data_6PEN
#
_model_server_result.job_id            VtgDqESERL2w47Ub104JVw 
_model_server_result.datetime_utc      '2024-11-22 10:35:12' 
_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          6pen 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":701}' 
#
_entry.id    6PEN 
#
_exptl.entry_id    6PEN 
_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    5 
_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            6PEN 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PEN 
_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    heptameric 
_pdbx_struct_assembly.oligomeric_count      7 
_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 
_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 H N N 
? 3 K N N 
? 3 N N N 
? 3 Q N N 
? 3 T 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 271 A THR 389 1_555 J MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc2 A OD2 ASP 323 A ASP 441 1_555 J MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? 
metalc ? metalc3 H O3B ADP . A ADP 701 1_555 I BE BEF . A BEF 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.596 ? 
metalc ? metalc4 H O1B ADP . A ADP 701 1_555 J MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? 
metalc ? metalc5 H O2B ADP . A ADP 701 1_555 J MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc6 I F1 BEF . A BEF 702 1_555 J MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc7 B OG1 THR 271 B THR 389 1_555 M MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? 
metalc ? metalc8 B OD2 ASP 323 B ASP 441 1_555 M MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? 
metalc ? metalc9 K O3B ADP . B ADP 701 1_555 L BE BEF . B BEF 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.597 ? 
metalc ? metalc10 K O1B ADP . B ADP 701 1_555 M MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.915 ? 
metalc ? metalc11 K O2B ADP . B ADP 701 1_555 M MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc12 L F1 BEF . B BEF 702 1_555 M MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc13 C OG1 THR 271 C THR 389 1_555 P MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? 
metalc ? metalc14 N O3B ADP . C ADP 701 1_555 O BE BEF . C BEF 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? 
metalc ? metalc15 N O1B ADP . C ADP 701 1_555 P MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.906 ? 
metalc ? metalc16 N O2B ADP . C ADP 701 1_555 P MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc17 O F1 BEF . C BEF 702 1_555 P MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc18 D OG1 THR 271 D THR 389 1_555 S MG MG . D MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? 
metalc ? metalc19 Q O3B ADP . D ADP 701 1_555 R BE BEF . D BEF 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.58 ? 
metalc ? metalc20 Q O1B ADP . D ADP 701 1_555 S MG MG . D MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? 
metalc ? metalc21 Q O2B ADP . D ADP 701 1_555 S MG MG . D MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc22 R F1 BEF . D BEF 702 1_555 S MG MG . D MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
#
_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                     6PEN 
_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
H 3 ADP A 1 701 711 ADP ADP . 
I 4 BEF A 1 702 712 BEF BEF . 
J 5 MG A 1 703 713 MG MG . 
K 3 ADP B 1 701 711 ADP ADP . 
L 4 BEF B 1 702 712 BEF BEF . 
M 5 MG B 1 703 713 MG MG . 
N 3 ADP C 1 701 711 ADP ADP . 
O 4 BEF C 1 702 712 BEF BEF . 
P 5 MG C 1 703 713 MG MG . 
Q 3 ADP D 1 701 711 ADP ADP . 
R 4 BEF D 1 702 712 BEF BEF . 
S 5 MG D 1 703 713 MG MG . 
T 3 ADP E 1 701 711 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 . . . N 3 154.289 110.749 134.687 1 57.4 ? PB ADP 701 C 1 
HETATM 2 O O1B ADP . . . N 3 154.556 112.101 134.007 1 57.4 ? O1B ADP 701 C 1 
HETATM 3 O O2B ADP . . . N 3 152.975 110.201 134.29 1 57.4 ? O2B ADP 701 C 1 
HETATM 4 O O3B ADP . . . N 3 154.434 111.025 136.244 1 57.4 ? O3B ADP 701 C 1 
HETATM 5 P PA ADP . . . N 3 156.84 109.899 133.675 1 57.4 ? PA ADP 701 C 1 
HETATM 6 O O1A ADP . . . N 3 157.317 111.335 133.945 1 57.4 ? O1A ADP 701 C 1 
HETATM 7 O O2A ADP . . . N 3 156.65 109.622 132.235 1 57.4 ? O2A ADP 701 C 1 
HETATM 8 O O3A ADP . . . N 3 155.454 109.713 134.413 1 57.4 ? O3A ADP 701 C 1 
HETATM 9 O O5' ADP . . . N 3 157.736 108.877 134.458 1 57.4 ? O5' ADP 701 C 1 
HETATM 10 C C5' ADP . . . N 3 159.013 109.286 134.981 1 57.4 ? C5' ADP 701 C 1 
HETATM 11 C C4' ADP . . . N 3 160.067 108.81 134.025 1 57.4 ? C4' ADP 701 C 1 
HETATM 12 O O4' ADP . . . N 3 160.921 107.857 134.699 1 57.4 ? O4' ADP 701 C 1 
HETATM 13 C C3' ADP . . . N 3 159.534 108.099 132.777 1 57.4 ? C3' ADP 701 C 1 
HETATM 14 O O3' ADP . . . N 3 159.426 109.008 131.688 1 57.4 ? O3' ADP 701 C 1 
HETATM 15 C C2' ADP . . . N 3 160.596 107.027 132.532 1 57.4 ? C2' ADP 701 C 1 
HETATM 16 O O2' ADP . . . N 3 161.697 107.53 131.802 1 57.4 ? O2' ADP 701 C 1 
HETATM 17 C C1' ADP . . . N 3 160.952 106.645 133.969 1 57.4 ? C1' ADP 701 C 1 
HETATM 18 N N9 ADP . . . N 3 160.026 105.722 134.609 1 57.4 ? N9 ADP 701 C 1 
HETATM 19 C C8 ADP . . . N 3 159.071 106.04 135.536 1 57.4 ? C8 ADP 701 C 1 
HETATM 20 N N7 ADP . . . N 3 158.369 105.015 135.955 1 57.4 ? N7 ADP 701 C 1 
HETATM 21 C C5 ADP . . . N 3 158.9 103.945 135.252 1 57.4 ? C5 ADP 701 C 1 
HETATM 22 C C6 ADP . . . N 3 158.593 102.574 135.243 1 57.4 ? C6 ADP 701 C 1 
HETATM 23 N N6 ADP . . . N 3 157.632 102.023 135.993 1 57.4 ? N6 ADP 701 C 1 
HETATM 24 N N1 ADP . . . N 3 159.315 101.772 134.424 1 57.4 ? N1 ADP 701 C 1 
HETATM 25 C C2 ADP . . . N 3 160.279 102.322 133.672 1 57.4 ? C2 ADP 701 C 1 
HETATM 26 N N3 ADP . . . N 3 160.656 103.602 133.598 1 57.4 ? N3 ADP 701 C 1 
HETATM 27 C C4 ADP . . . N 3 159.925 104.367 134.417 1 57.4 ? C4 ADP 701 C 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           386 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#