data_2Y8Q
#
_model_server_result.job_id            aYVVsBPgLqT-Mss5a7VZJA 
_model_server_result.datetime_utc      '2024-12-23 12:27:13' 
_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 
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_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1328}' 
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_entry.id    2Y8Q 
#
_exptl.entry_id    2Y8Q 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              347.221 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'ADENOSINE MONOPHOSPHATE' 
_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 
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_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 
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_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                      5 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C10 H14 N5 O7 P' 
_chem_comp.formula_weight    347.221 
_chem_comp.id                AMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'ADENOSINE MONOPHOSPHATE' 
_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
P O1P AMP doub 57 n n 
P O2P AMP sing 58 n n 
P O3P AMP sing 59 n n 
P O5' AMP sing 60 n n 
O2P HOP2 AMP sing 61 n n 
O3P HOP3 AMP sing 62 n n 
O5' C5' AMP sing 63 n n 
C5' C4' AMP sing 64 n n 
C5' "H5'1" AMP sing 65 n n 
C5' "H5'2" AMP sing 66 n n 
C4' O4' AMP sing 67 n n 
C4' C3' AMP sing 68 n n 
C4' H4' AMP sing 69 n n 
O4' C1' AMP sing 70 n n 
C3' O3' AMP sing 71 n n 
C3' C2' AMP sing 72 n n 
C3' H3' AMP sing 73 n n 
O3' HO3' AMP sing 74 n n 
C2' O2' AMP sing 75 n n 
C2' C1' AMP sing 76 n n 
C2' H2' AMP sing 77 n n 
O2' HO2' AMP sing 78 n n 
C1' N9 AMP sing 79 n n 
C1' H1' AMP sing 80 n n 
N9 C8 AMP sing 81 n y 
N9 C4 AMP sing 82 n y 
C8 N7 AMP doub 83 n y 
C8 H8 AMP sing 84 n n 
N7 C5 AMP sing 85 n y 
C5 C6 AMP sing 86 n y 
C5 C4 AMP doub 87 n y 
C6 N6 AMP sing 88 n n 
C6 N1 AMP doub 89 n y 
N6 HN61 AMP sing 90 n n 
N6 HN62 AMP sing 91 n n 
N1 C2 AMP sing 92 n y 
C2 N3 AMP doub 93 n y 
C2 H2 AMP sing 94 n n 
N3 C4 AMP sing 95 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 P AMP . . . E 5 24.922 72.947 18.933 1 45.43 ? P AMP 1328 E 1 
HETATM 2 O O1P AMP . . . E 5 26.091 72.123 19.441 1 46.63 ? O1P AMP 1328 E 1 
HETATM 3 O O2P AMP . . . E 5 23.858 73.25 19.959 1 46.41 ? O2P AMP 1328 E 1 
HETATM 4 O O3P AMP . . . E 5 24.385 72.447 17.628 1 45.52 ? O3P AMP 1328 E 1 
HETATM 5 O O5' AMP . . . E 5 25.511 74.396 18.55 1 43.63 ? O5' AMP 1328 E 1 
HETATM 6 C C5' AMP . . . E 5 25.54 75.514 19.431 1 41.46 ? C5' AMP 1328 E 1 
HETATM 7 C C4' AMP . . . E 5 25.778 76.765 18.58 1 42.12 ? C4' AMP 1328 E 1 
HETATM 8 O O4' AMP . . . E 5 26.872 76.585 17.659 1 41.68 ? O4' AMP 1328 E 1 
HETATM 9 C C3' AMP . . . E 5 24.567 77.105 17.718 1 41.21 ? C3' AMP 1328 E 1 
HETATM 10 O O3' AMP . . . E 5 24.41 78.529 17.689 1 41.85 ? O3' AMP 1328 E 1 
HETATM 11 C C2' AMP . . . E 5 24.913 76.59 16.334 1 39.13 ? C2' AMP 1328 E 1 
HETATM 12 O O2' AMP . . . E 5 24.342 77.378 15.294 1 38.18 ? O2' AMP 1328 E 1 
HETATM 13 C C1' AMP . . . E 5 26.429 76.639 16.299 1 39.36 ? C1' AMP 1328 E 1 
HETATM 14 N N9 AMP . . . E 5 26.975 75.493 15.525 1 38.98 ? N9 AMP 1328 E 1 
HETATM 15 C C8 AMP . . . E 5 26.535 74.218 15.506 1 38.24 ? C8 AMP 1328 E 1 
HETATM 16 N N7 AMP . . . E 5 27.274 73.459 14.648 1 37.98 ? N7 AMP 1328 E 1 
HETATM 17 C C5 AMP . . . E 5 28.211 74.252 14.108 1 37.41 ? C5 AMP 1328 E 1 
HETATM 18 C C6 AMP . . . E 5 29.322 74.109 13.145 1 37.68 ? C6 AMP 1328 E 1 
HETATM 19 N N6 AMP . . . E 5 29.622 72.933 12.55 1 37.64 ? N6 AMP 1328 E 1 
HETATM 20 N N1 AMP . . . E 5 30.056 75.21 12.872 1 39.75 ? N1 AMP 1328 E 1 
HETATM 21 C C2 AMP . . . E 5 29.81 76.417 13.421 1 39.71 ? C2 AMP 1328 E 1 
HETATM 22 N N3 AMP . . . E 5 28.819 76.612 14.304 1 39.77 ? N3 AMP 1328 E 1 
HETATM 23 C C4 AMP . . . E 5 28.007 75.59 14.684 1 38.93 ? C4 AMP 1328 E 1 
#
_model_server_stats.io_time_ms              67 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           370 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           23 
#