data_6RDB
#
_model_server_result.job_id            v-agbjyKUbBk91NgXNObeA 
_model_server_result.datetime_utc      '2025-09-01 01:04:14' 
_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          6rdb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"CA","auth_seq_id":601}' 
#
_entry.id    6RDB 
#
_exptl.entry_id    6RDB 
_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            6RDB 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6RDB 
_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               author_and_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,EA,FA,GA,HA,IA,JA 
_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
? 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 U O1G ATP . T ATP 1001 1_555 V MG MG . T MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc2 U O2B ATP . T ATP 1001 1_555 V MG MG . T MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
metalc ? metalc3 V MG MG . T MG 1002 1_555 EA O HOH . T HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? 
metalc ? metalc4 V MG MG . T MG 1002 1_555 EA O HOH . T HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? 
metalc ? metalc5 V MG MG . T MG 1002 1_555 HA O HOH . X HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc6 P OG1 THR 232 U THR 232 1_555 X MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? 
metalc ? metalc7 W O1G ATP . U ATP 1001 1_555 X MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc8 W O2B ATP . U ATP 1001 1_555 X MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? 
metalc ? metalc9 X MG MG . U MG 1002 1_555 FA O HOH . U HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? 
metalc ? metalc10 X MG MG . U MG 1002 1_555 FA O HOH . U HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc11 X MG MG . U MG 1002 1_555 FA O HOH . U HOH 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? 
metalc ? metalc12 Q OG1 THR 232 V THR 232 1_555 Z MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? 
metalc ? metalc13 Y O1G ATP . V ATP 1001 1_555 Z MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
metalc ? metalc14 Y O2B ATP . V ATP 1001 1_555 Z MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc15 Z MG MG . V MG 1002 1_555 GA O HOH . V HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? 
metalc ? metalc16 Z MG MG . V MG 1002 1_555 GA O HOH . V HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc17 Z MG MG . V MG 1002 1_555 IA O HOH . Y HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? 
metalc ? metalc18 R OG1 THR 190 X THR 190 1_555 BA MG MG . X MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc19 R OE2 GLU 215 X GLU 215 1_555 BA MG MG . X MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.869 ? 
metalc ? metalc20 AA O2B ADP . X ADP 601 1_555 BA MG MG . X MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? 
metalc ? metalc21 BA MG MG . X MG 602 1_555 HA O HOH . X HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc22 BA MG MG . X MG 602 1_555 HA O HOH . X HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? 
metalc ? metalc23 S OG1 THR 190 Y THR 190 1_555 DA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? 
metalc ? metalc24 S OE2 GLU 215 Y GLU 215 1_555 DA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? 
metalc ? metalc25 CA O3B ADP . Y ADP 601 1_555 DA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? 
metalc ? metalc26 DA MG MG . Y MG 602 1_555 IA O HOH . Y HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? 
metalc ? metalc27 DA MG MG . Y MG 602 1_555 IA O HOH . Y HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? 
metalc ? metalc28 DA MG MG . Y MG 602 1_555 IA O HOH . Y HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? 
#
_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                     6RDB 
_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 . 
EA 11 HOH T 1 1101 6 HOH HOH . 
EA 11 HOH T 2 1102 4 HOH HOH . 
EA 11 HOH T 3 1103 5 HOH HOH . 
EA 11 HOH T 4 1104 8 HOH HOH . 
EA 11 HOH T 5 1105 2 HOH HOH . 
EA 11 HOH T 6 1106 3 HOH HOH . 
EA 11 HOH T 7 1107 48 HOH HOH . 
FA 11 HOH U 1 1101 14 HOH HOH . 
FA 11 HOH U 2 1102 49 HOH HOH . 
FA 11 HOH U 3 1103 15 HOH HOH . 
FA 11 HOH U 4 1104 13 HOH HOH . 
FA 11 HOH U 5 1105 11 HOH HOH . 
FA 11 HOH U 6 1106 47 HOH HOH . 
FA 11 HOH U 7 1107 16 HOH HOH . 
FA 11 HOH U 8 1108 12 HOH HOH . 
FA 11 HOH U 9 1109 10 HOH HOH . 
GA 11 HOH V 1 1101 23 HOH HOH . 
GA 11 HOH V 2 1102 51 HOH HOH . 
GA 11 HOH V 3 1103 27 HOH HOH . 
GA 11 HOH V 4 1104 22 HOH HOH . 
GA 11 HOH V 5 1105 24 HOH HOH . 
GA 11 HOH V 6 1106 20 HOH HOH . 
GA 11 HOH V 7 1107 19 HOH HOH . 
HA 11 HOH X 1 701 29 HOH HOH . 
HA 11 HOH X 2 702 32 HOH HOH . 
HA 11 HOH X 3 703 33 HOH HOH . 
