data_8DGC
#
_model_server_result.job_id            V6yDg3dok7n9fb1IElilJQ 
_model_server_result.datetime_utc      '2025-07-01 21:43:35' 
_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          8dgc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":601}' 
#
_entry.id    8DGC 
#
_exptl.entry_id    8DGC 
_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    8 
_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            8DGC 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DGC 
_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,Q,R,S,T,U,V,W,X 
_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 
? 3 Q N N 
? 3 S N N 
? 3 U N N 
? 3 W 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 OG SER 294 A SER 294 1_555 J MG MG . A MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? 
metalc ? metalc2 I O1G ATP . A ATP 2101 1_555 J MG MG . A MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc3 B OG SER 294 B SER 294 1_555 L MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc4 K O1G ATP . B ATP 2101 1_555 L MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? 
metalc ? metalc5 K O2B ATP . B ATP 2101 1_555 L MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
metalc ? metalc6 C OG SER 294 C SER 294 1_555 N MG MG . C MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? 
metalc ? metalc7 M O1G ATP . C ATP 2101 1_555 N MG MG . C MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc8 D OG SER 294 D SER 294 1_555 P MG MG . D MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc9 O O1G ATP . D ATP 2101 1_555 P MG MG . D MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? 
metalc ? metalc10 O O2B ATP . D ATP 2101 1_555 P MG MG . D MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
metalc ? metalc11 Q O2G ATP . E ATP 601 1_555 R MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
metalc ? metalc12 Q O2B ATP . E ATP 601 1_555 R MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
metalc ? metalc13 Q O3B ATP . E ATP 601 1_555 R MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? 
metalc ? metalc14 S O2G ATP . F ATP 601 1_555 T MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc15 S O2B ATP . F ATP 601 1_555 T MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
metalc ? metalc16 S O3B ATP . F ATP 601 1_555 T MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.801 ? 
metalc ? metalc17 U O2G ATP . G ATP 601 1_555 V MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? 
metalc ? metalc18 U O2B ATP . G ATP 601 1_555 V MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
metalc ? metalc19 U O3B ATP . G ATP 601 1_555 V MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.801 ? 
metalc ? metalc20 W O2G ATP . H ATP 601 1_555 X MG MG . H MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? 
metalc ? metalc21 W O2B ATP . H ATP 601 1_555 X MG MG . H MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
metalc ? metalc22 W O3B ATP . H ATP 601 1_555 X MG MG . H MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? 
#
_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                     8DGC 
_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 2101 2101 ATP ATP . 
J 4 MG A 1 2102 2102 MG MG . 
K 3 ATP B 1 2101 2101 ATP ATP . 
L 4 MG B 1 2102 2102 MG MG . 
M 3 ATP C 1 2101 2101 ATP ATP . 
N 4 MG C 1 2102 2102 MG MG . 
O 3 ATP D 1 2101 2101 ATP ATP . 
P 4 MG D 1 2102 2102 MG MG . 
Q 3 ATP E 1 601 601 ATP ATP . 
R 4 MG E 1 602 602 MG MG . 
S 3 ATP F 1 601 601 ATP ATP . 
T 4 MG F 1 602 602 MG MG . 
U 3 ATP G 1 601 601 ATP ATP . 
V 4 MG G 1 602 602 MG MG . 
W 3 ATP H 1 601 601 ATP ATP . 
