data_5YZ2
#
_model_server_result.job_id            gmyFi8NKjkPjpEmeEVvgQQ 
_model_server_result.datetime_utc      '2025-03-05 19:28:54' 
_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          5yz2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":301}' 
#
_entry.id    5YZ2 
#
_exptl.entry_id    5YZ2 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          114.73 
_cell.angle_gamma         90 
_cell.entry_id            5YZ2 
_cell.length_a            53.898 
_cell.length_b            56.29 
_cell.length_c            54.349 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YZ2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 
_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 D N 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 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                     5YZ2 
_atom_sites.fract_transf_matrix[1][1]    0.018554 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.008546 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017765 
_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]    0.020258 
_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 AMP A 1 301 1 AMP AMP . 
D 2 AMP B 1 301 2 AMP AMP . 
E 3 HOH A 1 401 61 HOH HOH . 
E 3 HOH A 2 402 104 HOH HOH . 
E 3 HOH A 3 403 128 HOH HOH . 
E 3 HOH A 4 404 56 HOH HOH . 
E 3 HOH A 5 405 119 HOH HOH . 
E 3 HOH A 6 406 137 HOH HOH . 
E 3 HOH A 7 407 50 HOH HOH . 
E 3 HOH A 8 408 106 HOH HOH . 
E 3 HOH A 9 409 93 HOH HOH . 
E 3 HOH A 10 410 64 HOH HOH . 
E 3 HOH A 11 411 51 HOH HOH . 
E 3 HOH A 12 412 55 HOH HOH . 
E 3 HOH A 13 413 4 HOH HOH . 
E 3 HOH A 14 414 29 HOH HOH . 
E 3 HOH A 15 415 120 HOH HOH . 
E 3 HOH A 16 416 74 HOH HOH . 
E 3 HOH A 17 417 69 HOH HOH . 
E 3 HOH A 18 418 25 HOH HOH . 
E 3 HOH A 19 419 7 HOH HOH . 
E 3 HOH A 20 420 18 HOH HOH . 
E 3 HOH A 21 421 57 HOH HOH . 
E 3 HOH A 22 422 73 HOH HOH . 
E 3 HOH A 23 423 94 HOH HOH . 
E 3 HOH A 24 424 72 HOH HOH . 
E 3 HOH A 25 425 9 HOH HOH . 
E 3 HOH A 26 426 85 HOH HOH . 
E 3 HOH A 27 427 129 HOH HOH . 
E 3 HOH A 28 428 24 HOH HOH . 
E 3 HOH A 29 429 16 HOH HOH . 
E 3 HOH A 30 430 22 HOH HOH . 
E 3 HOH A 31 431 32 HOH HOH . 
E 3 HOH A 32 432 20 HOH HOH . 
E 3 HOH A 33 433 148 HOH HOH . 
E 3 HOH A 34 434 37 HOH HOH . 
E 3 HOH A 35 435 46 HOH HOH . 
E 3 HOH A 36 436 8 HOH HOH . 
E 3 HOH A 37 437 98 HOH HOH . 
E 3 HOH A 38 438 122 HOH HOH . 
E 3 HOH A 39 439 97 HOH HOH . 
E 3 HOH A 40 440 124 HOH HOH . 
E 3 HOH A 41 441 144 HOH HOH . 
E 3 HOH A 42 442 11 HOH HOH . 
E 3 HOH A 43 443 65 HOH HOH . 
E 3 HOH A 44 444 95 HOH HOH . 
E 3 HOH A 45 445 27 HOH HOH . 
E 3 HOH A 46 446 138 HOH HOH . 
E 3 HOH A 47 447 155 HOH HOH . 
E 3 HOH A 48 448 71 HOH HOH . 
E 3 HOH A 49 449 83 HOH HOH . 
E 3 HOH A 50 450 84 HOH HOH . 
E 3 HOH A 51 451 47 HOH HOH . 
E 3 HOH A 52 452 145 HOH HOH . 
E 3 HOH A 53 453 40 HOH HOH . 
E 3 HOH A 54 454 141 HOH HOH . 
E 3 HOH A 55 455 15 HOH HOH . 
E 3 HOH A 56 456 126 HOH HOH . 
E 3 HOH A 57 457 139 HOH HOH . 
E 3 HOH A 58 458 123 HOH HOH . 
E 3 HOH A 59 459 44 HOH HOH . 
E 3 HOH A 60 460 118 HOH HOH . 
E 3 HOH A 61 461 89 HOH HOH . 
E 3 HOH A 62 462 140 HOH HOH . 
E 3 HOH A 63 463 2 HOH HOH . 
E 3 HOH A 64 464 36 HOH HOH . 
E 3 HOH A 65 465 127 HOH HOH . 
E 3 HOH A 66 466 38 HOH HOH . 
E 3 HOH A 67 467 78 HOH HOH . 
E 3 HOH A 68 468 136 HOH HOH . 
