data_2Y8Q
#
_model_server_result.job_id            czsWNko0-VBDvFUdfFMpZA 
_model_server_result.datetime_utc      '2024-11-05 14:44:42' 
_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          2y8q 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1327}' 
#
_entry.id    2Y8Q 
#
_exptl.entry_id    2Y8Q 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            2Y8Q 
_cell.length_a            49.026 
_cell.length_b            119.918 
_cell.length_c            130.15 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2Y8Q 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
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_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_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                     2Y8Q 
_atom_sites.fract_transf_matrix[1][1]    0.020397 
_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]    0.008339 
_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]    0.007683 
_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
D 4 ADP E 1 1327 1327 ADP ADP . 
E 5 AMP E 1 1328 1328 AMP AMP . 
F 6 HOH A 1 2001 2001 HOH HOH . 
F 6 HOH A 2 2002 2002 HOH HOH . 
F 6 HOH A 3 2003 2003 HOH HOH . 
F 6 HOH A 4 2004 2004 HOH HOH . 
F 6 HOH A 5 2005 2005 HOH HOH . 
F 6 HOH A 6 2006 2006 HOH HOH . 
G 6 HOH B 1 2001 2001 HOH HOH . 
G 6 HOH B 2 2002 2002 HOH HOH . 
G 6 HOH B 3 2003 2003 HOH HOH . 
G 6 HOH B 4 2004 2004 HOH HOH . 
G 6 HOH B 5 2005 2005 HOH HOH . 
G 6 HOH B 6 2006 2006 HOH HOH . 
G 6 HOH B 7 2007 2007 HOH HOH . 
G 6 HOH B 8 2008 2008 HOH HOH . 
G 6 HOH B 9 2009 2009 HOH HOH . 
G 6 HOH B 10 2010 2010 HOH HOH . 
G 6 HOH B 11 2011 2011 HOH HOH . 
H 6 HOH E 1 2001 2001 HOH HOH . 
H 6 HOH E 2 2002 2002 HOH HOH . 
H 6 HOH E 3 2003 2003 HOH HOH . 
H 6 HOH E 4 2004 2004 HOH HOH . 
H 6 HOH E 5 2005 2005 HOH HOH . 
H 6 HOH E 6 2006 2006 HOH HOH . 
H 6 HOH E 7 2007 2007 HOH HOH . 
H 6 HOH E 8 2008 2008 HOH HOH . 
H 6 HOH E 9 2009 2009 HOH HOH . 
H 6 HOH E 10 2010 2010 HOH HOH . 
H 6 HOH E 11 2011 2011 HOH HOH . 
H 6 HOH E 12 2012 2012 HOH HOH . 
H 6 HOH E 13 2013 2013 HOH HOH . 
H 6 HOH E 14 2014 2014 HOH HOH . 
H 6 HOH E 15 2015 2015 HOH HOH . 
H 6 HOH E 16 2016 2016 HOH HOH . 
H 6 HOH E 17 2017 2017 HOH HOH . 
H 6 HOH E 18 2018 2018 HOH HOH . 
H 6 HOH E 19 2019 2019 HOH HOH . 
H 6 HOH E 20 2020 2020 HOH HOH . 
H 6 HOH E 21 2021 2021 HOH HOH . 
H 6 HOH E 22 2022 2022 HOH HOH . 
H 6 HOH E 23 2023 2023 HOH HOH . 
H 6 HOH E 24 2024 2024 HOH HOH . 
H 6 HOH E 25 2025 2025 HOH HOH . 
H 6 HOH E 26 2026 2026 HOH HOH . 
H 6 HOH E 27 2027 2027 HOH HOH . 
H 6 HOH E 28 2028 2028 HOH HOH . 
H 6 HOH E 29 2029 2029 HOH HOH . 
H 6 HOH E 30 2030 2030 HOH HOH . 
H 6 HOH E 31 2031 2031 HOH HOH . 
H 6 HOH E 32 2032 2032 HOH HOH . 
H 6 HOH E 33 2033 2033 HOH HOH . 
H 6 HOH E 34 2034 2034 HOH HOH . 
