data_6MRD
#
_model_server_result.job_id            hruhgw2zmV3aGdf3cTjYvg 
_model_server_result.datetime_utc      '2025-04-19 12:01:40' 
_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          6mrd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":601}' 
#
_entry.id    6MRD 
#
_exptl.entry_id    6MRD 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    7 
_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            6MRD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6MRD 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    tetradecameric 
_pdbx_struct_assembly.oligomeric_count      14 
_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 
_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
? 3 O N N 
? 3 Q N N 
? 3 S N N 
? 3 U N N 
? 3 W N N 
? 3 Y N N 
? 3 AA 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 OD1 ASP 87 A ASP 87 1_555 P MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
metalc ? metalc2 A OD2 ASP 87 A ASP 87 1_555 P MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? 
metalc ? metalc3 O O1B ADP . A ADP 601 1_555 P MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
metalc ? metalc4 O O3B ADP . A ADP 601 1_555 P MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc5 O O1A ADP . A ADP 601 1_555 P MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? 
metalc ? metalc6 O O3A ADP . A ADP 601 1_555 P MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.88 ? 
metalc ? metalc7 I OD1 ASP 87 G ASP 87 1_555 R MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc8 I OD2 ASP 87 G ASP 87 1_555 R MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? 
metalc ? metalc9 Q O1B ADP . G ADP 601 1_555 R MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
metalc ? metalc10 Q O3B ADP . G ADP 601 1_555 R MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
metalc ? metalc11 Q O1A ADP . G ADP 601 1_555 R MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? 
metalc ? metalc12 Q O3A ADP . G ADP 601 1_555 R MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? 
metalc ? metalc13 S O1A ADP . F ADP 601 1_555 T MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc14 S O3A ADP . F ADP 601 1_555 T MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? 
metalc ? metalc15 S O5' ADP . F ADP 601 1_555 T MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? 
metalc ? metalc16 K OD1 ASP 87 E ASP 87 1_555 V MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? 
metalc ? metalc17 K OD2 ASP 87 E ASP 87 1_555 V MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? 
metalc ? metalc18 U O1B ADP . E ADP 601 1_555 V MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
metalc ? metalc19 U O3B ADP . E ADP 601 1_555 V MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
metalc ? metalc20 U O1A ADP . E ADP 601 1_555 V MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? 
metalc ? metalc21 U O3A ADP . E ADP 601 1_555 V MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? 
metalc ? metalc22 L OD1 ASP 87 D ASP 87 1_555 X MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc23 L OD2 ASP 87 D ASP 87 1_555 X MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? 
metalc ? metalc24 W O1B ADP . D ADP 601 1_555 X MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
metalc ? metalc25 W O3B ADP . D ADP 601 1_555 X MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc26 W O1A ADP . D ADP 601 1_555 X MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? 
metalc ? metalc27 W O3A ADP . D ADP 601 1_555 X MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.898 ? 
metalc ? metalc28 Y O1B ADP . C ADP 601 1_555 Z MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? 
metalc ? metalc29 Y O1A ADP . C ADP 601 1_555 Z MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc30 Y O3A ADP . C ADP 601 1_555 Z MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc31 Y O5' ADP . C ADP 601 1_555 Z MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? 
metalc ? metalc32 N OD1 ASP 87 B ASP 87 1_555 BA MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? 
metalc ? metalc33 N OD2 ASP 87 B ASP 87 1_555 BA MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? 
metalc ? metalc34 AA O1B ADP . B ADP 601 1_555 BA MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? 
metalc ? metalc35 AA O3B ADP . B ADP 601 1_555 BA MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc36 AA O1A ADP . B ADP 601 1_555 BA MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? 
metalc ? metalc37 AA O3A ADP . B ADP 601 1_555 BA MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.817 ? 
#
_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                     6MRD 
_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
O 3 ADP A 1 601 529 ADP ADP . 
P 4 MG A 1 602 530 MG MG . 
Q 3 ADP G 1 601 529 ADP ADP . 
R 4 MG G 1 602 530 MG MG . 
S 3 ADP F 1 601 529 ADP ADP . 
T 4 MG F 1 602 530 MG MG . 
U 3 ADP E 1 601 529 ADP ADP . 
V 4 MG E 1 602 530 MG MG . 
