data_6EF3
#
_model_server_result.job_id            JD-0PQhOUzCZx1WVW3NM2Q 
_model_server_result.datetime_utc      '2024-12-22 06:21:25' 
_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          6ef3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"AA","auth_seq_id":501}' 
#
_entry.id    6EF3 
#
_exptl.entry_id    6EF3 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          25 
_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            6EF3 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6EF3 
_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    24-meric 
_pdbx_struct_assembly.oligomeric_count      24 
_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,Y,Z,AA,BA,CA,DA 
_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
? 25 Y N N 
? 25 Z N N 
? 25 AA N N 
? 25 DA 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
covale ? covale1 W NZ LYS 3 s LYS 108 1_555 X C GLY 76 u GLY 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
covale ? covale2 W NZ LYS 3 s LYS 108 1_555 X O GLY 76 u GLY 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? 
#
_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 114 n n 
PG O2G ATP sing 115 n n 
PG O3G ATP sing 116 n n 
PG O3B ATP sing 117 n n 
O2G HOG2 ATP sing 118 n n 
O3G HOG3 ATP sing 119 n n 
PB O1B ATP doub 120 n n 
PB O2B ATP sing 121 n n 
PB O3B ATP sing 122 n n 
PB O3A ATP sing 123 n n 
O2B HOB2 ATP sing 124 n n 
PA O1A ATP doub 125 n n 
PA O2A ATP sing 126 n n 
PA O3A ATP sing 127 n n 
PA O5' ATP sing 128 n n 
O2A HOA2 ATP sing 129 n n 
O5' C5' ATP sing 130 n n 
C5' C4' ATP sing 131 n n 
C5' "H5'1" ATP sing 132 n n 
C5' "H5'2" ATP sing 133 n n 
C4' O4' ATP sing 134 n n 
C4' C3' ATP sing 135 n n 
C4' H4' ATP sing 136 n n 
O4' C1' ATP sing 137 n n 
C3' O3' ATP sing 138 n n 
C3' C2' ATP sing 139 n n 
C3' H3' ATP sing 140 n n 
O3' HO3' ATP sing 141 n n 
C2' O2' ATP sing 142 n n 
C2' C1' ATP sing 143 n n 
C2' H2' ATP sing 144 n n 
O2' HO2' ATP sing 145 n n 
C1' N9 ATP sing 146 n n 
C1' H1' ATP sing 147 n n 
N9 C8 ATP sing 148 n y 
N9 C4 ATP sing 149 n y 
C8 N7 ATP doub 150 n y 
C8 H8 ATP sing 151 n n 
N7 C5 ATP sing 152 n y 
C5 C6 ATP sing 153 n y 
C5 C4 ATP doub 154 n y 
C6 N6 ATP sing 155 n n 
C6 N1 ATP doub 156 n y 
N6 HN61 ATP sing 157 n n 
N6 HN62 ATP sing 158 n n 
N1 C2 ATP sing 159 n y 
C2 N3 ATP doub 160 n y 
C2 H2 ATP sing 161 n n 
N3 C4 ATP sing 162 n y 
#
_atom_sites.entry_id                     6EF3 
_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
Y 25 ATP H 1 501 501 ATP ATP . 
Z 25 ATP I 1 501 501 ATP ATP . 
AA 25 ATP J 1 501 501 ATP ATP . 
BA 26 ADP K 1 501 501 ADP ADP . 
CA 26 ADP L 1 501 501 ADP ADP . 
DA 25 ATP M 1 501 501 ATP ATP . 
