data_3U06
#
_model_server_result.job_id            zzW9MQAf5IeHgRNp8LttGg 
_model_server_result.datetime_utc      '2024-11-15 05:47:15' 
_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          3u06 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":1}' 
#
_entry.id    3U06 
#
_exptl.entry_id    3U06 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_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          98.91 
_cell.angle_gamma         90 
_cell.entry_id            3U06 
_cell.length_a            160.539 
_cell.length_b            67.094 
_cell.length_c            94.369 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3U06 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 2 C N N 
? 2 I 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 C O3B ADP . A ADP 1 1_555 D MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
metalc ? metalc2 A OG1 THR 153 A THR 441 1_555 D MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc3 D MG MG . A MG 701 1_555 K O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
metalc ? metalc4 D MG MG . A MG 701 1_555 K O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc5 D MG MG . A MG 701 1_555 K O HOH . A HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc6 D MG MG . A MG 701 1_555 K O HOH . A HOH 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
#
_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                     3U06 
_atom_sites.fract_transf_matrix[1][1]    0.006229 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000977 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014904 
_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]    0.010726 
_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
C 2 ADP A 1 1 1 ADP ADP . 
D 3 MG A 1 701 1 MG MG . 
E 4 GOL A 1 702 1 GOL GOL . 
F 4 GOL A 1 2 2 GOL GOL . 
G 4 GOL A 1 3 3 GOL GOL . 
H 4 GOL A 1 4 4 GOL GOL . 
I 2 ADP B 1 1 1 ADP ADP . 
J 4 GOL B 1 5 5 GOL GOL . 
K 5 HOH A 1 5 5 HOH HOH . 
K 5 HOH A 2 6 6 HOH HOH . 
K 5 HOH A 3 7 7 HOH HOH . 
K 5 HOH A 4 9 9 HOH HOH . 
K 5 HOH A 5 14 14 HOH HOH . 
K 5 HOH A 6 15 15 HOH HOH . 
K 5 HOH A 7 18 18 HOH HOH . 
K 5 HOH A 8 19 19 HOH HOH . 
K 5 HOH A 9 20 20 HOH HOH . 
K 5 HOH A 10 21 21 HOH HOH . 
K 5 HOH A 11 22 22 HOH HOH . 
K 5 HOH A 12 24 24 HOH HOH . 
K 5 HOH A 13 25 25 HOH HOH . 
K 5 HOH A 14 26 26 HOH HOH . 
K 5 HOH A 15 28 28 HOH HOH . 
K 5 HOH A 16 30 30 HOH HOH . 
K 5 HOH A 17 31 31 HOH HOH . 
K 5 HOH A 18 34 34 HOH HOH . 
K 5 HOH A 19 35 35 HOH HOH . 
K 5 HOH A 20 36 36 HOH HOH . 
K 5 HOH A 21 37 37 HOH HOH . 
K 5 HOH A 22 38 38 HOH HOH . 
K 5 HOH A 23 39 39 HOH HOH . 
K 5 HOH A 24 40 40 HOH HOH . 
K 5 HOH A 25 41 41 HOH HOH . 
K 5 HOH A 26 42 42 HOH HOH . 
K 5 HOH A 27 44 44 HOH HOH . 
K 5 HOH A 28 45 45 HOH HOH . 
K 5 HOH A 29 46 46 HOH HOH . 
K 5 HOH A 30 48 48 HOH HOH . 
K 5 HOH A 31 49 49 HOH HOH . 
K 5 HOH A 32 51 51 HOH HOH . 
K 5 HOH A 33 52 52 HOH HOH . 
K 5 HOH A 34 53 53 HOH HOH . 
K 5 HOH A 35 54 54 HOH HOH . 
K 5 HOH A 36 58 58 HOH HOH . 
K 5 HOH A 37 60 60 HOH HOH . 
K 5 HOH A 38 61 61 HOH HOH . 
K 5 HOH A 39 62 62 HOH HOH . 
K 5 HOH A 40 63 63 HOH HOH . 
K 5 HOH A 41 64 64 HOH HOH . 
K 5 HOH A 42 65 65 HOH HOH . 
K 5 HOH A 43 66 66 HOH HOH . 
K 5 HOH A 44 67 67 HOH HOH . 
K 5 HOH A 45 68 68 HOH HOH . 
K 5 HOH A 46 69 69 HOH HOH . 
K 5 HOH A 47 70 70 HOH HOH . 
K 5 HOH A 48 71 71 HOH HOH . 
K 5 HOH A 49 72 72 HOH HOH . 
K 5 HOH A 50 73 73 HOH HOH . 
K 5 HOH A 51 75 75 HOH HOH . 
K 5 HOH A 52 77 77 HOH HOH . 
K 5 HOH A 53 78 78 HOH HOH . 
K 5 HOH A 54 79 79 HOH HOH . 
