH A 19 719 940 HOH HOH . 
T 7 HOH A 20 720 801 HOH HOH . 
T 7 HOH A 21 721 971 HOH HOH . 
T 7 HOH A 22 722 781 HOH HOH . 
T 7 HOH A 23 723 795 HOH HOH . 
T 7 HOH A 24 724 793 HOH HOH . 
T 7 HOH A 25 725 991 HOH HOH . 
T 7 HOH A 26 726 846 HOH HOH . 
T 7 HOH A 27 727 832 HOH HOH . 
T 7 HOH A 28 728 820 HOH HOH . 
T 7 HOH A 29 729 841 HOH HOH . 
T 7 HOH A 30 730 809 HOH HOH . 
T 7 HOH A 31 731 768 HOH HOH . 
T 7 HOH A 32 732 754 HOH HOH . 
T 7 HOH A 33 733 1005 HOH HOH . 
T 7 HOH A 34 734 837 HOH HOH . 
T 7 HOH A 35 735 899 HOH HOH . 
T 7 HOH A 36 736 753 HOH HOH . 
T 7 HOH A 37 737 847 HOH HOH . 
T 7 HOH A 38 738 979 HOH HOH . 
T 7 HOH A 39 739 790 HOH HOH . 
T 7 HOH A 40 740 947 HOH HOH . 
T 7 HOH A 41 741 769 HOH HOH . 
T 7 HOH A 42 742 834 HOH HOH . 
T 7 HOH A 43 743 868 HOH HOH . 
T 7 HOH A 44 744 798 HOH HOH . 
T 7 HOH A 45 745 762 HOH HOH . 
T 7 HOH A 46 746 814 HOH HOH . 
T 7 HOH A 47 747 813 HOH HOH . 
T 7 HOH A 48 748 2 HOH HOH . 
T 7 HOH A 49 749 1003 HOH HOH . 
T 7 HOH A 50 750 808 HOH HOH . 
T 7 HOH A 51 751 960 HOH HOH . 
T 7 HOH A 52 752 804 HOH HOH . 
T 7 HOH A 53 753 831 HOH HOH . 
T 7 HOH A 54 754 812 HOH HOH . 
T 7 HOH A 55 755 802 HOH HOH . 
T 7 HOH A 56 756 765 HOH HOH . 
T 7 HOH A 57 757 779 HOH HOH . 
T 7 HOH A 58 758 752 HOH HOH . 
T 7 HOH A 59 759 818 HOH HOH . 
T 7 HOH A 60 760 766 HOH HOH . 
T 7 HOH A 61 761 998 HOH HOH . 
T 7 HOH A 62 762 757 HOH HOH . 
T 7 HOH A 63 763 3 HOH HOH . 
T 7 HOH A 64 764 883 HOH HOH . 
T 7 HOH A 65 765 807 HOH HOH . 
T 7 HOH A 66 766 760 HOH HOH . 
T 7 HOH A 67 767 952 HOH HOH . 
T 7 HOH A 68 768 859 HOH HOH . 
T 7 HOH A 69 769 776 HOH HOH . 
T 7 HOH A 70 770 822 HOH HOH . 
T 7 HOH A 71 771 909 HOH HOH . 
T 7 HOH A 72 772 982 HOH HOH . 
T 7 HOH A 73 773 773 HOH HOH . 
T 7 HOH A 74 774 955 HOH HOH . 
T 7 HOH A 75 775 756 HOH HOH . 
T 7 HOH A 76 776 815 HOH HOH . 
T 7 HOH A 77 777 788 HOH HOH . 
T 7 HOH A 78 778 864 HOH HOH . 
T 7 HOH A 79 779 900 HOH HOH . 
T 7 HOH A 80 780 835 HOH HOH . 
T 7 HOH A 81 781 824 HOH HOH . 
T 7 HOH A 82 782 806 HOH HOH . 
T 7 HOH A 83 783 902 HOH HOH . 
T 7 HOH A 84 784 770 HOH HOH . 
T 7 HOH A 85 785 821 HOH HOH . 
T 7 HOH A 86 786 817 HOH HOH . 
T 7 HOH A 87 787 767 HOH HOH . 
