data_6VFX
#
_model_server_result.job_id            TPCFfOCL9Ute5Ld6w6sSwQ 
_model_server_result.datetime_utc      '2025-07-07 17:10:07' 
_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":"EA","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 . . . EA 4 141.446 130.552 93.221 1 57.02 ? PG ATP 501 A 1 
HETATM 2 O O1G ATP . . . EA 4 140.452 131.488 93.862 1 57.02 ? O1G ATP 501 A 1 
HETATM 3 O O2G ATP . . . EA 4 142.793 130.516 93.899 1 57.02 ? O2G ATP 501 A 1 
HETATM 4 O O3G ATP . . . EA 4 141.52 130.657 91.717 1 57.02 ? O3G ATP 501 A 1 
HETATM 5 P PB ATP . . . EA 4 139.47 128.579 92.831 1 57.02 ? PB ATP 501 A 1 
HETATM 6 O O1B ATP . . . EA 4 139.494 128.905 91.358 1 57.02 ? O1B ATP 501 A 1 
HETATM 7 O O2B ATP . . . EA 4 138.319 129.058 93.684 1 57.02 ? O2B ATP 501 A 1 
HETATM 8 O O3B ATP . . . EA 4 140.845 129.084 93.502 1 57.02 ? O3B ATP 501 A 1 
HETATM 9 P PA ATP . . . EA 4 139.332 125.989 91.769 1 57.02 ? PA ATP 501 A 1 
HETATM 10 O O1A ATP . . . EA 4 140.253 126.384 90.64 1 57.02 ? O1A ATP 501 A 1 
HETATM 11 O O2A ATP . . . EA 4 137.847 125.894 91.511 1 57.02 ? O2A ATP 501 A 1 
HETATM 12 O O3A ATP . . . EA 4 139.602 126.984 93.006 1 57.02 ? O3A ATP 501 A 1 
HETATM 13 O O5' ATP . . . EA 4 139.856 124.573 92.324 1 57.02 ? O5' ATP 501 A 1 
HETATM 14 C C5' ATP . . . EA 4 140.843 123.853 91.587 1 57.02 ? C5' ATP 501 A 1 
HETATM 15 C C4' ATP . . . EA 4 140.795 122.374 91.945 1 57.02 ? C4' ATP 501 A 1 
HETATM 16 O O4' ATP . . . EA 4 140.335 122.202 93.288 1 57.02 ? O4' ATP 501 A 1 
HETATM 17 C C3' ATP . . . EA 4 139.837 121.626 91.036 1 57.02 ? C3' ATP 501 A 1 
HETATM 18 O O3' ATP . . . EA 4 140.562 120.796 90.125 1 57.02 ? O3' ATP 501 A 1 
HETATM 19 C C2' ATP . . . EA 4 138.979 120.78 91.953 1 57.02 ? C2' ATP 501 A 1 
HETATM 20 O O2' ATP . . . EA 4 139.261 119.393 91.744 1 57.02 ? O2' ATP 501 A 1 
HETATM 21 C C1' ATP . . . EA 4 139.342 121.176 93.376 1 57.02 ? C1' ATP 501 A 1 
HETATM 22 N N9 ATP . . . EA 4 138.156 121.74 94.07 1 57.02 ? N9 ATP 501 A 1 
HETATM 23 C C8 ATP . . . EA 4 138.134 122.921 94.716 1 57.02 ? C8 ATP 501 A 1 
HETATM 24 N N7 ATP . . . EA 4 136.914 123.169 95.256 1 57.02 ? N7 ATP 501 A 1 
HETATM 25 C C5 ATP . . . EA 4 136.124 122.122 94.957 1 57.02 ? C5 ATP 501 A 1 
HETATM 26 C C6 ATP . . . EA 4 134.716 121.743 95.223 1 57.02 ? C6 ATP 501 A 1 
HETATM 27 N N6 ATP . . . EA 4 133.895 122.554 95.932 1 57.02 ? N6 ATP 501 A 1 
HETATM 28 N N1 ATP . . . EA 4 134.28 120.561 94.734 1 57.02 ? N1 ATP 501 A 1 
HETATM 29 C C2 ATP . . . EA 4 135.087 119.748 94.028 1 57.02 ? C2 ATP 501 A 1 
HETATM 30 N N3 ATP . . . EA 4 136.373 120.029 93.751 1 57.02 ? N3 ATP 501 A 1 
HETATM 31 C C4 ATP . . . EA 4 136.948 121.177 94.186 1 57.02 ? C4 ATP 501 A 1 
HETATM 32 H "H5'1" ATP . . . EA 4 141.833 124.251 91.819 1 57.02 ? "H5'1" ATP 501 A 1 
HETATM 33 H "H5'2" ATP . . . EA 4 140.672 123.981 90.516 1 57.02 ? "H5'2" ATP 501 A 1 
HETATM 34 H H4' ATP . . . EA 4 141.801 121.946 91.833 1 57.02 ? H4' ATP 501 A 1 
HETATM 35 H H3' ATP . . . EA 4 139.2 122.339 90.494 1 57.02 ? H3' ATP 501 A 1 
HETATM 36 H HO3' ATP . . . EA 4 139.957 120.438 89.461 1 57.02 ? HO3' ATP 501 A 1 
HETATM 37 H H2' ATP . . . EA 4 137.926 120.972 91.753 1 57.02 ? H2' ATP 501 A 1 
HETATM 38 H HO2' ATP . . . EA 4 138.903 119.113 90.89 1 57.02 ? HO2' ATP 501 A 1 
HETATM 39 H H1' ATP . . . EA 4 139.732 120.301 93.916 1 57.02 ? H1' ATP 501 A 1 
HETATM 40 H H8 ATP . . . EA 4 138.981 123.591 94.793 1 57.02 ? H8 ATP 501 A 1 
HETATM 41 H HN61 ATP . . . EA 4 132.94 122.282 96.101 1 57.02 ? HN61 ATP 501 A 1 
HETATM 42 H HN62 ATP . . . EA 4 134.239 123.432 96.288 1 57.02 ? HN62 ATP 501 A 1 
HETATM 43 H H2 ATP . . . EA 4 134.679 118.813 93.664 1 57.02 ? H2 ATP 501 A 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    78 
_model_server_stats.query_time_ms           259 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#