K 5 HOH A 55 82 82 HOH HOH . 
K 5 HOH A 56 83 83 HOH HOH . 
K 5 HOH A 57 84 84 HOH HOH . 
K 5 HOH A 58 85 85 HOH HOH . 
K 5 HOH A 59 86 86 HOH HOH . 
K 5 HOH A 60 88 88 HOH HOH . 
K 5 HOH A 61 89 89 HOH HOH . 
K 5 HOH A 62 91 91 HOH HOH . 
K 5 HOH A 63 92 92 HOH HOH . 
K 5 HOH A 64 94 94 HOH HOH . 
K 5 HOH A 65 95 95 HOH HOH . 
K 5 HOH A 66 96 96 HOH HOH . 
K 5 HOH A 67 97 97 HOH HOH . 
K 5 HOH A 68 98 98 HOH HOH . 
K 5 HOH A 69 99 99 HOH HOH . 
K 5 HOH A 70 101 101 HOH HOH . 
K 5 HOH A 71 103 103 HOH HOH . 
K 5 HOH A 72 104 104 HOH HOH . 
K 5 HOH A 73 105 105 HOH HOH . 
K 5 HOH A 74 106 106 HOH HOH . 
K 5 HOH A 75 107 107 HOH HOH . 
K 5 HOH A 76 108 108 HOH HOH . 
K 5 HOH A 77 109 109 HOH HOH . 
K 5 HOH A 78 110 110 HOH HOH . 
K 5 HOH A 79 111 111 HOH HOH . 
K 5 HOH A 80 112 112 HOH HOH . 
K 5 HOH A 81 113 113 HOH HOH . 
K 5 HOH A 82 114 114 HOH HOH . 
K 5 HOH A 83 120 120 HOH HOH . 
K 5 HOH A 84 122 122 HOH HOH . 
K 5 HOH A 85 703 1 HOH HOH . 
K 5 HOH A 86 704 2 HOH HOH . 
K 5 HOH A 87 705 3 HOH HOH . 
K 5 HOH A 88 706 4 HOH HOH . 
L 5 HOH B 1 8 8 HOH HOH . 
L 5 HOH B 2 10 10 HOH HOH . 
L 5 HOH B 3 11 11 HOH HOH . 
L 5 HOH B 4 12 12 HOH HOH . 
L 5 HOH B 5 13 13 HOH HOH . 
L 5 HOH B 6 16 16 HOH HOH . 
L 5 HOH B 7 17 17 HOH HOH . 
L 5 HOH B 8 23 23 HOH HOH . 
L 5 HOH B 9 27 27 HOH HOH . 
L 5 HOH B 10 29 29 HOH HOH . 
L 5 HOH B 11 32 32 HOH HOH . 
L 5 HOH B 12 33 33 HOH HOH . 
L 5 HOH B 13 43 43 HOH HOH . 
L 5 HOH B 14 47 47 HOH HOH . 
L 5 HOH B 15 50 50 HOH HOH . 
L 5 HOH B 16 55 55 HOH HOH . 
L 5 HOH B 17 56 56 HOH HOH . 
L 5 HOH B 18 57 57 HOH HOH . 
L 5 HOH B 19 59 59 HOH HOH . 
L 5 HOH B 20 74 74 HOH HOH . 
L 5 HOH B 21 76 76 HOH HOH . 
L 5 HOH B 22 80 80 HOH HOH . 
L 5 HOH B 23 81 81 HOH HOH . 
L 5 HOH B 24 87 87 HOH HOH . 
L 5 HOH B 25 90 90 HOH HOH . 
L 5 HOH B 26 93 93 HOH HOH . 
L 5 HOH B 27 100 100 HOH HOH . 
L 5 HOH B 28 102 102 HOH HOH . 
L 5 HOH B 29 115 115 HOH HOH . 
L 5 HOH B 30 116 116 HOH HOH . 
L 5 HOH B 31 117 117 HOH HOH . 
L 5 HOH B 32 118 118 HOH HOH . 
L 5 HOH B 33 119 119 HOH HOH . 
