data_1MND
#
_model_server_result.job_id            XPRHsC15FyJjTU7P-q6RjA 
_model_server_result.datetime_utc      '2024-12-01 20:33:13' 
_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          1mnd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":998}' 
#
_entry.id    1MND 
#
_exptl.entry_id    1MND 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_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            1MND 
_cell.length_a            87.9 
_cell.length_b            149 
_cell.length_c            153.8 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1MND 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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
covale ? covale1 D O2B ADP . A ADP 998 1_555 C F4 ALF . A ALF 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
metalc ? metalc1 A OG1 THR 186 A THR 186 1_555 B MG MG . A MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
metalc ? metalc2 A OG SER 237 A SER 237 1_555 B MG MG . A MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? 
metalc ? metalc3 B MG MG . A MG 997 1_555 D O2B ADP . A ADP 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
metalc ? metalc4 B MG MG . A MG 997 1_555 C F4 ALF . A ALF 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
metalc ? metalc5 B MG MG . A MG 997 1_555 C F2 ALF . A ALF 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.961 ? 
metalc ? metalc6 B MG MG . A MG 997 1_555 C AL ALF . A ALF 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.431 ? 
metalc ? metalc7 B MG MG . A MG 997 1_555 E O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.84 ? 
metalc ? metalc8 D O3B ADP . A ADP 998 1_555 C AL ALF . A ALF 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc9 D O2B ADP . A ADP 998 1_555 C AL ALF . A ALF 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.477 ? 
metalc ? metalc10 D O1B ADP . A ADP 998 1_555 C AL ALF . A ALF 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.586 ? 
metalc ? metalc11 C AL ALF . A ALF 999 1_555 E O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.713 ? 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
PB O1B ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 n y 
#
_atom_sites.entry_id                     1MND 
_atom_sites.fract_transf_matrix[1][1]    0.011377 
_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]    0.006711 
_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]    0.006502 
_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 MG A 1 997 997 MG MG . 
C 3 ALF A 1 999 999 ALF ALF . 
D 4 ADP A 1 998 998 ADP ADP . 
E 5 HOH A 1 1000 700 HOH HOH . 
E 5 HOH A 2 1001 701 HOH HOH . 
E 5 HOH A 3 1002 702 HOH HOH . 
E 5 HOH A 4 1003 703 HOH HOH . 
E 5 HOH A 5 1004 704 HOH HOH . 
E 5 HOH A 6 1005 705 HOH HOH . 
E 5 HOH A 7 1006 706 HOH HOH . 
E 5 HOH A 8 1007 707 HOH HOH . 
E 5 HOH A 9 1008 708 HOH HOH . 
E 5 HOH A 10 1009 709 HOH HOH . 
E 5 HOH A 11 1010 710 HOH HOH . 
E 5 HOH A 12 1011 711 HOH HOH . 
E 5 HOH A 13 1012 712 HOH HOH . 
E 5 HOH A 14 1013 713 HOH HOH . 
E 5 HOH A 15 1014 714 HOH HOH . 
E 5 HOH A 16 1015 715 HOH HOH . 
E 5 HOH A 17 1016 716 HOH HOH . 
E 5 HOH A 18 1017 717 HOH HOH . 
E 5 HOH A 19 1018 718 HOH HOH . 
E 5 HOH A 20 1019 719 HOH HOH . 
E 5 HOH A 21 1020 720 HOH HOH . 
E 5 HOH A 22 1021 721 HOH HOH . 
E 5 HOH A 23 1022 722 HOH HOH . 
E 5 HOH A 24 1023 723 HOH HOH . 
E 5 HOH A 25 1024 724 HOH HOH . 
E 5 HOH A 26 1025 725 HOH HOH . 
E 5 HOH A 27 1026 726 HOH HOH . 
E 5 HOH A 28 1027 727 HOH HOH . 
E 5 HOH A 29 1028 728 HOH HOH . 
E 5 HOH A 30 1029 729 HOH HOH . 
E 5 HOH A 31 1030 730 HOH HOH . 
E 5 HOH A 32 1031 731 HOH HOH . 
E 5 HOH A 33 1032 732 HOH HOH . 
