data_1PYG
#
_model_server_result.job_id            8S8sFzmHB2rpUXREANi-2A 
_model_server_result.datetime_utc      '2025-02-05 12:03:54' 
_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          1pyg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":843}' 
#
_entry.id    1PYG 
#
_exptl.entry_id    1PYG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              347.221 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'ADENOSINE MONOPHOSPHATE' 
_entity.pdbx_number_of_molecules    4 
_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            1PYG 
_cell.length_a            169.9 
_cell.length_b            209.9 
_cell.length_c            123.4 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1PYG 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        PQS 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 E N N 
? 2 G N N 
? 2 I N N 
? 2 K 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
covale ? covale1 A NZ LYS 680 A LYS 680 1_555 F C4A PDP . A PDP 860 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.594 ? 
covale ? covale2 A NZ LYS 680 A LYS 680 1_555 F C4A PDP . A PDP 860 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.439 ? 
covale ? covale3 B NZ LYS 680 B LYS 680 1_555 H C4A PDP . B PDP 860 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.458 ? 
covale ? covale4 B NZ LYS 680 B LYS 680 1_555 H C4A PDP . B PDP 860 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.449 ? 
covale ? covale5 C NZ LYS 680 C LYS 680 1_555 J C4A PDP . C PDP 860 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.428 ? 
covale ? covale6 C NZ LYS 680 C LYS 680 1_555 J C4A PDP . C PDP 860 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.563 ? 
covale ? covale7 D NZ LYS 680 D LYS 680 1_555 L C4A PDP . D PDP 860 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.347 ? 
covale ? covale8 D NZ LYS 680 D LYS 680 1_555 L C4A PDP . D PDP 860 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.445 ? 
#
_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 13 n n 
P O2P AMP sing 14 n n 
P O3P AMP sing 15 n n 
P O5' AMP sing 16 n n 
O2P HOP2 AMP sing 17 n n 
O3P HOP3 AMP sing 18 n n 
O5' C5' AMP sing 19 n n 
C5' C4' AMP sing 20 n n 
C5' "H5'1" AMP sing 21 n n 
C5' "H5'2" AMP sing 22 n n 
C4' O4' AMP sing 23 n n 
C4' C3' AMP sing 24 n n 
C4' H4' AMP sing 25 n n 
O4' C1' AMP sing 26 n n 
C3' O3' AMP sing 27 n n 
C3' C2' AMP sing 28 n n 
C3' H3' AMP sing 29 n n 
O3' HO3' AMP sing 30 n n 
C2' O2' AMP sing 31 n n 
C2' C1' AMP sing 32 n n 
C2' H2' AMP sing 33 n n 
O2' HO2' AMP sing 34 n n 
C1' N9 AMP sing 35 n n 
C1' H1' AMP sing 36 n n 
N9 C8 AMP sing 37 n y 
N9 C4 AMP sing 38 n y 
C8 N7 AMP doub 39 n y 
C8 H8 AMP sing 40 n n 
N7 C5 AMP sing 41 n y 
C5 C6 AMP sing 42 n y 
C5 C4 AMP doub 43 n y 
C6 N6 AMP sing 44 n n 
C6 N1 AMP doub 45 n y 
N6 HN61 AMP sing 46 n n 
N6 HN62 AMP sing 47 n n 
N1 C2 AMP sing 48 n y 
C2 N3 AMP doub 49 n y 
C2 H2 AMP sing 50 n n 
N3 C4 AMP sing 51 n y 
#
_atom_sites.entry_id                     1PYG 
_atom_sites.fract_transf_matrix[1][1]    0.005886 
_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]    0.004764 
_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]    0.008104 
_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
E 2 AMP A 1 843 841 AMP AMP . 
F 3 PDP A 1 860 860 PDP PDP . 
G 2 AMP B 1 843 841 AMP AMP . 
H 3 PDP B 1 860 860 PDP PDP . 
I 2 AMP C 1 843 841 AMP AMP . 
J 3 PDP C 1 860 860 PDP PDP . 
K 2 AMP D 1 843 841 AMP AMP . 
L 3 PDP D 1 860 860 PDP PDP . 
#
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 . . . I 2 20.127 83.029 26.277 1 15.56 ? P AMP 843 C 1 
HETATM 2 O O1P AMP . . . I 2 19.496 82.795 24.968 1 18.49 ? O1P AMP 843 C 1 
HETATM 3 O O2P AMP . . . I 2 19.453 82.409 27.433 1 17.15 ? O2P AMP 843 C 1 
HETATM 4 O O3P AMP . . . I 2 21.592 82.846 26.338 1 17.08 ? O3P AMP 843 C 1 
HETATM 5 O O5' AMP . . . I 2 19.854 84.59 26.486 1 11.81 ? O5' AMP 843 C 1 
HETATM 6 C C5' AMP . . . I 2 20.263 85.665 25.664 1 10.18 ? C5' AMP 843 C 1 
HETATM 7 C C4' AMP . . . I 2 19.357 86.906 25.894 1 9.88 ? C4' AMP 843 C 1 
HETATM 8 O O4' AMP . . . I 2 17.992 86.575 25.55 1 9.44 ? O4' AMP 843 C 1 
HETATM 9 C C3' AMP . . . I 2 19.284 87.404 27.336 1 8.16 ? C3' AMP 843 C 1 
HETATM 10 O O3' AMP . . . I 2 20.198 88.414 27.691 1 7.8 ? O3' AMP 843 C 1 
HETATM 11 C C2' AMP . . . I 2 17.958 88.047 27.369 1 8.58 ? C2' AMP 843 C 1 
HETATM 12 O O2' AMP . . . I 2 18.023 89.353 26.831 1 11.3 ? O2' AMP 843 C 1 
HETATM 13 C C1' AMP . . . I 2 17.103 87.136 26.516 1 9.59 ? C1' AMP 843 C 1 
HETATM 14 N N9 AMP . . . I 2 16.418 86.095 27.321 1 8.86 ? N9 AMP 843 C 1 
HETATM 15 C C8 AMP . . . I 2 16.89 84.889 27.733 1 7.95 ? C8 AMP 843 C 1 
HETATM 16 N N7 AMP . . . I 2 15.963 84.072 28.124 1 10.98 ? N7 AMP 843 C 1 
HETATM 17 C C5 AMP . . . I 2 14.79 84.815 28.02 1 8.28 ? C5 AMP 843 C 1 
HETATM 18 C C6 AMP . . . I 2 13.438 84.501 28.218 1 8.53 ? C6 AMP 843 C 1 
HETATM 19 N N6 AMP . . . I 2 12.984 83.31 28.62 1 7.88 ? N6 AMP 843 C 1 
HETATM 20 N N1 AMP . . . I 2 12.566 85.465 27.945 1 10.66 ? N1 AMP 843 C 1 
HETATM 21 C C2 AMP . . . I 2 12.973 86.601 27.431 1 7.4 ? C2 AMP 843 C 1 
HETATM 22 N N3 AMP . . . I 2 14.188 87.024 27.252 1 6.74 ? N3 AMP 843 C 1 
HETATM 23 C C4 AMP . . . I 2 15.07 86.061 27.561 1 7.18 ? C4 AMP 843 C 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           265 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           23 
#