data_9B03
#
_model_server_result.job_id            lBaiMBlqxlst8FG7vH-fqg 
_model_server_result.datetime_utc      '2024-11-17 13:29:04' 
_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          9b03 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":401}' 
#
_entry.id    9B03 
#
_exptl.entry_id    9B03 
_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    6 
_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            9B03 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9B03 
_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    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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 
_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
? 3 I N N 
? 3 K N N 
? 3 M N N 
? 3 O N N 
? 3 Q N N 
? 3 S 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
covale ? covale1 A C GLU 68 A GLU 72 1_555 A N HIC 69 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale2 A C HIC 69 A HIC 73 1_555 A N GLY 70 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale3 B C GLU 68 B GLU 72 1_555 B N HIC 69 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale4 B C HIC 69 B HIC 73 1_555 B N GLY 70 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale5 C C GLU 68 C GLU 72 1_555 C N HIC 69 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale6 C C HIC 69 C HIC 73 1_555 C N GLY 70 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale7 D C GLU 68 D GLU 72 1_555 D N HIC 69 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale8 D C HIC 69 D HIC 73 1_555 D N GLY 70 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale9 E C GLU 68 E GLU 72 1_555 E N HIC 69 E HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? 
covale ? covale10 E C HIC 69 E HIC 73 1_555 E N GLY 70 E GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale11 F C GLU 68 F GLU 72 1_555 F N HIC 69 F HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale12 F C HIC 69 F HIC 73 1_555 F N GLY 70 F GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
metalc ? metalc1 I O1B ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? 
metalc ? metalc2 I O3B ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? 
metalc ? metalc3 I O1A ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.914 ? 
metalc ? metalc4 M O1B ADP . C ADP 401 1_555 N MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? 
metalc ? metalc5 M O3B ADP . C ADP 401 1_555 N MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc6 Q O1A ADP . E ADP 401 1_555 R MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.93 ? 
metalc ? metalc7 S O1B ADP . F ADP 401 1_555 T MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
metalc ? metalc8 S O3B ADP . F ADP 401 1_555 T MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? 
metalc ? metalc9 S O1A ADP . F ADP 401 1_555 T MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? 
metalc ? metalc10 S O3A ADP . F ADP 401 1_555 T MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? 
#
_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                     9B03 
_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
I 3 ADP A 1 401 401 ADP ADP . 
J 4 MG A 1 402 402 MG MG . 
K 3 ADP B 1 401 401 ADP ADP . 
L 4 MG B 1 402 402 MG MG . 
M 3 ADP C 1 401 401 ADP ADP . 
N 4 MG C 1 402 402 MG MG . 
O 3 ADP D 1 401 401 ADP ADP . 
P 4 MG D 1 402 402 MG MG . 
Q 3 ADP E 1 401 401 ADP ADP . 
R 4 MG E 1 402 402 MG MG . 
S 3 ADP F 1 401 401 ADP ADP . 
T 4 MG F 1 402 402 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 . . . M 3 171.007 146.183 176.72 1 101.06 ? PB ADP 401 C 1 
HETATM 2 O O1B ADP . . . M 3 172.498 146.28 176.534 1 94.68 ? O1B ADP 401 C 1 
HETATM 3 O O2B ADP . . . M 3 170.514 146.597 178.086 1 73.58 ? O2B ADP 401 C 1 
HETATM 4 O O3B ADP . . . M 3 170.221 146.776 175.575 1 93.49 ? O3B ADP 401 C 1 
HETATM 5 P PA ADP . . . M 3 171.398 143.534 177.651 1 74.68 ? PA ADP 401 C 1 
HETATM 6 O O1A ADP . . . M 3 172.067 142.454 176.84 1 92.95 ? O1A ADP 401 C 1 
HETATM 7 O O2A ADP . . . M 3 172.158 144.272 178.723 1 74.87 ? O2A ADP 401 C 1 
HETATM 8 O O3A ADP . . . M 3 170.722 144.599 176.648 1 91.27 ? O3A ADP 401 C 1 
HETATM 9 O O5' ADP . . . M 3 170.092 142.903 178.343 1 70 ? O5' ADP 401 C 1 
HETATM 10 C C5' ADP . . . M 3 170.071 142.67 179.749 1 76.47 ? C5' ADP 401 C 1 
HETATM 11 C C4' ADP . . . M 3 168.649 142.348 180.189 1 77.32 ? C4' ADP 401 C 1 
HETATM 12 O O4' ADP . . . M 3 168.296 141.03 179.772 1 90.79 ? O4' ADP 401 C 1 
HETATM 13 C C3' ADP . . . M 3 168.505 142.39 181.7 1 78.87 ? C3' ADP 401 C 1 
HETATM 14 O O3' ADP . . . M 3 167.768 143.549 182.094 1 81.94 ? O3' ADP 401 C 1 
HETATM 15 C C2' ADP . . . M 3 167.734 141.145 182.082 1 82.05 ? C2' ADP 401 C 1 
HETATM 16 O O2' ADP . . . M 3 166.435 141.511 182.553 1 88.66 ? O2' ADP 401 C 1 
HETATM 17 C C1' ADP . . . M 3 167.609 140.328 180.81 1 81.29 ? C1' ADP 401 C 1 
HETATM 18 N N9 ADP . . . M 3 168.252 139.008 181.015 1 81.46 ? N9 ADP 401 C 1 
HETATM 19 C C8 ADP . . . M 3 169.543 138.813 181.339 1 85.42 ? C8 ADP 401 C 1 
HETATM 20 N N7 ADP . . . M 3 169.823 137.491 181.456 1 85.29 ? N7 ADP 401 C 1 
HETATM 21 C C5 ADP . . . M 3 168.688 136.815 181.204 1 81.94 ? C5 ADP 401 C 1 
HETATM 22 C C6 ADP . . . M 3 168.279 135.393 181.158 1 79.17 ? C6 ADP 401 C 1 
HETATM 23 N N6 ADP . . . M 3 169.167 134.403 181.411 1 82.69 ? N6 ADP 401 C 1 
HETATM 24 N N1 ADP . . . M 3 166.992 135.117 180.854 1 77.45 ? N1 ADP 401 C 1 
HETATM 25 C C2 ADP . . . M 3 166.097 136.09 180.6 1 75.2 ? C2 ADP 401 C 1 
HETATM 26 N N3 ADP . . . M 3 166.4 137.399 180.625 1 76.5 ? N3 ADP 401 C 1 
HETATM 27 C C4 ADP . . . M 3 167.653 137.819 180.921 1 81.64 ? C4 ADP 401 C 1 
#
_model_server_stats.io_time_ms              67 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    173 
_model_server_stats.query_time_ms           471 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           27 
#