E 5 HOH A 34 1033 733 HOH HOH . 
E 5 HOH A 35 1034 734 HOH HOH . 
E 5 HOH A 36 1035 735 HOH HOH . 
E 5 HOH A 37 1036 736 HOH HOH . 
E 5 HOH A 38 1037 737 HOH HOH . 
E 5 HOH A 39 1038 738 HOH HOH . 
E 5 HOH A 40 1039 739 HOH HOH . 
E 5 HOH A 41 1040 740 HOH HOH . 
E 5 HOH A 42 1041 741 HOH HOH . 
E 5 HOH A 43 1042 742 HOH HOH . 
E 5 HOH A 44 1043 743 HOH HOH . 
E 5 HOH A 45 1044 744 HOH HOH . 
E 5 HOH A 46 1045 745 HOH HOH . 
E 5 HOH A 47 1046 746 HOH HOH . 
E 5 HOH A 48 1047 747 HOH HOH . 
E 5 HOH A 49 1048 748 HOH HOH . 
E 5 HOH A 50 1049 749 HOH HOH . 
E 5 HOH A 51 1050 750 HOH HOH . 
E 5 HOH A 52 1051 751 HOH HOH . 
E 5 HOH A 53 1052 752 HOH HOH . 
E 5 HOH A 54 1053 753 HOH HOH . 
E 5 HOH A 55 1054 754 HOH HOH . 
E 5 HOH A 56 1055 755 HOH HOH . 
E 5 HOH A 57 1056 756 HOH HOH . 
E 5 HOH A 58 1057 757 HOH HOH . 
E 5 HOH A 59 1058 758 HOH HOH . 
E 5 HOH A 60 1059 759 HOH HOH . 
E 5 HOH A 61 1060 760 HOH HOH . 
E 5 HOH A 62 1061 761 HOH HOH . 
E 5 HOH A 63 1062 762 HOH HOH . 
E 5 HOH A 64 1063 763 HOH HOH . 
E 5 HOH A 65 1064 764 HOH HOH . 
E 5 HOH A 66 1065 765 HOH HOH . 
E 5 HOH A 67 1066 766 HOH HOH . 
E 5 HOH A 68 1067 767 HOH HOH . 
E 5 HOH A 69 1068 768 HOH HOH . 
E 5 HOH A 70 1069 769 HOH HOH . 
E 5 HOH A 71 1070 770 HOH HOH . 
E 5 HOH A 72 1071 771 HOH HOH . 
E 5 HOH A 73 1072 772 HOH HOH . 
E 5 HOH A 74 1073 773 HOH HOH . 
E 5 HOH A 75 1074 774 HOH HOH . 
E 5 HOH A 76 1075 775 HOH HOH . 
E 5 HOH A 77 1076 776 HOH HOH . 
E 5 HOH A 78 1077 777 HOH HOH . 
E 5 HOH A 79 1078 778 HOH HOH . 
E 5 HOH A 80 1079 779 HOH HOH . 
E 5 HOH A 81 1080 780 HOH HOH . 
E 5 HOH A 82 1081 781 HOH HOH . 
E 5 HOH A 83 1082 782 HOH HOH . 
E 5 HOH A 84 1083 783 HOH HOH . 
E 5 HOH A 85 1084 784 HOH HOH . 
E 5 HOH A 86 1085 785 HOH HOH . 
E 5 HOH A 87 1086 786 HOH HOH . 
E 5 HOH A 88 1087 787 HOH HOH . 
E 5 HOH A 89 1088 788 HOH HOH . 
E 5 HOH A 90 1089 789 HOH HOH . 
E 5 HOH A 91 1090 790 HOH HOH . 
E 5 HOH A 92 1091 791 HOH HOH . 
E 5 HOH A 93 1092 792 HOH HOH . 
E 5 HOH A 94 1093 793 HOH HOH . 
E 5 HOH A 95 1094 794 HOH HOH . 
E 5 HOH A 96 1095 795 HOH HOH . 
E 5 HOH A 97 1096 796 HOH HOH . 
E 5 HOH A 98 1097 797 HOH HOH . 
