data_7DYJ
#
_model_server_result.job_id            qXyHH5aeplbiGBQX8LVCAQ 
_model_server_result.datetime_utc      '2024-11-17 02:26:23' 
_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          7dyj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":602}' 
#
_entry.id    7DYJ 
#
_exptl.entry_id    7DYJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_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            7DYJ 
_cell.length_a            94.582 
_cell.length_b            94.582 
_cell.length_c            179.858 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7DYJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_445 -y-1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -47.291 -81.910415 0 
3 'crystal symmetry operation' 3_545 -x+y,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 47.291 -81.910415 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
? 2 G N N 
? 2 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 OG1 THR 53 A THR 53 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
metalc ? metalc2 A OG1 THR 295 A THR 295 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc3 C O3G ATP . A ATP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? 
metalc ? metalc4 C O2B ATP . A ATP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? 
metalc ? metalc5 D O1G ATP . A ATP 602 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? 
metalc ? metalc6 D O2B ATP . A ATP 602 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.808 ? 
metalc ? metalc7 D O3B ATP . A ATP 602 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.851 ? 
metalc ? metalc8 E MG MG . A MG 603 1_555 K O HOH . A HOH 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? 
metalc ? metalc9 E MG MG . A MG 603 1_555 K O HOH . A HOH 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? 
metalc ? metalc10 E MG MG . A MG 603 1_555 K O HOH . A HOH 727 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? 
metalc ? metalc11 F MG MG . A MG 604 1_555 K O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc12 F MG MG . A MG 604 1_555 K O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc13 F MG MG . A MG 604 1_555 K O HOH . A HOH 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? 
metalc ? metalc14 B OG1 THR 53 B THR 53 1_555 I MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc15 B OG1 THR 295 B THR 295 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? 
metalc ? metalc16 G O2G ATP . B ATP 601 1_555 I MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? 
metalc ? metalc17 G O2B ATP . B ATP 601 1_555 I MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
metalc ? metalc18 G O3B ATP . B ATP 601 1_555 I MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? 
metalc ? metalc19 H O3G ATP . B ATP 602 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.929 ? 
metalc ? metalc20 H O2B ATP . B ATP 602 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.833 ? 
metalc ? metalc21 I MG MG . B MG 603 1_555 L O HOH . B HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.89 ? 
metalc ? metalc22 I MG MG . B MG 603 1_555 L O HOH . B HOH 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
metalc ? metalc23 I MG MG . B MG 603 1_555 L O HOH . B HOH 721 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc24 J MG MG . B MG 604 1_555 L O HOH . B HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? 
metalc ? metalc25 J MG MG . B MG 604 1_555 L O HOH . B HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
metalc ? metalc26 J MG MG . B MG 604 1_555 L O HOH . B HOH 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
#
_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                     7DYJ 
_atom_sites.fract_transf_matrix[1][1]    0.010573 
_atom_sites.fract_transf_matrix[1][2]    0.006104 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012208 
_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]    0.00556 
_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 ATP A 1 601 501 ATP ATP . 
D 2 ATP A 1 602 601 ATP ATP . 
E 3 MG A 1 603 1 MG MG . 
F 3 MG A 1 604 2 MG MG . 
G 2 ATP B 1 601 501 ATP ATP . 
H 2 ATP B 1 602 601 ATP ATP . 
I 3 MG B 1 603 3 MG MG . 
J 3 MG B 1 604 4 MG MG . 
K 4 HOH A 1 701 65 HOH HOH . 
K 4 HOH A 2 702 77 HOH HOH . 
K 4 HOH A 3 703 74 HOH HOH . 
K 4 HOH A 4 704 64 HOH HOH . 
K 4 HOH A 5 705 11 HOH HOH . 
K 4 HOH A 6 706 58 HOH HOH . 
K 4 HOH A 7 707 76 HOH HOH . 
K 4 HOH A 8 708 1 HOH HOH . 
K 4 HOH A 9 709 56 HOH HOH . 
K 4 HOH A 10 710 70 HOH HOH . 
K 4 HOH A 11 711 86 HOH HOH . 
K 4 HOH A 12 712 63 HOH HOH . 
K 4 HOH A 13 713 73 HOH HOH . 
K 4 HOH A 14 714 15 HOH HOH . 
K 4 HOH A 15 715 27 HOH HOH . 
K 4 HOH A 16 716 23 HOH HOH . 
K 4 HOH A 17 717 9 HOH HOH . 
K 4 HOH A 18 718 6 HOH HOH . 
K 4 HOH A 19 719 88 HOH HOH . 
K 4 HOH A 20 720 71 HOH HOH . 
K 4 HOH A 21 721 45 HOH HOH . 
K 4 HOH A 22 722 2 HOH HOH . 
K 4 HOH A 23 723 82 HOH HOH . 
K 4 HOH A 24 724 30 HOH HOH . 
K 4 HOH A 25 725 42 HOH HOH . 
K 4 HOH A 26 726 84 HOH HOH . 
K 4 HOH A 27 727 57 HOH HOH . 
K 4 HOH A 28 728 59 HOH HOH . 
K 4 HOH A 29 729 75 HOH HOH . 
K 4 HOH A 30 730 53 HOH HOH . 
L 4 HOH B 1 701 68 HOH HOH . 
L 4 HOH B 2 702 79 HOH HOH . 
L 4 HOH B 3 703 67 HOH HOH . 
L 4 HOH B 4 704 81 HOH HOH . 
L 4 HOH B 5 705 61 HOH HOH . 
L 4 HOH B 6 706 85 HOH HOH . 