HA 11 HOH X 4 704 34 HOH HOH . 
HA 11 HOH X 5 705 7 HOH HOH . 
HA 11 HOH X 6 706 31 HOH HOH . 
HA 11 HOH X 7 707 30 HOH HOH . 
HA 11 HOH X 8 708 9 HOH HOH . 
HA 11 HOH X 9 709 1 HOH HOH . 
IA 11 HOH Y 1 701 25 HOH HOH . 
IA 11 HOH Y 2 702 41 HOH HOH . 
IA 11 HOH Y 3 703 42 HOH HOH . 
IA 11 HOH Y 4 704 43 HOH HOH . 
IA 11 HOH Y 5 705 52 HOH HOH . 
IA 11 HOH Y 6 706 21 HOH HOH . 
JA 11 HOH Z 1 601 46 HOH HOH . 
JA 11 HOH Z 2 602 18 HOH HOH . 
#
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 10 147.433 272.905 272.217 1 48.78 ? PB ADP 601 Y 1 
HETATM 2 O O1B ADP . . . CA 10 146.466 272.88 271.059 1 48.78 ? O1B ADP 601 Y 1 
HETATM 3 O O2B ADP . . . CA 10 147.799 271.524 272.701 1 48.78 ? O2B ADP 601 Y 1 
HETATM 4 O O3B ADP . . . CA 10 146.981 273.814 273.334 1 48.78 ? O3B ADP 601 Y 1 
HETATM 5 P PA ADP . . . CA 10 149.912 274.497 272.302 1 48.78 ? PA ADP 601 Y 1 
HETATM 6 O O1A ADP . . . CA 10 149.366 275.883 272.401 1 48.78 ? O1A ADP 601 Y 1 
HETATM 7 O O2A ADP . . . CA 10 150.418 273.846 273.546 1 48.78 ? O2A ADP 601 Y 1 
HETATM 8 O O3A ADP . . . CA 10 148.796 273.551 271.643 1 48.78 ? O3A ADP 601 Y 1 
HETATM 9 O O5' ADP . . . CA 10 151.054 274.454 271.176 1 48.78 ? O5' ADP 601 Y 1 
HETATM 10 C C5' ADP . . . CA 10 151.557 273.163 270.749 1 48.78 ? C5' ADP 601 Y 1 
HETATM 11 C C4' ADP . . . CA 10 153.059 273.232 270.615 1 48.78 ? C4' ADP 601 Y 1 
HETATM 12 O O4' ADP . . . CA 10 153.403 273.428 269.218 1 48.78 ? O4' ADP 601 Y 1 
HETATM 13 C C3' ADP . . . CA 10 153.752 274.372 271.372 1 48.78 ? C3' ADP 601 Y 1 
HETATM 14 O O3' ADP . . . CA 10 154.17 273.954 272.666 1 48.78 ? O3' ADP 601 Y 1 
HETATM 15 C C2' ADP . . . CA 10 154.947 274.684 270.469 1 48.78 ? C2' ADP 601 Y 1 
HETATM 16 O O2' ADP . . . CA 10 156.039 273.818 270.688 1 48.78 ? O2' ADP 601 Y 1 
HETATM 17 C C1' ADP . . . CA 10 154.333 274.48 269.088 1 48.78 ? C1' ADP 601 Y 1 
HETATM 18 N N9 ADP . . . CA 10 153.638 275.653 268.573 1 48.78 ? N9 ADP 601 Y 1 
HETATM 19 C C8 ADP . . . CA 10 152.291 275.907 268.647 1 48.78 ? C8 ADP 601 Y 1 
HETATM 20 N N7 ADP . . . CA 10 151.946 277.044 268.097 1 48.78 ? N7 ADP 601 Y 1 
HETATM 21 C C5 ADP . . . CA 10 153.139 277.577 267.631 1 48.78 ? C5 ADP 601 Y 1 
HETATM 22 C C6 ADP . . . CA 10 153.439 278.772 266.95 1 48.78 ? C6 ADP 601 Y 1 
HETATM 23 N N6 ADP . . . CA 10 152.527 279.679 266.611 1 48.78 ? N6 ADP 601 Y 1 
HETATM 24 N N1 ADP . . . CA 10 154.735 279 266.63 1 48.78 ? N1 ADP 601 Y 1 
HETATM 25 C C2 ADP . . . CA 10 155.648 278.083 266.974 1 48.78 ? C2 ADP 601 Y 1 
HETATM 26 N N3 ADP . . . CA 10 155.483 276.928 267.612 1 48.78 ? N3 ADP 601 Y 1 
HETATM 27 C C4 ADP . . . CA 10 154.19 276.728 267.918 1 48.78 ? C4 ADP 601 Y 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    83 
_model_server_stats.query_time_ms           408 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#