W 3 ADP D 1 601 529 ADP ADP . 
X 4 MG D 1 602 530 MG MG . 
Y 3 ADP C 1 601 529 ADP ADP . 
Z 4 MG C 1 602 530 MG MG . 
AA 3 ADP B 1 601 529 ADP ADP . 
BA 4 MG B 1 602 530 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 . . . O 3 231.089 210.249 210.693 1 124.46 ? PB ADP 601 A 1 
HETATM 2 O O1B ADP . . . O 3 230.493 209.136 209.841 1 124.46 ? O1B ADP 601 A 1 
HETATM 3 O O2B ADP . . . O 3 229.997 211.169 211.149 1 124.46 ? O2B ADP 601 A 1 
HETATM 4 O O3B ADP . . . O 3 232.127 210.993 209.883 1 124.46 ? O3B ADP 601 A 1 
HETATM 5 P PA ADP . . . O 3 233.379 208.838 211.838 1 124.46 ? PA ADP 601 A 1 
HETATM 6 O O1A ADP . . . O 3 233.882 209.085 210.446 1 124.46 ? O1A ADP 601 A 1 
HETATM 7 O O2A ADP . . . O 3 233.267 207.345 212.029 1 124.46 ? O2A ADP 601 A 1 
HETATM 8 O O3A ADP . . . O 3 231.896 209.569 212.006 1 124.46 ? O3A ADP 601 A 1 
HETATM 9 O O5' ADP . . . O 3 234.447 209.492 212.883 1 124.46 ? O5' ADP 601 A 1 
HETATM 10 C C5' ADP . . . O 3 235.739 209.821 212.354 1 124.46 ? C5' ADP 601 A 1 
HETATM 11 C C4' ADP . . . O 3 236.238 211.115 213.039 1 124.46 ? C4' ADP 601 A 1 
HETATM 12 O O4' ADP . . . O 3 236.96 210.796 214.07 1 124.46 ? O4' ADP 601 A 1 
HETATM 13 C C3' ADP . . . O 3 237.152 211.89 212.096 1 124.46 ? C3' ADP 601 A 1 
HETATM 14 O O3' ADP . . . O 3 236.543 213.065 211.753 1 124.46 ? O3' ADP 601 A 1 
HETATM 15 C C2' ADP . . . O 3 238.435 212.192 212.861 1 124.46 ? C2' ADP 601 A 1 
HETATM 16 O O2' ADP . . . O 3 238.511 213.678 213.137 1 124.46 ? O2' ADP 601 A 1 
HETATM 17 C C1' ADP . . . O 3 238.37 211.539 213.982 1 124.46 ? C1' ADP 601 A 1 
HETATM 18 N N9 ADP . . . O 3 239.426 210.519 213.989 1 124.46 ? N9 ADP 601 A 1 
HETATM 19 C C8 ADP . . . O 3 239.524 209.468 213.146 1 124.46 ? C8 ADP 601 A 1 
HETATM 20 N N7 ADP . . . O 3 240.625 208.769 213.488 1 124.46 ? N7 ADP 601 A 1 
HETATM 21 C C5 ADP . . . O 3 241.196 209.391 214.539 1 124.46 ? C5 ADP 601 A 1 
HETATM 22 C C6 ADP . . . O 3 242.317 209.101 215.261 1 124.46 ? C6 ADP 601 A 1 
HETATM 23 N N6 ADP . . . O 3 243.296 208.073 215.205 1 124.46 ? N6 ADP 601 A 1 
HETATM 24 N N1 ADP . . . O 3 242.674 209.864 216.249 1 124.46 ? N1 ADP 601 A 1 
HETATM 25 C C2 ADP . . . O 3 241.932 210.957 216.566 1 124.46 ? C2 ADP 601 A 1 
HETATM 26 N N3 ADP . . . O 3 240.815 211.251 215.852 1 124.46 ? N3 ADP 601 A 1 
HETATM 27 C C4 ADP . . . O 3 240.459 210.473 214.853 1 124.46 ? C4 ADP 601 A 1 
#
_model_server_stats.io_time_ms              90 
_model_server_stats.parse_time_ms           29 
_model_server_stats.create_model_time_ms    77 
_model_server_stats.query_time_ms           428 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#