T 7 HOH A 88 788 789 HOH HOH . 
T 7 HOH A 89 789 763 HOH HOH . 
T 7 HOH A 90 790 755 HOH HOH . 
T 7 HOH A 91 791 994 HOH HOH . 
T 7 HOH A 92 792 961 HOH HOH . 
T 7 HOH A 93 793 787 HOH HOH . 
T 7 HOH A 94 794 870 HOH HOH . 
T 7 HOH A 95 795 975 HOH HOH . 
T 7 HOH A 96 796 780 HOH HOH . 
T 7 HOH A 97 797 764 HOH HOH . 
T 7 HOH A 98 798 791 HOH HOH . 
T 7 HOH A 99 799 843 HOH HOH . 
T 7 HOH A 100 800 761 HOH HOH . 
T 7 HOH A 101 801 872 HOH HOH . 
T 7 HOH A 102 802 828 HOH HOH . 
T 7 HOH A 103 803 827 HOH HOH . 
T 7 HOH A 104 804 973 HOH HOH . 
T 7 HOH A 105 805 856 HOH HOH . 
T 7 HOH A 106 806 792 HOH HOH . 
T 7 HOH A 107 807 1006 HOH HOH . 
T 7 HOH A 108 808 892 HOH HOH . 
T 7 HOH A 109 809 842 HOH HOH . 
T 7 HOH A 110 810 865 HOH HOH . 
T 7 HOH A 111 811 799 HOH HOH . 
T 7 HOH A 112 812 903 HOH HOH . 
T 7 HOH A 113 813 830 HOH HOH . 
T 7 HOH A 114 814 890 HOH HOH . 
T 7 HOH A 115 815 829 HOH HOH . 
T 7 HOH A 116 816 976 HOH HOH . 
T 7 HOH A 117 817 948 HOH HOH . 
T 7 HOH A 118 818 889 HOH HOH . 
T 7 HOH A 119 819 981 HOH HOH . 
T 7 HOH A 120 820 992 HOH HOH . 
T 7 HOH A 121 821 912 HOH HOH . 
T 7 HOH A 122 822 985 HOH HOH . 
T 7 HOH A 123 823 862 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 . . . Q 4 -4.091 21.311 -0.978 1 26.84 ? C1 NAG 616 A 1 
HETATM 2 C C2 NAG . . . Q 4 -5.168 21.713 -1.984 1 68.07 ? C2 NAG 616 A 1 
HETATM 3 C C3 NAG . . . Q 4 -6.554 21.561 -1.367 1 42.64 ? C3 NAG 616 A 1 
HETATM 4 C C4 NAG . . . Q 4 -6.74 20.157 -0.809 1 55.11 ? C4 NAG 616 A 1 
HETATM 5 C C5 NAG . . . Q 4 -5.609 19.822 0.158 1 56.13 ? C5 NAG 616 A 1 
HETATM 6 C C6 NAG . . . Q 4 -5.664 18.399 0.664 1 44.3 ? C6 NAG 616 A 1 
HETATM 7 C C7 NAG . . . Q 4 -4.39 23.37 -3.62 1 85.43 ? C7 NAG 616 A 1 
HETATM 8 C C8 NAG . . . Q 4 -4.263 24.829 -3.94 1 89.38 ? C8 NAG 616 A 1 
HETATM 9 N N2 NAG . . . Q 4 -4.964 23.076 -2.449 1 46.59 ? N2 NAG 616 A 1 
HETATM 10 O O3 NAG . . . Q 4 -7.54 21.824 -2.359 1 59.79 ? O3 NAG 616 A 1 
HETATM 11 O O4 NAG . . . Q 4 -7.986 20.07 -0.128 1 63.53 ? O4 NAG 616 A 1 
HETATM 12 O O5 NAG . . . Q 4 -4.344 19.975 -0.504 1 34.78 ? O5 NAG 616 A 1 
HETATM 13 O O6 NAG . . . Q 4 -5.595 17.466 -0.406 1 79.6 ? O6 NAG 616 A 1 
HETATM 14 O O7 NAG . . . Q 4 -3.991 22.498 -4.386 1 76.53 ? O7 NAG 616 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#