data_6RDM
#
_model_server_result.job_id            if7UEY6tWWMAxH9E8oPvng 
_model_server_result.datetime_utc      '2024-11-30 17:15:27' 
_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":"CA","auth_seq_id":601}' 
#
_entry.id    6RDM 
#
_exptl.entry_id    6RDM 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          10 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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
? 10 AA N N 
? 10 CA 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 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-5'-DIPHOSPHATE" 
_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
PB O1B ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 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 PB ADP . . . CA 10 146.469 272.313 271.093 1 48.78 ? PB ADP 601 Y 1 
HETATM 2 O O1B ADP . . . CA 10 145.455 272.145 269.995 1 48.78 ? O1B ADP 601 Y 1 
HETATM 3 O O2B ADP . . . CA 10 146.69 271.073 271.918 1 48.78 ? O2B ADP 601 Y 1 
HETATM 4 O O3B ADP . . . CA 10 146.334 273.589 271.883 1 48.78 ? O3B ADP 601 Y 1 
HETATM 5 P PA ADP . . . CA 10 148.938 273.568 270.788 1 48.78 ? PA ADP 601 Y 1 
HETATM 6 O O1A ADP . . . CA 10 148.523 274.937 270.333 1 48.78 ? O1A ADP 601 Y 1 
HETATM 7 O O2A ADP . . . CA 10 149.237 273.316 272.242 1 48.78 ? O2A ADP 601 Y 1 
HETATM 8 O O3A ADP . . . CA 10 147.836 272.519 270.281 1 48.78 ? O3A ADP 601 Y 1 
HETATM 9 O O5' ADP . . . CA 10 150.216 273.113 269.936 1 48.78 ? O5' ADP 601 Y 1 
HETATM 10 C C5' ADP . . . CA 10 151.52 273.563 270.282 1 48.78 ? C5' ADP 601 Y 1 
HETATM 11 C C4' ADP . . . CA 10 152.518 272.955 269.307 1 48.78 ? C4' ADP 601 Y 1 
HETATM 12 O O4' ADP . . . CA 10 152.168 273.331 267.977 1 48.78 ? O4' ADP 601 Y 1 
HETATM 13 C C3' ADP . . . CA 10 153.918 273.457 269.579 1 48.78 ? C3' ADP 601 Y 1 
HETATM 14 O O3' ADP . . . CA 10 154.796 272.347 269.756 1 48.78 ? O3' ADP 601 Y 1 
HETATM 15 C C2' ADP . . . CA 10 154.332 274.205 268.339 1 48.78 ? C2' ADP 601 Y 1 
HETATM 16 O O2' ADP . . . CA 10 155.58 273.68 267.886 1 48.78 ? O2' ADP 601 Y 1 
HETATM 17 C C1' ADP . . . CA 10 153.256 273.956 267.303 1 48.78 ? C1' ADP 601 Y 1 
HETATM 18 N N9 ADP . . . CA 10 152.769 275.244 266.767 1 48.78 ? N9 ADP 601 Y 1 
HETATM 19 C C8 ADP . . . CA 10 151.513 275.695 266.903 1 48.78 ? C8 ADP 601 Y 1 
HETATM 20 N N7 ADP . . . CA 10 151.35 276.9 266.309 1 48.78 ? N7 ADP 601 Y 1 
HETATM 21 C C5 ADP . . . CA 10 152.531 277.237 265.773 1 48.78 ? C5 ADP 601 Y 1 
HETATM 22 C C6 ADP . . . CA 10 153.052 278.386 265.011 1 48.78 ? C6 ADP 601 Y 1 
HETATM 23 N N6 ADP . . . CA 10 152.252 279.425 264.69 1 48.78 ? N6 ADP 601 Y 1 
HETATM 24 N N1 ADP . . . CA 10 154.343 278.357 264.632 1 48.78 ? N1 ADP 601 Y 1 
HETATM 25 C C2 ADP . . . CA 10 155.144 277.322 264.942 1 48.78 ? C2 ADP 601 Y 1 
HETATM 26 N N3 ADP . . . CA 10 154.74 276.246 265.635 1 48.78 ? N3 ADP 601 Y 1 
HETATM 27 C C4 ADP . . . CA 10 153.465 276.143 266.072 1 48.78 ? C4 ADP 601 Y 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           27 
#