X 4 MG H 1 602 602 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 . . . Q 3 233.986 177.792 193.067 1 85.98 ? PG ATP 601 E 1 
HETATM 2 O O1G ATP . . . Q 3 234.672 177.834 191.756 1 97.28 ? O1G ATP 601 E 1 
HETATM 3 O O2G ATP . . . Q 3 233.481 179.144 193.522 1 87.55 ? O2G ATP 601 E 1 
HETATM 4 O O3G ATP . . . Q 3 232.853 176.784 193.128 1 87.59 ? O3G ATP 601 E 1 
HETATM 5 P PB ATP . . . Q 3 236.398 177.739 194.808 1 92.95 ? PB ATP 601 E 1 
HETATM 6 O O1B ATP . . . Q 3 237.496 177.653 193.825 1 99.41 ? O1B ATP 601 E 1 
HETATM 7 O O2B ATP . . . Q 3 236.225 179.124 195.427 1 91.62 ? O2B ATP 601 E 1 
HETATM 8 O O3B ATP . . . Q 3 234.998 177.333 194.204 1 90.78 ? O3B ATP 601 E 1 
HETATM 9 P PA ATP . . . Q 3 235.838 176.425 197.387 1 92.13 ? PA ATP 601 E 1 
HETATM 10 O O1A ATP . . . Q 3 234.504 175.818 197.218 1 97.09 ? O1A ATP 601 E 1 
HETATM 11 O O2A ATP . . . Q 3 235.818 177.743 198.145 1 95.69 ? O2A ATP 601 E 1 
HETATM 12 O O3A ATP . . . Q 3 236.538 176.692 195.997 1 88.42 ? O3A ATP 601 E 1 
HETATM 13 O O5' ATP . . . Q 3 236.833 175.45 198.127 1 95.59 ? O5' ATP 601 E 1 
HETATM 14 C C5' ATP . . . Q 3 237.01 174.089 197.683 1 94.77 ? C5' ATP 601 E 1 
HETATM 15 C C4' ATP . . . Q 3 236.133 173.18 198.504 1 95.03 ? C4' ATP 601 E 1 
HETATM 16 O O4' ATP . . . Q 3 236.724 171.865 198.561 1 94.34 ? O4' ATP 601 E 1 
HETATM 17 C C3' ATP . . . Q 3 235.941 173.584 199.96 1 95.06 ? C3' ATP 601 E 1 
HETATM 18 O O3' ATP . . . Q 3 234.709 173.079 200.462 1 93.69 ? O3' ATP 601 E 1 
HETATM 19 C C2' ATP . . . Q 3 237.137 172.926 200.651 1 95.27 ? C2' ATP 601 E 1 
HETATM 20 O O2' ATP . . . Q 3 236.814 172.594 201.996 1 98.03 ? O2' ATP 601 E 1 
HETATM 21 C C1' ATP . . . Q 3 237.345 171.654 199.822 1 93.83 ? C1' ATP 601 E 1 
HETATM 22 N N9 ATP . . . Q 3 238.748 171.327 199.589 1 95.89 ? N9 ATP 601 E 1 
HETATM 23 C C8 ATP . . . Q 3 239.771 172.21 199.362 1 96.42 ? C8 ATP 601 E 1 
HETATM 24 N N7 ATP . . . Q 3 240.936 171.643 199.17 1 97.3 ? N7 ATP 601 E 1 
HETATM 25 C C5 ATP . . . Q 3 240.666 170.291 199.296 1 95.54 ? C5 ATP 601 E 1 
HETATM 26 C C6 ATP . . . Q 3 241.485 169.154 199.203 1 94.52 ? C6 ATP 601 E 1 
HETATM 27 N N6 ATP . . . Q 3 242.797 169.207 198.952 1 97.16 ? N6 ATP 601 E 1 
HETATM 28 N N1 ATP . . . Q 3 240.905 167.947 199.376 1 92.65 ? N1 ATP 601 E 1 
HETATM 29 C C2 ATP . . . Q 3 239.594 167.894 199.626 1 92.8 ? C2 ATP 601 E 1 
HETATM 30 N N3 ATP . . . Q 3 238.722 168.899 199.736 1 93.65 ? N3 ATP 601 E 1 
HETATM 31 C C4 ATP . . . Q 3 239.324 170.079 199.562 1 94.79 ? C4 ATP 601 E 1 
#
_model_server_stats.io_time_ms              201 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    108 
_model_server_stats.query_time_ms           289 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           31 
#