L 5 HOH B 34 121 121 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 . . . I 2 26.697 -39.03 28.755 1 60.8 ? PB ADP 1 B 1 
HETATM 2 O O1B ADP . . . I 2 26.857 -40.531 28.695 1 60.42 ? O1B ADP 1 B 1 
HETATM 3 O O2B ADP . . . I 2 25.341 -38.537 28.312 1 60.83 ? O2B ADP 1 B 1 
HETATM 4 O O3B ADP . . . I 2 27.221 -38.404 30.027 1 60.31 ? O3B ADP 1 B 1 
HETATM 5 P PA ADP . . . I 2 29.018 -37.67 28.015 1 68.9 ? PA ADP 1 B 1 
HETATM 6 O O1A ADP . . . I 2 29.967 -38.619 28.704 1 70.12 ? O1A ADP 1 B 1 
HETATM 7 O O2A ADP . . . I 2 28.571 -36.408 28.713 1 69.97 ? O2A ADP 1 B 1 
HETATM 8 O O3A ADP . . . I 2 27.7 -38.501 27.611 1 67.93 ? O3A ADP 1 B 1 
HETATM 9 O O5' ADP . . . I 2 29.662 -37.283 26.596 1 66.61 ? O5' ADP 1 B 1 
HETATM 10 C C5' ADP . . . I 2 30.235 -38.286 25.761 1 68.11 ? C5' ADP 1 B 1 
HETATM 11 C C4' ADP . . . I 2 31.59 -37.769 25.301 1 69.32 ? C4' ADP 1 B 1 
HETATM 12 O O4' ADP . . . I 2 31.409 -36.733 24.336 1 69.24 ? O4' ADP 1 B 1 
HETATM 13 C C3' ADP . . . I 2 32.371 -37.189 26.472 1 70.66 ? C3' ADP 1 B 1 
HETATM 14 O O3' ADP . . . I 2 33.614 -37.88 26.629 1 71.52 ? O3' ADP 1 B 1 
HETATM 15 C C2' ADP . . . I 2 32.599 -35.725 26.144 1 70.63 ? C2' ADP 1 B 1 
HETATM 16 O O2' ADP . . . I 2 33.991 -35.391 26.187 1 72.54 ? O2' ADP 1 B 1 
HETATM 17 C C1' ADP . . . I 2 32.071 -35.53 24.734 1 69.33 ? C1' ADP 1 B 1 
HETATM 18 N N9 ADP . . . I 2 31.108 -34.401 24.655 1 67.81 ? N9 ADP 1 B 1 
HETATM 19 C C8 ADP . . . I 2 29.872 -34.393 25.193 1 67.26 ? C8 ADP 1 B 1 
HETATM 20 N N7 ADP . . . I 2 29.242 -33.219 24.936 1 66.14 ? N7 ADP 1 B 1 
HETATM 21 C C5 ADP . . . I 2 30.081 -32.454 24.219 1 65.56 ? C5 ADP 1 B 1 
HETATM 22 C C6 ADP . . . I 2 30.041 -31.101 23.621 1 65.05 ? C6 ADP 1 B 1 
HETATM 23 N N6 ADP . . . I 2 28.946 -30.316 23.747 1 64.46 ? N6 ADP 1 B 1 
HETATM 24 N N1 ADP . . . I 2 31.134 -30.679 22.948 1 65.35 ? N1 ADP 1 B 1 
HETATM 25 C C2 ADP . . . I 2 32.231 -31.446 22.813 1 64.98 ? C2 ADP 1 B 1 
HETATM 26 N N3 ADP . . . I 2 32.329 -32.684 23.333 1 65.55 ? N3 ADP 1 B 1 
HETATM 27 C C4 ADP . . . I 2 31.311 -33.235 24.034 1 66.46 ? C4 ADP 1 B 1 
HETATM 28 H "H5'1" ADP . . . I 2 30.356 -39.217 26.319 1 81.73 ? "H5'1" ADP 1 B 1 
HETATM 29 H "H5'2" ADP . . . I 2 29.59 -38.475 24.9 1 81.73 ? "H5'2" ADP 1 B 1 
HETATM 30 H H4' ADP . . . I 2 32.162 -38.599 24.864 1 83.18 ? H4' ADP 1 B 1 
HETATM 31 H H3' ADP . . . I 2 31.768 -37.268 27.387 1 84.79 ? H3' ADP 1 B 1 
HETATM 32 H HO3' ADP . . . I 2 34.1 -37.503 27.374 1 85.83 ? HO3' ADP 1 B 1 
HETATM 33 H H2' ADP . . . I 2 32.026 -35.098 26.842 1 84.76 ? H2' ADP 1 B 1 
HETATM 34 H HO2' ADP . . . I 2 34.332 -35.543 27.079 1 87.05 ? HO2' ADP 1 B 1 
HETATM 35 H H1' ADP . . . I 2 32.922 -35.337 24.065 1 83.19 ? H1' ADP 1 B 1 
HETATM 36 H H8 ADP . . . I 2 29.441 -35.213 25.755 1 80.72 ? H8 ADP 1 B 1 
HETATM 37 H HN61 ADP . . . I 2 28.14 -30.65 24.255 1 77.35 ? HN61 ADP 1 B 1 
HETATM 38 H HN62 ADP . . . I 2 28.935 -29.394 23.333 1 77.35 ? HN62 ADP 1 B 1 
HETATM 39 H H2 ADP . . . I 2 33.075 -31.05 22.261 1 77.97 ? H2 ADP 1 B 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          17 
_model_server_stats.element_count           39 
#