data_7Y3S
#
_model_server_result.job_id            dp-vzu8wHVmUBqG2wQRChQ 
_model_server_result.datetime_utc      '2024-11-26 08:01:31' 
_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          7y3s 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":2602}' 
#
_entry.id    7Y3S 
#
_exptl.entry_id    7Y3S 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          108.16 
_cell.angle_gamma         90 
_cell.entry_id            7Y3S 
_cell.length_a            71.897 
_cell.length_b            92.017 
_cell.length_c            87.326 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7Y3S 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 3 D N N 
? 3 H N 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
metalc ? metalc1 A OE1 GLN 223 A GLN 1237 1_555 F MG MG . A MG 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? 
metalc ? metalc2 D O1G ATP . A ATP 2602 1_555 E MG MG . A MG 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.855 ? 
metalc ? metalc3 D O1B ATP . A ATP 2602 1_555 E MG MG . A MG 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.643 ? 
metalc ? metalc4 D O2G ATP . A ATP 2602 1_555 F MG MG . A MG 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? 
metalc ? metalc5 D O3B ATP . A ATP 2602 1_555 F MG MG . A MG 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? 
metalc ? metalc6 B OE1 GLU 200 B GLU 1214 1_555 K MG MG . B MG 2605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? 
metalc ? metalc7 B SG CYS 434 B CYS 1448 1_555 I ZN ZN . B ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? 
metalc ? metalc8 B SG CYS 439 B CYS 1453 1_555 I ZN ZN . B ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? 
metalc ? metalc9 B SG CYS 481 B CYS 1495 1_555 I ZN ZN . B ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc10 B SG CYS 483 B CYS 1497 1_555 I ZN ZN . B ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc11 H O2B ATP . B ATP 2602 1_555 J MG MG . B MG 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc12 H O1B ATP . B ATP 2602 1_555 K MG MG . B MG 2605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? 
#
_chem_comp.formula           'C10 H16 N5 O13 P3' 
_chem_comp.formula_weight    507.181 
_chem_comp.id                ATP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "ADENOSINE-5'-TRIPHOSPHATE" 
_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
PG O1G ATP doub 70 n n 
PG O2G ATP sing 71 n n 
PG O3G ATP sing 72 n n 
PG O3B ATP sing 73 n n 
O2G HOG2 ATP sing 74 n n 
O3G HOG3 ATP sing 75 n n 
PB O1B ATP doub 76 n n 
PB O2B ATP sing 77 n n 
PB O3B ATP sing 78 n n 
PB O3A ATP sing 79 n n 
O2B HOB2 ATP sing 80 n n 
PA O1A ATP doub 81 n n 
PA O2A ATP sing 82 n n 
PA O3A ATP sing 83 n n 
PA O5' ATP sing 84 n n 
O2A HOA2 ATP sing 85 n n 
O5' C5' ATP sing 86 n n 
C5' C4' ATP sing 87 n n 
C5' "H5'1" ATP sing 88 n n 
C5' "H5'2" ATP sing 89 n n 
C4' O4' ATP sing 90 n n 
C4' C3' ATP sing 91 n n 
C4' H4' ATP sing 92 n n 
O4' C1' ATP sing 93 n n 
C3' O3' ATP sing 94 n n 
C3' C2' ATP sing 95 n n 
C3' H3' ATP sing 96 n n 
O3' HO3' ATP sing 97 n n 
C2' O2' ATP sing 98 n n 
C2' C1' ATP sing 99 n n 
C2' H2' ATP sing 100 n n 
O2' HO2' ATP sing 101 n n 
C1' N9 ATP sing 102 n n 
C1' H1' ATP sing 103 n n 
N9 C8 ATP sing 104 n y 
N9 C4 ATP sing 105 n y 
C8 N7 ATP doub 106 n y 
C8 H8 ATP sing 107 n n 
N7 C5 ATP sing 108 n y 
C5 C6 ATP sing 109 n y 
C5 C4 ATP doub 110 n y 
C6 N6 ATP sing 111 n n 
C6 N1 ATP doub 112 n y 
N6 HN61 ATP sing 113 n n 
N6 HN62 ATP sing 114 n n 
N1 C2 ATP sing 115 n y 
C2 N3 ATP doub 116 n y 
C2 H2 ATP sing 117 n n 
N3 C4 ATP sing 118 n y 
#
_atom_sites.entry_id                     7Y3S 
_atom_sites.fract_transf_matrix[1][1]    0.013909 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004562 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010868 
_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]    0.012052 
_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
C 2 F9C A 1 2601 2601 F9C 761 . 
