data_8UB4
#
_model_server_result.job_id            V7ec0Dm7UmfU8e1p_HrGhw 
_model_server_result.datetime_utc      '2024-11-28 08:05:55' 
_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          8ub4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"AA","auth_seq_id":901}' 
#
_entry.id    8UB4 
#
_exptl.entry_id    8UB4 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          6 
_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            8UB4 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8UB4 
_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    decameric 
_pdbx_struct_assembly.oligomeric_count      10 
_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
? 6 AA N N 
? 6 BA 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 OG1 THR 262 A THR 262 1_555 L MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.804 ? 
metalc ? metalc2 A OG1 THR 535 A THR 535 1_555 N MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.839 ? 
metalc ? metalc3 K O2B 08T . A 08T 901 1_555 L MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? 
metalc ? metalc4 B OG1 THR 262 B THR 262 1_555 P MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.775 ? 
metalc ? metalc5 B OG1 THR 535 B THR 535 1_555 R MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? 
metalc ? metalc6 O O2B 08T . B 08T 901 1_555 P MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? 
metalc ? metalc7 Q O2B 08T . B 08T 903 1_555 R MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? 
metalc ? metalc8 C OG1 THR 262 C THR 262 1_555 T MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.785 ? 
metalc ? metalc9 C OG1 THR 535 C THR 535 1_555 V MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? 
metalc ? metalc10 S O2B 08T . C 08T 901 1_555 T MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc11 U O2B 08T . C 08T 903 1_555 V MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? 
metalc ? metalc12 D OG1 THR 262 D THR 262 1_555 X MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.778 ? 
metalc ? metalc13 D OG1 THR 535 D THR 535 1_555 Z MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? 
metalc ? metalc14 W O2B 08T . D 08T 901 1_555 X MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? 
metalc ? metalc15 Y O2B 08T . D 08T 903 1_555 Z MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? 
#
_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 48 n n 
PB O2B ADP sing 49 n n 
PB O3B ADP sing 50 n n 
PB O3A ADP sing 51 n n 
O2B HOB2 ADP sing 52 n n 
O3B HOB3 ADP sing 53 n n 
PA O1A ADP doub 54 n n 
PA O2A ADP sing 55 n n 
PA O3A ADP sing 56 n n 
PA O5' ADP sing 57 n n 
O2A HOA2 ADP sing 58 n n 
O5' C5' ADP sing 59 n n 
C5' C4' ADP sing 60 n n 
C5' "H5'1" ADP sing 61 n n 
C5' "H5'2" ADP sing 62 n n 
C4' O4' ADP sing 63 n n 
C4' C3' ADP sing 64 n n 
C4' H4' ADP sing 65 n n 
O4' C1' ADP sing 66 n n 
C3' O3' ADP sing 67 n n 
C3' C2' ADP sing 68 n n 
C3' H3' ADP sing 69 n n 
O3' HO3' ADP sing 70 n n 
C2' O2' ADP sing 71 n n 
C2' C1' ADP sing 72 n n 
C2' H2' ADP sing 73 n n 
O2' HO2' ADP sing 74 n n 
C1' N9 ADP sing 75 n n 
C1' H1' ADP sing 76 n n 
N9 C8 ADP sing 77 n y 
N9 C4 ADP sing 78 n y 
C8 N7 ADP doub 79 n y 
C8 H8 ADP sing 80 n n 
N7 C5 ADP sing 81 n y 
C5 C6 ADP sing 82 n y 
C5 C4 ADP doub 83 n y 
C6 N6 ADP sing 84 n n 
C6 N1 ADP doub 85 n y 
N6 HN61 ADP sing 86 n n 
N6 HN62 ADP sing 87 n n 
N1 C2 ADP sing 88 n y 
C2 N3 ADP doub 89 n y 
C2 H2 ADP sing 90 n n 
N3 C4 ADP sing 91 n y 
#
_atom_sites.entry_id                     8UB4 
_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
K 4 08T A 1 901 901 08T ADP . 
L 5 MG A 1 902 903 MG MG . 
M 4 08T A 1 903 904 08T ADP . 
N 5 MG A 1 904 906 MG MG . 
O 4 08T B 1 901 901 08T ADP . 
P 5 MG B 1 902 903 MG MG . 
Q 4 08T B 1 903 904 08T ADP . 
R 5 MG B 1 904 906 MG MG . 
S 4 08T C 1 901 901 08T ADP . 
T 5 MG C 1 902 903 MG MG . 
U 4 08T C 1 903 904 08T ADP . 
V 5 MG C 1 904 906 MG MG . 
W 4 08T D 1 901 901 08T ADP . 
X 5 MG D 1 902 903 MG MG . 
Y 4 08T D 1 903 904 08T ADP . 
Z 5 MG D 1 904 906 MG MG . 
AA 6 ADP E 1 901 901 ADP ADP . 
BA 6 ADP E 1 902 904 ADP ADP . 