#
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 . . . AA 25 195.88 174.664 163.448 1 49.86 ? PG ATP 501 J 1 
HETATM 2 O O1G ATP . . . AA 25 195.734 175.041 161.994 1 49.86 ? O1G ATP 501 J 1 
HETATM 3 O O2G ATP . . . AA 25 196.351 175.792 164.337 1 49.86 ? O2G ATP 501 J 1 
HETATM 4 O O3G ATP . . . AA 25 194.732 173.859 164.008 1 49.86 ? O3G ATP 501 J 1 
HETATM 5 P PB ATP . . . AA 25 198.011 173.556 164.77 1 49.86 ? PB ATP 501 J 1 
HETATM 6 O O1B ATP . . . AA 25 198.815 174.821 164.831 1 49.86 ? O1B ATP 501 J 1 
HETATM 7 O O2B ATP . . . AA 25 197.156 173.143 165.935 1 49.86 ? O2B ATP 501 J 1 
HETATM 8 O O3B ATP . . . AA 25 197.104 173.62 163.455 1 49.86 ? O3B ATP 501 J 1 
HETATM 9 P PA ATP . . . AA 25 200.4 172.578 165.371 1 49.86 ? PA ATP 501 J 1 
HETATM 10 O O1A ATP . . . AA 25 201.451 173.164 164.48 1 49.86 ? O1A ATP 501 J 1 
HETATM 11 O O2A ATP . . . AA 25 200.036 173.273 166.65 1 49.86 ? O2A ATP 501 J 1 
HETATM 12 O O3A ATP . . . AA 25 199.065 172.391 164.52 1 49.86 ? O3A ATP 501 J 1 
HETATM 13 O O5' ATP . . . AA 25 200.784 171.097 165.795 1 49.86 ? O5' ATP 501 J 1 
HETATM 14 C C5' ATP . . . AA 25 200.992 170.892 167.174 1 49.86 ? C5' ATP 501 J 1 
HETATM 15 C C4' ATP . . . AA 25 201.511 169.489 167.401 1 49.86 ? C4' ATP 501 J 1 
HETATM 16 O O4' ATP . . . AA 25 202.806 169.37 166.823 1 49.86 ? O4' ATP 501 J 1 
HETATM 17 C C3' ATP . . . AA 25 201.648 169.148 168.865 1 49.86 ? C3' ATP 501 J 1 
HETATM 18 O O3' ATP . . . AA 25 201.01 167.899 169.123 1 49.86 ? O3' ATP 501 J 1 
HETATM 19 C C2' ATP . . . AA 25 203.123 169.107 169.132 1 49.86 ? C2' ATP 501 J 1 
HETATM 20 O O2' ATP . . . AA 25 203.486 168.083 170.056 1 49.86 ? O2' ATP 501 J 1 
HETATM 21 C C1' ATP . . . AA 25 203.756 168.903 167.773 1 49.86 ? C1' ATP 501 J 1 
HETATM 22 N N9 ATP . . . AA 25 204.992 169.684 167.593 1 49.86 ? N9 ATP 501 J 1 
HETATM 23 C C8 ATP . . . AA 25 205.368 170.221 166.431 1 49.86 ? C8 ATP 501 J 1 
HETATM 24 N N7 ATP . . . AA 25 206.541 170.873 166.552 1 49.86 ? N7 ATP 501 J 1 
HETATM 25 C C5 ATP . . . AA 25 206.92 170.736 167.817 1 49.86 ? C5 ATP 501 J 1 
HETATM 26 C C6 ATP . . . AA 25 208.056 171.162 168.608 1 49.86 ? C6 ATP 501 J 1 
HETATM 27 N N6 ATP . . . AA 25 208.989 171.884 168.004 1 49.86 ? N6 ATP 501 J 1 
HETATM 28 N N1 ATP . . . AA 25 208.123 170.839 169.902 1 49.86 ? N1 ATP 501 J 1 
HETATM 29 C C2 ATP . . . AA 25 207.158 170.111 170.468 1 49.86 ? C2 ATP 501 J 1 
HETATM 30 N N3 ATP . . . AA 25 206.084 169.68 169.8 1 49.86 ? N3 ATP 501 J 1 
HETATM 31 C C4 ATP . . . AA 25 205.919 169.944 168.495 1 49.86 ? C4 ATP 501 J 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    59 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#