data_8DGF
#
_model_server_result.job_id            yx0VXuaO5kKNq2PY3jPdww 
_model_server_result.datetime_utc      '2024-11-27 14:27:46' 
_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          8dgf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":1601}' 
#
_entry.id    8DGF 
#
_exptl.entry_id    8DGF 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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    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         90 
_cell.entry_id            8DGF 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DGF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_pdbx_struct_assembly.details               author_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 
_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    ? 
_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 I N N 
? 3 K N N 
? 3 M N N 
? 3 O 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
disulf ? disulf1 A SG CYS 1439 A CYS 1439 1_555 A SG CYS 1490 A CYS 1490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
disulf ? disulf2 B SG CYS 1439 B CYS 1439 1_555 B SG CYS 1490 B CYS 1490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf3 C SG CYS 1439 C CYS 1439 1_555 C SG CYS 1490 C CYS 1490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
disulf ? disulf4 D SG CYS 1439 D CYS 1439 1_555 D SG CYS 1490 D CYS 1490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
covale ? covale1 A C FME 1 A FME 1 1_555 A N VAL 2 A VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale2 C C FME 1 C FME 1 1_555 C N VAL 2 C VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
metalc ? metalc1 A OG1 THR 240 A THR 240 1_555 J MG MG . A MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
metalc ? metalc2 I O1G ATP . A ATP 1601 1_555 J MG MG . A MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc3 I O2B ATP . A ATP 1601 1_555 J MG MG . A MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? 
metalc ? metalc4 B OG1 THR 240 B THR 240 1_555 L MG MG . B MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? 
metalc ? metalc5 K O1G ATP . B ATP 1601 1_555 L MG MG . B MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc6 K O2B ATP . B ATP 1601 1_555 L MG MG . B MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc7 C OG1 THR 240 C THR 240 1_555 N MG MG . C MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
metalc ? metalc8 M O1G ATP . C ATP 1601 1_555 N MG MG . C MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
metalc ? metalc9 M O2B ATP . C ATP 1601 1_555 N MG MG . C MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc10 D OG1 THR 240 D THR 240 1_555 P MG MG . D MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? 
metalc ? metalc11 O O1G ATP . D ATP 1601 1_555 P MG MG . D MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc12 O O2B ATP . D ATP 1601 1_555 P MG MG . D MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
#
_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                     8DGF 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
I 3 ATP A 1 1601 1601 ATP ATP . 
J 4 MG A 1 1602 1602 MG MG . 
K 3 ATP B 1 1601 1601 ATP ATP . 
L 4 MG B 1 1602 1602 MG MG . 
M 3 ATP C 1 1601 1601 ATP ATP . 
N 4 MG C 1 1602 1602 MG MG . 
O 3 ATP D 1 1601 1601 ATP ATP . 
P 4 MG D 1 1602 1602 MG MG . 
#
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 . . . M 3 197.181 162.86 173.875 1 33.7 ? PG ATP 1601 C 1 
HETATM 2 O O1G ATP . . . M 3 196.818 163.344 172.525 1 72.23 ? O1G ATP 1601 C 1 
HETATM 3 O O2G ATP . . . M 3 198.03 163.836 174.649 1 55.56 ? O2G ATP 1601 C 1 
HETATM 4 O O3G ATP . . . M 3 195.968 162.465 174.68 1 68.29 ? O3G ATP 1601 C 1 
HETATM 5 P PB ATP . . . M 3 198.122 160.16 173.045 1 8.47 ? PB ATP 1601 C 1 
HETATM 6 O O1B ATP . . . M 3 197.501 159.096 173.838 1 54.16 ? O1B ATP 1601 C 1 
HETATM 7 O O2B ATP . . . M 3 197.547 160.405 171.646 1 65.54 ? O2B ATP 1601 C 1 
HETATM 8 O O3B ATP . . . M 3 198.073 161.528 173.789 1 56.72 ? O3B ATP 1601 C 1 
HETATM 9 P PA ATP . . . M 3 200.666 159.819 171.64 1 14.98 ? PA ATP 1601 C 1 
HETATM 10 O O1A ATP . . . M 3 201.003 161.123 171.042 1 60.09 ? O1A ATP 1601 C 1 
HETATM 11 O O2A ATP . . . M 3 200.036 158.836 170.662 1 68.32 ? O2A ATP 1601 C 1 
HETATM 12 O O3A ATP . . . M 3 199.691 159.951 172.84 1 55.52 ? O3A ATP 1601 C 1 
HETATM 13 O O5' ATP . . . M 3 201.96 159.117 172.212 1 61.73 ? O5' ATP 1601 C 1 
HETATM 14 C C5' ATP . . . M 3 202.693 159.7 173.304 1 66.72 ? C5' ATP 1601 C 1 
HETATM 15 C C4' ATP . . . M 3 204.103 159.182 173.331 1 59.86 ? C4' ATP 1601 C 1 
HETATM 16 O O4' ATP . . . M 3 204.11 157.784 173.668 1 64.46 ? O4' ATP 1601 C 1 
HETATM 17 C C3' ATP . . . M 3 204.865 159.268 172.017 1 59.94 ? C3' ATP 1601 C 1 
HETATM 18 O O3' ATP . . . M 3 205.401 160.577 171.866 1 65.62 ? O3' ATP 1601 C 1 
HETATM 19 C C2' ATP . . . M 3 205.937 158.192 172.182 1 59.45 ? C2' ATP 1601 C 1 
HETATM 20 O O2' ATP . . . M 3 207.026 158.752 172.896 1 65.74 ? O2' ATP 1601 C 1 
HETATM 21 C C1' ATP . . . M 3 205.242 157.159 173.078 1 59.83 ? C1' ATP 1601 C 1 
HETATM 22 N N9 ATP . . . M 3 204.814 155.93 172.417 1 60.84 ? N9 ATP 1601 C 1 
HETATM 23 C C8 ATP . . . M 3 203.657 155.743 171.71 1 66.08 ? C8 ATP 1601 C 1 
HETATM 24 N N7 ATP . . . M 3 203.511 154.529 171.234 1 66.9 ? N7 ATP 1601 C 1 
HETATM 25 C C5 ATP . . . M 3 204.66 153.871 171.65 1 62.89 ? C5 ATP 1601 C 1 
HETATM 26 C C6 ATP . . . M 3 205.116 152.551 171.468 1 62.72 ? C6 ATP 1601 C 1 
HETATM 27 N N6 ATP . . . M 3 204.426 151.615 170.799 1 66.15 ? N6 ATP 1601 C 1 
HETATM 28 N N1 ATP . . . M 3 206.313 152.223 172.017 1 63.59 ? N1 ATP 1601 C 1 
HETATM 29 C C2 ATP . . . M 3 206.993 153.159 172.691 1 63.32 ? C2 ATP 1601 C 1 
HETATM 30 N N3 ATP . . . M 3 206.661 154.434 172.926 1 66.58 ? N3 ATP 1601 C 1 
HETATM 31 C C4 ATP . . . M 3 205.478 154.727 172.375 1 62.99 ? C4 ATP 1601 C 1 
#
_model_server_stats.io_time_ms              34 
_model_server_stats.parse_time_ms           38 
_model_server_stats.create_model_time_ms    78 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          15 
_model_server_stats.element_count           31 
#