data_6RDM
#
_model_server_result.job_id            UcLJXvv0lGdcgR2OPdefcA 
_model_server_result.datetime_utc      '2024-11-27 19:48:51' 
_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          6rdm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"W","auth_seq_id":1001}' 
#
_entry.id    6RDM 
#
_exptl.entry_id    6RDM 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          8 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_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            6RDM 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6RDM 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    eicosameric 
_pdbx_struct_assembly.oligomeric_count      20 
_pdbx_struct_assembly.details               software_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    x,y,z 
_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
? 8 U N N 
? 8 W N N 
? 8 Y 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 O OG1 THR 232 T THR 232 1_555 V MG MG . T MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc2 U O1G ATP . T ATP 1001 1_555 V MG MG . T MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? 
metalc ? metalc3 U O2B ATP . T ATP 1001 1_555 V MG MG . T MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc4 P OG1 THR 232 U THR 232 1_555 X MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc5 W O1G ATP . U ATP 1001 1_555 X MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? 
metalc ? metalc6 W O2B ATP . U ATP 1001 1_555 X MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
metalc ? metalc7 Q OG1 THR 232 V THR 232 1_555 Z MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc8 Y O1G ATP . V ATP 1001 1_555 Z MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc9 Y O2B ATP . V ATP 1001 1_555 Z MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? 
metalc ? metalc10 R OG1 THR 190 X THR 190 1_555 BA MG MG . X MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
metalc ? metalc11 R OE2 GLU 215 X GLU 215 1_555 BA MG MG . X MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc12 AA O2B ADP . X ADP 601 1_555 BA MG MG . X MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc13 S OG1 THR 190 Y THR 190 1_555 DA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? 
metalc ? metalc14 S OE2 GLU 215 Y GLU 215 1_555 DA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3 ? 
metalc ? metalc15 CA O2B ADP . Y ADP 601 1_555 DA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? 
metalc ? metalc16 CA O3B ADP . Y ADP 601 1_555 DA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
#
_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                     6RDM 
_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
U 8 ATP T 1 1001 1001 ATP ATP . 
V 9 MG T 1 1002 1002 MG MG . 
W 8 ATP U 1 1001 1001 ATP ATP . 
X 9 MG U 1 1002 1002 MG MG . 
Y 8 ATP V 1 1001 1001 ATP ATP . 
Z 9 MG V 1 1002 1002 MG MG . 
AA 10 ADP X 1 601 1028 ADP ADP . 
BA 9 MG X 1 602 1029 MG MG . 
CA 10 ADP Y 1 601 1028 ADP ADP . 
DA 9 MG Y 1 602 1029 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 . . . W 8 122.002 226.382 251.754 1 30.66 ? PG ATP 1001 U 1 
HETATM 2 O O1G ATP . . . W 8 122.613 225.782 252.991 1 30.66 ? O1G ATP 1001 U 1 
HETATM 3 O O2G ATP . . . W 8 122.215 227.864 251.602 1 30.66 ? O2G ATP 1001 U 1 
HETATM 4 O O3G ATP . . . W 8 120.597 225.923 251.462 1 30.66 ? O3G ATP 1001 U 1 
HETATM 5 P PB ATP . . . W 8 123.279 224.19 250.736 1 30.66 ? PB ATP 1001 U 1 
HETATM 6 O O1B ATP . . . W 8 124.591 224.152 251.466 1 30.66 ? O1B ATP 1001 U 1 
HETATM 7 O O2B ATP . . . W 8 122.094 223.465 251.314 1 30.66 ? O2B ATP 1001 U 1 
HETATM 8 O O3B ATP . . . W 8 122.881 225.731 250.583 1 30.66 ? O3B ATP 1001 U 1 
HETATM 9 P PA ATP . . . W 8 122.879 222.461 248.534 1 30.66 ? PA ATP 1001 U 1 
HETATM 10 O O1A ATP . . . W 8 123.655 221.236 248.919 1 30.66 ? O1A ATP 1001 U 1 
HETATM 11 O O2A ATP . . . W 8 121.393 222.463 248.761 1 30.66 ? O2A ATP 1001 U 1 
HETATM 12 O O3A ATP . . . W 8 123.564 223.741 249.222 1 30.66 ? O3A ATP 1001 U 1 
HETATM 13 O O5' ATP . . . W 8 123.126 222.758 246.978 1 30.66 ? O5' ATP 1001 U 1 
HETATM 14 C C5' ATP . . . W 8 122.572 223.92 246.363 1 30.66 ? C5' ATP 1001 U 1 
HETATM 15 C C4' ATP . . . W 8 122.295 223.595 244.906 1 30.66 ? C4' ATP 1001 U 1 
HETATM 16 O O4' ATP . . . W 8 123.504 223.154 244.297 1 30.66 ? O4' ATP 1001 U 1 
HETATM 17 C C3' ATP . . . W 8 121.294 222.46 244.802 1 30.66 ? C3' ATP 1001 U 1 
HETATM 18 O O3' ATP . . . W 8 120.228 222.845 243.936 1 30.66 ? O3' ATP 1001 U 1 
HETATM 19 C C2' ATP . . . W 8 122.033 221.301 244.181 1 30.66 ? C2' ATP 1001 U 1 
HETATM 20 O O2' ATP . . . W 8 121.258 220.752 243.116 1 30.66 ? O2' ATP 1001 U 1 
HETATM 21 C C1' ATP . . . W 8 123.325 221.894 243.657 1 30.66 ? C1' ATP 1001 U 1 
HETATM 22 N N9 ATP . . . W 8 124.444 221.004 244.021 1 30.66 ? N9 ATP 1001 U 1 
HETATM 23 C C8 ATP . . . W 8 125.127 221.031 245.175 1 30.66 ? C8 ATP 1001 U 1 
HETATM 24 N N7 ATP . . . W 8 126.09 220.078 245.189 1 30.66 ? N7 ATP 1001 U 1 
HETATM 25 C C5 ATP . . . W 8 126.025 219.424 244.02 1 30.66 ? C5 ATP 1001 U 1 
HETATM 26 C C6 ATP . . . W 8 126.752 218.309 243.38 1 30.66 ? C6 ATP 1001 U 1 
HETATM 27 N N6 ATP . . . W 8 127.771 217.682 244.012 1 30.66 ? N6 ATP 1001 U 1 
HETATM 28 N N1 ATP . . . W 8 126.365 217.939 242.146 1 30.66 ? N1 ATP 1001 U 1 
HETATM 29 C C2 ATP . . . W 8 125.36 218.554 241.505 1 30.66 ? C2 ATP 1001 U 1 
HETATM 30 N N3 ATP . . . W 8 124.658 219.568 242.027 1 30.66 ? N3 ATP 1001 U 1 
HETATM 31 C C4 ATP . . . W 8 124.939 220.039 243.256 1 30.66 ? C4 ATP 1001 U 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    44 
_model_server_stats.query_time_ms           270 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           31 
#