data_6VFX
#
_model_server_result.job_id            wybfKa3ndSpEVdV76kw3Ng 
_model_server_result.datetime_utc      '2025-07-06 06:40:48' 
_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          6vfx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"CA","auth_seq_id":501}' 
#
_entry.id    6VFX 
#
_exptl.entry_id    6VFX 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    21-meric 
_pdbx_struct_assembly.oligomeric_count      21 
_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,EA,FA 
_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
? 4 V N N 
? 4 X N N 
? 4 Z N N 
? 4 CA N N 
? 4 EA 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 126 C THR 126 1_555 W MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? 
metalc ? metalc2 A OD2 ASP 184 C ASP 184 1_555 W MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? 
metalc ? metalc3 V O3G ATP . C ATP 501 1_555 W MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc4 V O1B ATP . C ATP 501 1_555 W MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? 
metalc ? metalc5 B OG1 THR 126 B THR 126 1_555 Y MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? 
metalc ? metalc6 B OD2 ASP 184 B ASP 184 1_555 Y MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? 
metalc ? metalc7 X O3G ATP . B ATP 501 1_555 Y MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc8 X O1B ATP . B ATP 501 1_555 Y MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? 
metalc ? metalc9 C OG1 THR 126 E THR 126 1_555 AA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc10 Z O3G ATP . E ATP 501 1_555 AA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc11 Z O1B ATP . E ATP 501 1_555 AA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? 
metalc ? metalc12 E OG1 THR 126 D THR 126 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? 
metalc ? metalc13 E OD2 ASP 184 D ASP 184 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? 
metalc ? metalc14 CA O3G ATP . D ATP 501 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
metalc ? metalc15 CA O1B ATP . D ATP 501 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? 
metalc ? metalc16 F OG1 THR 126 A THR 126 1_555 FA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc17 F OD2 ASP 184 A ASP 184 1_555 FA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? 
metalc ? metalc18 EA O3G ATP . A ATP 501 1_555 FA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc19 EA O1B ATP . A ATP 501 1_555 FA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? 
#
_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                     6VFX 
_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
V 4 ATP C 1 501 1 ATP ATP . 
W 5 MG C 1 502 2 MG MG . 
X 4 ATP B 1 501 1 ATP ATP . 
Y 5 MG B 1 502 1 MG MG . 
Z 4 ATP E 1 501 1 ATP ATP . 
AA 5 MG E 1 502 4 MG MG . 
BA 6 ADP F 1 501 1 ADP ADP . 
CA 4 ATP D 1 501 1 ATP ATP . 
DA 5 MG D 1 502 3 MG MG . 
EA 4 ATP A 1 501 1 ATP ATP . 
FA 5 MG A 1 502 5 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 . . . CA 4 169.622 182.997 95.774 1 43.25 ? PG ATP 501 D 1 
HETATM 2 O O1G ATP . . . CA 4 170.848 182.357 96.373 1 43.25 ? O1G ATP 501 D 1 
HETATM 3 O O2G ATP . . . CA 4 168.502 183.226 96.761 1 43.25 ? O2G ATP 501 D 1 
HETATM 4 O O3G ATP . . . CA 4 169.172 182.384 94.47 1 43.25 ? O3G ATP 501 D 1 
HETATM 5 P PB ATP . . . CA 4 171.178 184.763 94.221 1 43.25 ? PB ATP 501 D 1 