D 3 ATP A 1 2602 2602 ATP ATP . 
E 4 MG A 1 2603 2604 MG MG . 
F 4 MG A 1 2604 2605 MG MG . 
G 2 F9C B 1 2601 2601 F9C 761 . 
H 3 ATP B 1 2602 2602 ATP ATP . 
I 5 ZN B 1 2603 2603 ZN ZN . 
J 4 MG B 1 2604 2604 MG MG . 
K 4 MG B 1 2605 2605 MG MG . 
L 6 HOH A 1 2701 21 HOH HOH . 
L 6 HOH A 2 2702 10 HOH HOH . 
L 6 HOH A 3 2703 12 HOH HOH . 
L 6 HOH A 4 2704 65 HOH HOH . 
L 6 HOH A 5 2705 50 HOH HOH . 
L 6 HOH A 6 2706 54 HOH HOH . 
L 6 HOH A 7 2707 15 HOH HOH . 
L 6 HOH A 8 2708 35 HOH HOH . 
L 6 HOH A 9 2709 32 HOH HOH . 
L 6 HOH A 10 2710 36 HOH HOH . 
L 6 HOH A 11 2711 6 HOH HOH . 
L 6 HOH A 12 2712 59 HOH HOH . 
L 6 HOH A 13 2713 1 HOH HOH . 
L 6 HOH A 14 2714 30 HOH HOH . 
L 6 HOH A 15 2715 51 HOH HOH . 
L 6 HOH A 16 2716 42 HOH HOH . 
L 6 HOH A 17 2717 48 HOH HOH . 
L 6 HOH A 18 2718 55 HOH HOH . 
L 6 HOH A 19 2719 47 HOH HOH . 
L 6 HOH A 20 2720 26 HOH HOH . 
L 6 HOH A 21 2721 66 HOH HOH . 
L 6 HOH A 22 2722 8 HOH HOH . 
L 6 HOH A 23 2723 24 HOH HOH . 
L 6 HOH A 24 2724 2 HOH HOH . 
L 6 HOH A 25 2725 23 HOH HOH . 
L 6 HOH A 26 2726 7 HOH HOH . 
L 6 HOH A 27 2727 22 HOH HOH . 
L 6 HOH A 28 2728 28 HOH HOH . 
L 6 HOH A 29 2729 4 HOH HOH . 
L 6 HOH A 30 2730 61 HOH HOH . 
L 6 HOH A 31 2731 44 HOH HOH . 
L 6 HOH A 32 2732 63 HOH HOH . 
L 6 HOH A 33 2733 56 HOH HOH . 
L 6 HOH A 34 2734 60 HOH HOH . 
L 6 HOH A 35 2735 57 HOH HOH . 
L 6 HOH A 36 2736 39 HOH HOH . 
L 6 HOH A 37 2737 20 HOH HOH . 
L 6 HOH A 38 2738 62 HOH HOH . 
L 6 HOH A 39 2739 14 HOH HOH . 
L 6 HOH A 40 2740 64 HOH HOH . 
L 6 HOH A 41 2741 9 HOH HOH . 
M 6 HOH B 1 2701 5 HOH HOH . 
M 6 HOH B 2 2702 52 HOH HOH . 
M 6 HOH B 3 2703 33 HOH HOH . 
M 6 HOH B 4 2704 19 HOH HOH . 
M 6 HOH B 5 2705 45 HOH HOH . 
M 6 HOH B 6 2706 58 HOH HOH . 
M 6 HOH B 7 2707 38 HOH HOH . 
M 6 HOH B 8 2708 18 HOH HOH . 
M 6 HOH B 9 2709 13 HOH HOH . 
M 6 HOH B 10 2710 11 HOH HOH . 
M 6 HOH B 11 2711 16 HOH HOH . 
M 6 HOH B 12 2712 25 HOH HOH . 
M 6 HOH B 13 2713 68 HOH HOH . 
M 6 HOH B 14 2714 43 HOH HOH . 
M 6 HOH B 15 2715 41 HOH HOH . 
M 6 HOH B 16 2716 40 HOH HOH . 
M 6 HOH B 17 2717 53 HOH HOH . 
M 6 HOH B 18 2718 34 HOH HOH . 
M 6 HOH B 19 2719 3 HOH HOH . 
M 6 HOH B 20 2720 49 HOH HOH . 
M 6 HOH B 21 2721 17 HOH HOH . 
M 6 HOH B 22 2722 27 HOH HOH . 
M 6 HOH B 23 2723 67 HOH HOH . 