#
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 . . . AA 6 148.347 169.303 128.605 1 169.37 ? PB ADP 901 E 1 
HETATM 2 O O1B ADP . . . AA 6 148.866 168.643 127.325 1 162.25 ? O1B ADP 901 E 1 
HETATM 3 O O2B ADP . . . AA 6 147.656 168.358 129.52 1 153.84 ? O2B ADP 901 E 1 
HETATM 4 O O3B ADP . . . AA 6 149.475 170.081 129.281 1 166.77 ? O3B ADP 901 E 1 
HETATM 5 P PA ADP . . . AA 6 146.716 170.97 126.741 1 167.94 ? PA ADP 901 E 1 
HETATM 6 O O1A ADP . . . AA 6 146.557 169.864 125.78 1 167.25 ? O1A ADP 901 E 1 
HETATM 7 O O2A ADP . . . AA 6 145.419 171.693 127.094 1 169.86 ? O2A ADP 901 E 1 
HETATM 8 O O3A ADP . . . AA 6 147.335 170.427 128.093 1 168.1 ? O3A ADP 901 E 1 
HETATM 9 O O5' ADP . . . AA 6 147.777 172.036 126.263 1 168.2 ? O5' ADP 901 E 1 
HETATM 10 C C5' ADP . . . AA 6 147.759 173.388 126.766 1 169.22 ? C5' ADP 901 E 1 
HETATM 11 C C4' ADP . . . AA 6 147.619 174.329 125.597 1 171.56 ? C4' ADP 901 E 1 
HETATM 12 O O4' ADP . . . AA 6 148.185 173.662 124.453 1 174.04 ? O4' ADP 901 E 1 
HETATM 13 C C3' ADP . . . AA 6 146.149 174.562 125.235 1 171.33 ? C3' ADP 901 E 1 
HETATM 14 O O3' ADP . . . AA 6 145.971 175.972 125.191 1 172.63 ? O3' ADP 901 E 1 
HETATM 15 C C2' ADP . . . AA 6 146.038 174.054 123.79 1 169.67 ? C2' ADP 901 E 1 
HETATM 16 O O2' ADP . . . AA 6 145.344 175.055 123.057 1 169.19 ? O2' ADP 901 E 1 
HETATM 17 C C1' ADP . . . AA 6 147.487 174.141 123.335 1 168.29 ? C1' ADP 901 E 1 
HETATM 18 N N9 ADP . . . AA 6 147.779 173.221 122.242 1 165.01 ? N9 ADP 901 E 1 
HETATM 19 C C8 ADP . . . AA 6 148.663 172.175 122.279 1 166.86 ? C8 ADP 901 E 1 
HETATM 20 N N7 ADP . . . AA 6 148.742 171.499 121.16 1 163.63 ? N7 ADP 901 E 1 
HETATM 21 C C5 ADP . . . AA 6 147.85 172.148 120.322 1 162.35 ? C5 ADP 901 E 1 
HETATM 22 C C6 ADP . . . AA 6 147.468 171.921 118.986 1 167.3 ? C6 ADP 901 E 1 
HETATM 23 N N6 ADP . . . AA 6 147.96 170.936 118.23 1 168.8 ? N6 ADP 901 E 1 
HETATM 24 N N1 ADP . . . AA 6 146.551 172.753 118.445 1 171.23 ? N1 ADP 901 E 1 
HETATM 25 C C2 ADP . . . AA 6 146.056 173.74 119.197 1 170.78 ? C2 ADP 901 E 1 
HETATM 26 N N3 ADP . . . AA 6 146.342 174.05 120.464 1 166.35 ? N3 ADP 901 E 1 
HETATM 27 C C4 ADP . . . AA 6 147.248 173.212 120.975 1 162.84 ? C4 ADP 901 E 1 
HETATM 28 H "H5'1" ADP . . . AA 6 148.645 173.618 127.4 1 169.49 ? "H5'1" ADP 901 E 1 
HETATM 29 H "H5'2" ADP . . . AA 6 147.019 173.57 127.579 1 169.58 ? "H5'2" ADP 901 E 1 
HETATM 30 H H4' ADP . . . AA 6 148.135 175.296 125.805 1 171.3 ? H4' ADP 901 E 1 
HETATM 31 H H3' ADP . . . AA 6 145.438 174.056 125.929 1 171.07 ? H3' ADP 901 E 1 
HETATM 32 H HO3' ADP . . . AA 6 145.811 176.225 124.289 1 171.14 ? HO3' ADP 901 E 1 
HETATM 33 H H2' ADP . . . AA 6 145.608 173.029 123.703 1 169.34 ? H2' ADP 901 E 1 
HETATM 34 H HO2' ADP . . . AA 6 145.287 175.062 122.111 1 169.56 ? HO2' ADP 901 E 1 
HETATM 35 H H1' ADP . . . AA 6 147.772 175.186 123.069 1 168.96 ? H1' ADP 901 E 1 
HETATM 36 H H8 ADP . . . AA 6 149.252 171.921 123.176 1 167.01 ? H8 ADP 901 E 1 
HETATM 37 H HN61 ADP . . . AA 6 148.882 170.864 117.801 1 170.98 ? HN61 ADP 901 E 1 
HETATM 38 H HN62 ADP . . . AA 6 147.33 170.152 118.059 1 171.44 ? HN62 ADP 901 E 1 
HETATM 39 H H2 ADP . . . AA 6 145.312 174.387 118.703 1 172.22 ? H2 ADP 901 E 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    56 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           39 
#