HETATM 6 O O1B ATP . . . CA 4 170.803 183.946 93.012 1 43.25 ? O1B ATP 501 D 1 
HETATM 7 O O2B ATP . . . CA 4 172.564 184.637 94.805 1 43.25 ? O2B ATP 501 D 1 
HETATM 8 O O3B ATP . . . CA 4 170.101 184.486 95.388 1 43.25 ? O3B ATP 501 D 1 
HETATM 9 P PA ATP . . . CA 4 170.697 186.821 92.378 1 43.25 ? PA ATP 501 D 1 
HETATM 10 O O1A ATP . . . CA 4 169.555 186.042 91.773 1 43.25 ? O1A ATP 501 D 1 
HETATM 11 O O2A ATP . . . CA 4 172.028 186.849 91.664 1 43.25 ? O2A ATP 501 D 1 
HETATM 12 O O3A ATP . . . CA 4 170.903 186.316 93.894 1 43.25 ? O3A ATP 501 D 1 
HETATM 13 O O5' ATP . . . CA 4 170.179 188.332 92.572 1 43.25 ? O5' ATP 501 D 1 
HETATM 14 C C5' ATP . . . CA 4 168.953 188.736 91.967 1 43.25 ? C5' ATP 501 D 1 
HETATM 15 C C4' ATP . . . CA 4 168.936 190.247 91.785 1 43.25 ? C4' ATP 501 D 1 
HETATM 16 O O4' ATP . . . CA 4 169.735 190.87 92.792 1 43.25 ? O4' ATP 501 D 1 
HETATM 17 C C3' ATP . . . CA 4 169.517 190.635 90.436 1 43.25 ? C3' ATP 501 D 1 
HETATM 18 O O3' ATP . . . CA 4 168.484 191.129 89.579 1 43.25 ? O3' ATP 501 D 1 
HETATM 19 C C2' ATP . . . CA 4 170.532 191.722 90.719 1 43.25 ? C2' ATP 501 D 1 
HETATM 20 O O2' ATP . . . CA 4 170.082 192.958 90.157 1 43.25 ? O2' ATP 501 D 1 
HETATM 21 C C1' ATP . . . CA 4 170.609 191.853 92.231 1 43.25 ? C1' ATP 501 D 1 
HETATM 22 N N9 ATP . . . CA 4 171.988 191.587 92.72 1 43.25 ? N9 ATP 501 D 1 
HETATM 23 C C8 ATP . . . CA 4 172.294 190.756 93.733 1 43.25 ? C8 ATP 501 D 1 
HETATM 24 N N7 ATP . . . CA 4 173.631 190.723 93.961 1 43.25 ? N7 ATP 501 D 1 
HETATM 25 C C5 ATP . . . CA 4 174.21 191.555 93.077 1 43.25 ? C5 ATP 501 D 1 
HETATM 26 C C6 ATP . . . CA 4 175.594 191.987 92.771 1 43.25 ? C6 ATP 501 D 1 
HETATM 27 N N6 ATP . . . CA 4 176.649 191.509 93.473 1 43.25 ? N6 ATP 501 D 1 
HETATM 28 N N1 ATP . . . CA 4 175.774 192.873 91.769 1 43.25 ? N1 ATP 501 D 1 
HETATM 29 C C2 ATP . . . CA 4 174.736 193.352 91.065 1 43.25 ? C2 ATP 501 D 1 
HETATM 30 N N3 ATP . . . CA 4 173.455 193.002 91.288 1 43.25 ? N3 ATP 501 D 1 
HETATM 31 C C4 ATP . . . CA 4 173.124 192.128 92.266 1 43.25 ? C4 ATP 501 D 1 
HETATM 32 H "H5'1" ATP . . . CA 4 168.831 188.241 91.001 1 43.25 ? "H5'1" ATP 501 D 1 
HETATM 33 H "H5'2" ATP . . . CA 4 168.119 188.442 92.604 1 43.25 ? "H5'2" ATP 501 D 1 
HETATM 34 H H4' ATP . . . CA 4 167.899 190.606 91.847 1 43.25 ? H4' ATP 501 D 1 
HETATM 35 H H3' ATP . . . CA 4 170.023 189.772 89.982 1 43.25 ? H3' ATP 501 D 1 
HETATM 36 H HO3' ATP . . . CA 4 168.829 191.231 88.681 1 43.25 ? HO3' ATP 501 D 1 
HETATM 37 H H2' ATP . . . CA 4 171.505 191.43 90.302 1 43.25 ? H2' ATP 501 D 1 
HETATM 38 H HO2' ATP . . . CA 4 170.158 192.924 89.194 1 43.25 ? HO2' ATP 501 D 1 
HETATM 39 H H1' ATP . . . CA 4 170.287 192.862 92.524 1 43.25 ? H1' ATP 501 D 1 
HETATM 40 H H8 ATP . . . CA 4 171.566 190.185 94.295 1 43.25 ? H8 ATP 501 D 1 
HETATM 41 H HN61 ATP . . . CA 4 177.582 191.813 93.247 1 43.25 ? HN61 ATP 501 D 1 
HETATM 42 H HN62 ATP . . . CA 4 176.5 190.848 94.22 1 43.25 ? HN62 ATP 501 D 1 
HETATM 43 H H2 ATP . . . CA 4 174.94 194.061 90.273 1 43.25 ? H2 ATP 501 D 1 
#
_model_server_stats.io_time_ms              63 
_model_server_stats.parse_time_ms           30 
_model_server_stats.create_model_time_ms    137 
_model_server_stats.query_time_ms           470 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#