M 6 HOH B 24 2724 29 HOH HOH . 
M 6 HOH B 25 2725 37 HOH HOH . 
M 6 HOH B 26 2726 46 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 PG ATP . . . D 3 72.079 17.077 30.538 1 58.99 ? PG ATP 2602 A 1 
HETATM 2 O O1G ATP . . . D 3 72.922 18.018 29.71 1 31.51 ? O1G ATP 2602 A 1 
HETATM 3 O O2G ATP . . . D 3 70.926 17.734 31.257 1 73.44 ? O2G ATP 2602 A 1 
HETATM 4 O O3G ATP . . . D 3 73.026 16.283 31.492 1 34.13 ? O3G ATP 2602 A 1 
HETATM 5 P PB ATP . . . D 3 71.73 15.323 28.242 1 44.07 ? PB ATP 2602 A 1 
HETATM 6 O O1B ATP . . . D 3 71.475 16.175 27.069 1 26.85 ? O1B ATP 2602 A 1 
HETATM 7 O O2B ATP . . . D 3 73.21 15.022 28.388 1 62.02 ? O2B ATP 2602 A 1 
HETATM 8 O O3B ATP . . . D 3 71.43 15.994 29.597 1 112.48 ? O3B ATP 2602 A 1 
HETATM 9 P PA ATP . . . D 3 71.216 12.626 27.237 1 37.39 ? PA ATP 2602 A 1 
HETATM 10 O O1A ATP . . . D 3 71.71 13.21 25.973 1 25.02 ? O1A ATP 2602 A 1 
HETATM 11 O O2A ATP . . . D 3 69.943 11.793 27.189 1 48.82 ? O2A ATP 2602 A 1 
HETATM 12 O O3A ATP . . . D 3 71.05 13.873 28.195 1 36.8 ? O3A ATP 2602 A 1 
HETATM 13 O O5' ATP . . . D 3 72.465 11.833 27.783 1 26.93 ? O5' ATP 2602 A 1 
HETATM 14 C C5' ATP . . . D 3 72.385 10.441 28.151 1 37.91 ? C5' ATP 2602 A 1 
HETATM 15 C C4' ATP . . . D 3 73.214 10.378 29.399 1 46.01 ? C4' ATP 2602 A 1 
HETATM 16 O O4' ATP . . . D 3 74.556 10.769 29.061 1 33.5 ? O4' ATP 2602 A 1 
HETATM 17 C C3' ATP . . . D 3 72.757 11.377 30.452 1 37.51 ? C3' ATP 2602 A 1 
HETATM 18 O O3' ATP . . . D 3 71.842 10.743 31.337 1 30.49 ? O3' ATP 2602 A 1 
HETATM 19 C C2' ATP . . . D 3 74.057 11.79 31.155 1 32.34 ? C2' ATP 2602 A 1 
HETATM 20 O O2' ATP . . . D 3 74.26 11.021 32.331 1 35.97 ? O2' ATP 2602 A 1 
HETATM 21 C C1' ATP . . . D 3 75.154 11.483 30.127 1 33.34 ? C1' ATP 2602 A 1 
HETATM 22 N N9 ATP . . . D 3 75.819 12.643 29.551 1 32.59 ? N9 ATP 2602 A 1 
HETATM 23 C C8 ATP . . . D 3 75.228 13.622 28.81 1 29.58 ? C8 ATP 2602 A 1 
HETATM 24 N N7 ATP . . . D 3 76.052 14.552 28.385 1 23.84 ? N7 ATP 2602 A 1 
HETATM 25 C C5 ATP . . . D 3 77.291 14.122 28.846 1 32.05 ? C5 ATP 2602 A 1 
HETATM 26 C C6 ATP . . . D 3 78.6 14.639 28.733 1 24.27 ? C6 ATP 2602 A 1 
HETATM 27 N N6 ATP . . . D 3 78.916 15.762 28.083 1 25.37 ? N6 ATP 2602 A 1 
HETATM 28 N N1 ATP . . . D 3 79.601 13.949 29.318 1 22.97 ? N1 ATP 2602 A 1 
HETATM 29 C C2 ATP . . . D 3 79.315 12.823 29.968 1 26.25 ? C2 ATP 2602 A 1 
HETATM 30 N N3 ATP . . . D 3 78.132 12.243 30.143 1 25.48 ? N3 ATP 2602 A 1 
HETATM 31 C C4 ATP . . . D 3 77.157 12.939 29.556 1 31.23 ? C4 ATP 2602 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           265 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#