E 5 HOH A 99 1098 798 HOH HOH . 
E 5 HOH A 100 1099 799 HOH HOH . 
E 5 HOH A 101 1100 800 HOH HOH . 
E 5 HOH A 102 1101 801 HOH HOH . 
E 5 HOH A 103 1102 802 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 P PB ADP . . . D 4 63.961 39.809 -25.696 1 43.58 ? PB ADP 998 A 1 
HETATM 2 O O1B ADP . . . D 4 63.967 38.305 -25.738 1 22.32 ? O1B ADP 998 A 1 
HETATM 3 O O2B ADP . . . D 4 65.294 40.328 -26.138 1 48.9 ? O2B ADP 998 A 1 
HETATM 4 O O3B ADP . . . D 4 62.878 40.395 -26.559 1 34.25 ? O3B ADP 998 A 1 
HETATM 5 P PA ADP . . . D 4 63.959 41.468 -23.263 1 39.75 ? PA ADP 998 A 1 
HETATM 6 O O1A ADP . . . D 4 65.417 41.479 -22.891 1 42.39 ? O1A ADP 998 A 1 
HETATM 7 O O2A ADP . . . D 4 63.604 42.726 -23.995 1 26.4 ? O2A ADP 998 A 1 
HETATM 8 O O3A ADP . . . D 4 63.632 40.204 -24.184 1 23.06 ? O3A ADP 998 A 1 
HETATM 9 O O5' ADP . . . D 4 63.086 41.432 -21.94 1 56.32 ? O5' ADP 998 A 1 
HETATM 10 C C5' ADP . . . D 4 62.013 42.392 -21.971 1 52.04 ? C5' ADP 998 A 1 
HETATM 11 C C4' ADP . . . D 4 61.615 42.969 -20.624 1 40.79 ? C4' ADP 998 A 1 
HETATM 12 O O4' ADP . . . D 4 61.774 42.006 -19.538 1 28.4 ? O4' ADP 998 A 1 
HETATM 13 C C3' ADP . . . D 4 62.325 44.246 -20.241 1 29.75 ? C3' ADP 998 A 1 
HETATM 14 O O3' ADP . . . D 4 61.664 45.378 -20.849 1 40 ? O3' ADP 998 A 1 
HETATM 15 C C2' ADP . . . D 4 62.387 44.131 -18.694 1 13.62 ? C2' ADP 998 A 1 
HETATM 16 O O2' ADP . . . D 4 61.352 44.842 -17.985 1 80 ? O2' ADP 998 A 1 
HETATM 17 C C1' ADP . . . D 4 62.331 42.623 -18.436 1 80 ? C1' ADP 998 A 1 
HETATM 18 N N9 ADP . . . D 4 63.628 42.001 -18.139 1 14.6 ? N9 ADP 998 A 1 
HETATM 19 C C8 ADP . . . D 4 64.133 40.836 -18.615 1 16.71 ? C8 ADP 998 A 1 
HETATM 20 N N7 ADP . . . D 4 65.061 40.285 -17.808 1 29.19 ? N7 ADP 998 A 1 
HETATM 21 C C5 ADP . . . D 4 65.247 41.242 -16.82 1 43.84 ? C5 ADP 998 A 1 
HETATM 22 C C6 ADP . . . D 4 66.139 41.293 -15.715 1 68.97 ? C6 ADP 998 A 1 
HETATM 23 N N6 ADP . . . D 4 67.026 40.34 -15.409 1 26.53 ? N6 ADP 998 A 1 
HETATM 24 N N1 ADP . . . D 4 66.05 42.399 -14.925 1 34.11 ? N1 ADP 998 A 1 
HETATM 25 C C2 ADP . . . D 4 65.132 43.366 -15.24 1 32.57 ? C2 ADP 998 A 1 
HETATM 26 N N3 ADP . . . D 4 64.273 43.405 -16.221 1 54.87 ? N3 ADP 998 A 1 
HETATM 27 C C4 ADP . . . D 4 64.42 42.332 -17.04 1 54.08 ? C4 ADP 998 A 1 
#
_model_server_stats.io_time_ms              54 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           237 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           27 
#