L 4 HOH B 7 707 5 HOH HOH . 
L 4 HOH B 8 708 20 HOH HOH . 
L 4 HOH B 9 709 25 HOH HOH . 
L 4 HOH B 10 710 66 HOH HOH . 
L 4 HOH B 11 711 4 HOH HOH . 
L 4 HOH B 12 712 19 HOH HOH . 
L 4 HOH B 13 713 78 HOH HOH . 
L 4 HOH B 14 714 8 HOH HOH . 
L 4 HOH B 15 715 60 HOH HOH . 
L 4 HOH B 16 716 72 HOH HOH . 
L 4 HOH B 17 717 31 HOH HOH . 
L 4 HOH B 18 718 44 HOH HOH . 
L 4 HOH B 19 719 83 HOH HOH . 
L 4 HOH B 20 720 87 HOH HOH . 
L 4 HOH B 21 721 62 HOH HOH . 
L 4 HOH B 22 722 13 HOH HOH . 
L 4 HOH B 23 723 39 HOH HOH . 
L 4 HOH B 24 724 55 HOH HOH . 
L 4 HOH B 25 725 80 HOH HOH . 
L 4 HOH B 26 726 54 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 2 -9.488 -30.1 20.514 1 45.97 ? PG ATP 602 A 1 
HETATM 2 O O1G ATP . . . D 2 -8.769 -29.228 19.517 1 46.84 ? O1G ATP 602 A 1 
HETATM 3 O O2G ATP . . . D 2 -8.886 -31.473 20.617 1 46.05 ? O2G ATP 602 A 1 
HETATM 4 O O3G ATP . . . D 2 -10.98 -30.13 20.295 1 46.49 ? O3G ATP 602 A 1 
HETATM 5 P PB ATP . . . D 2 -7.971 -28.839 22.698 1 44.41 ? PB ATP 602 A 1 
HETATM 6 O O1B ATP . . . D 2 -7.177 -29.975 23.254 1 43.72 ? O1B ATP 602 A 1 
HETATM 7 O O2B ATP . . . D 2 -7.309 -27.844 21.805 1 44.1 ? O2B ATP 602 A 1 
HETATM 8 O O3B ATP . . . D 2 -9.267 -29.419 21.959 1 45.41 ? O3B ATP 602 A 1 
HETATM 9 P PA ATP . . . D 2 -9.28 -26.586 24.033 1 43.38 ? PA ATP 602 A 1 
HETATM 10 O O1A ATP . . . D 2 -10.468 -26.476 23.134 1 43.29 ? O1A ATP 602 A 1 
HETATM 11 O O2A ATP . . . D 2 -8.181 -25.588 23.886 1 43.17 ? O2A ATP 602 A 1 
HETATM 12 O O3A ATP . . . D 2 -8.664 -28.06 23.91 1 43.68 ? O3A ATP 602 A 1 
HETATM 13 O O5' ATP . . . D 2 -9.765 -26.609 25.559 1 41.9 ? O5' ATP 602 A 1 
HETATM 14 C C5' ATP . . . D 2 -11.181 -26.741 25.813 1 40.25 ? C5' ATP 602 A 1 
HETATM 15 C C4' ATP . . . D 2 -11.392 -27.438 27.131 1 39.21 ? C4' ATP 602 A 1 
HETATM 16 O O4' ATP . . . D 2 -11.082 -26.513 28.203 1 38.91 ? O4' ATP 602 A 1 
HETATM 17 C C3' ATP . . . D 2 -12.825 -27.913 27.396 1 39.02 ? C3' ATP 602 A 1 
HETATM 18 O O3' ATP . . . D 2 -13.008 -29.26 26.977 1 38.68 ? O3' ATP 602 A 1 
HETATM 19 C C2' ATP . . . D 2 -12.959 -27.738 28.912 1 38.83 ? C2' ATP 602 A 1 
HETATM 20 O O2' ATP . . . D 2 -12.431 -28.818 29.652 1 38.67 ? O2' ATP 602 A 1 
HETATM 21 C C1' ATP . . . D 2 -12.122 -26.487 29.153 1 38.73 ? C1' ATP 602 A 1 
HETATM 22 N N9 ATP . . . D 2 -12.846 -25.225 29.006 1 38.6 ? N9 ATP 602 A 1 
HETATM 23 C C8 ATP . . . D 2 -13.161 -24.55 27.847 1 38.28 ? C8 ATP 602 A 1 
HETATM 24 N N7 ATP . . . D 2 -13.811 -23.431 28.076 1 37.97 ? N7 ATP 602 A 1 
HETATM 25 C C5 ATP . . . D 2 -13.927 -23.368 29.459 1 37.97 ? C5 ATP 602 A 1 
HETATM 26 C C6 ATP . . . D 2 -14.512 -22.424 30.324 1 38.08 ? C6 ATP 602 A 1 
HETATM 27 N N6 ATP . . . D 2 -15.115 -21.315 29.907 1 38.23 ? N6 ATP 602 A 1 
HETATM 28 N N1 ATP . . . D 2 -14.447 -22.673 31.655 1 38.51 ? N1 ATP 602 A 1 
HETATM 29 C C2 ATP . . . D 2 -13.836 -23.793 32.07 1 38.49 ? C2 ATP 602 A 1 
HETATM 30 N N3 ATP . . . D 2 -13.249 -24.747 31.35 1 38.29 ? N3 ATP 602 A 1 
HETATM 31 C C4 ATP . . . D 2 -13.333 -24.469 30.038 1 38.25 ? C4 ATP 602 A 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#