H 6 HOH E 35 2035 2035 HOH HOH . 
H 6 HOH E 36 2036 2036 HOH HOH . 
H 6 HOH E 37 2037 2037 HOH HOH . 
H 6 HOH E 38 2038 2038 HOH HOH . 
H 6 HOH E 39 2039 2039 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 . . . D 4 26.993 67.287 25.489 1 48.26 ? PB ADP 1327 E 1 
HETATM 2 O O1B ADP . . . D 4 26.369 65.912 25.699 1 48.34 ? O1B ADP 1327 E 1 
HETATM 3 O O2B ADP . . . D 4 28.483 67.338 25.674 1 48.18 ? O2B ADP 1327 E 1 
HETATM 4 O O3B ADP . . . D 4 26.445 68.009 24.273 1 45.9 ? O3B ADP 1327 E 1 
HETATM 5 P PA ADP . . . D 4 27.064 69.651 27.074 1 48.34 ? PA ADP 1327 E 1 
HETATM 6 O O1A ADP . . . D 4 26.065 70.211 28.058 1 50.23 ? O1A ADP 1327 E 1 
HETATM 7 O O2A ADP . . . D 4 27.366 70.405 25.813 1 47.48 ? O2A ADP 1327 E 1 
HETATM 8 O O3A ADP . . . D 4 26.539 68.157 26.766 1 48.26 ? O3A ADP 1327 E 1 
HETATM 9 O O5' ADP . . . D 4 28.455 69.478 27.844 1 48.89 ? O5' ADP 1327 E 1 
HETATM 10 C C5' ADP . . . D 4 29.219 70.666 28.054 1 49.51 ? C5' ADP 1327 E 1 
HETATM 11 C C4' ADP . . . D 4 30.105 70.558 29.297 1 51.32 ? C4' ADP 1327 E 1 
HETATM 12 O O4' ADP . . . D 4 29.43 71.077 30.452 1 51.66 ? O4' ADP 1327 E 1 
HETATM 13 C C3' ADP . . . D 4 30.481 69.122 29.64 1 51.59 ? C3' ADP 1327 E 1 
HETATM 14 O O3' ADP . . . D 4 31.844 69.137 30.079 1 53.55 ? O3' ADP 1327 E 1 
HETATM 15 C C2' ADP . . . D 4 29.537 68.721 30.763 1 49.78 ? C2' ADP 1327 E 1 
HETATM 16 O O2' ADP . . . D 4 30.112 67.775 31.67 1 48.61 ? O2' ADP 1327 E 1 
HETATM 17 C C1' ADP . . . D 4 29.21 70.048 31.437 1 50.32 ? C1' ADP 1327 E 1 
HETATM 18 N N9 ADP . . . D 4 27.798 70.053 31.901 1 47.94 ? N9 ADP 1327 E 1 
HETATM 19 C C8 ADP . . . D 4 26.751 69.544 31.223 1 46.88 ? C8 ADP 1327 E 1 
HETATM 20 N N7 ADP . . . D 4 25.6 69.702 31.93 1 47.29 ? N7 ADP 1327 E 1 
HETATM 21 C C5 ADP . . . D 4 25.905 70.336 33.079 1 46.64 ? C5 ADP 1327 E 1 
HETATM 22 C C6 ADP . . . D 4 25.147 70.818 34.263 1 46.82 ? C6 ADP 1327 E 1 
HETATM 23 N N6 ADP . . . D 4 23.807 70.631 34.35 1 44.82 ? N6 ADP 1327 E 1 
HETATM 24 N N1 ADP . . . D 4 25.847 71.439 35.244 1 47.87 ? N1 ADP 1327 E 1 
HETATM 25 C C2 ADP . . . D 4 27.185 71.609 35.151 1 48.53 ? C2 ADP 1327 E 1 
HETATM 26 N N3 ADP . . . D 4 27.93 71.2 34.101 1 47.09 ? N3 ADP 1327 E 1 
HETATM 27 C C4 ADP . . . D 4 27.358 70.567 33.053 1 46.91 ? C4 ADP 1327 E 1 
#
_model_server_stats.io_time_ms              71 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#