E 3 HOH A 69 469 63 HOH HOH . 
E 3 HOH A 70 470 66 HOH HOH . 
E 3 HOH A 71 471 45 HOH HOH . 
E 3 HOH A 72 472 153 HOH HOH . 
E 3 HOH A 73 473 111 HOH HOH . 
E 3 HOH A 74 474 117 HOH HOH . 
E 3 HOH A 75 475 88 HOH HOH . 
E 3 HOH A 76 476 52 HOH HOH . 
E 3 HOH A 77 477 114 HOH HOH . 
F 3 HOH B 1 401 99 HOH HOH . 
F 3 HOH B 2 402 107 HOH HOH . 
F 3 HOH B 3 403 49 HOH HOH . 
F 3 HOH B 4 404 115 HOH HOH . 
F 3 HOH B 5 405 26 HOH HOH . 
F 3 HOH B 6 406 125 HOH HOH . 
F 3 HOH B 7 407 60 HOH HOH . 
F 3 HOH B 8 408 62 HOH HOH . 
F 3 HOH B 9 409 5 HOH HOH . 
F 3 HOH B 10 410 142 HOH HOH . 
F 3 HOH B 11 411 3 HOH HOH . 
F 3 HOH B 12 412 12 HOH HOH . 
F 3 HOH B 13 413 103 HOH HOH . 
F 3 HOH B 14 414 76 HOH HOH . 
F 3 HOH B 15 415 80 HOH HOH . 
F 3 HOH B 16 416 143 HOH HOH . 
F 3 HOH B 17 417 48 HOH HOH . 
F 3 HOH B 18 418 135 HOH HOH . 
F 3 HOH B 19 419 30 HOH HOH . 
F 3 HOH B 20 420 70 HOH HOH . 
F 3 HOH B 21 421 134 HOH HOH . 
F 3 HOH B 22 422 39 HOH HOH . 
F 3 HOH B 23 423 146 HOH HOH . 
F 3 HOH B 24 424 67 HOH HOH . 
F 3 HOH B 25 425 10 HOH HOH . 
F 3 HOH B 26 426 14 HOH HOH . 
F 3 HOH B 27 427 112 HOH HOH . 
F 3 HOH B 28 428 131 HOH HOH . 
F 3 HOH B 29 429 43 HOH HOH . 
F 3 HOH B 30 430 17 HOH HOH . 
F 3 HOH B 31 431 28 HOH HOH . 
F 3 HOH B 32 432 86 HOH HOH . 
F 3 HOH B 33 433 101 HOH HOH . 
F 3 HOH B 34 434 33 HOH HOH . 
F 3 HOH B 35 435 6 HOH HOH . 
F 3 HOH B 36 436 54 HOH HOH . 
F 3 HOH B 37 437 77 HOH HOH . 
F 3 HOH B 38 438 23 HOH HOH . 
F 3 HOH B 39 439 58 HOH HOH . 
F 3 HOH B 40 440 154 HOH HOH . 
F 3 HOH B 41 441 100 HOH HOH . 
F 3 HOH B 42 442 79 HOH HOH . 
F 3 HOH B 43 443 91 HOH HOH . 
F 3 HOH B 44 444 31 HOH HOH . 
F 3 HOH B 45 445 96 HOH HOH . 
F 3 HOH B 46 446 92 HOH HOH . 
F 3 HOH B 47 447 90 HOH HOH . 
F 3 HOH B 48 448 59 HOH HOH . 
F 3 HOH B 49 449 105 HOH HOH . 
F 3 HOH B 50 450 150 HOH HOH . 
F 3 HOH B 51 451 34 HOH HOH . 
F 3 HOH B 52 452 133 HOH HOH . 
F 3 HOH B 53 453 82 HOH HOH . 
F 3 HOH B 54 454 19 HOH HOH . 
F 3 HOH B 55 455 53 HOH HOH . 
F 3 HOH B 56 456 42 HOH HOH . 
F 3 HOH B 57 457 21 HOH HOH . 
F 3 HOH B 58 458 13 HOH HOH . 
F 3 HOH B 59 459 1 HOH HOH . 
F 3 HOH B 60 460 109 HOH HOH . 
F 3 HOH B 61 461 149 HOH HOH . 
F 3 HOH B 62 462 151 HOH HOH . 
F 3 HOH B 63 463 116 HOH HOH . 
F 3 HOH B 64 464 132 HOH HOH . 
F 3 HOH B 65 465 121 HOH HOH . 
F 3 HOH B 66 466 152 HOH HOH . 
F 3 HOH B 67 467 130 HOH HOH . 
F 3 HOH B 68 468 113 HOH HOH . 
F 3 HOH B 69 469 87 HOH HOH . 
F 3 HOH B 70 470 110 HOH HOH . 
F 3 HOH B 71 471 35 HOH HOH . 
F 3 HOH B 72 472 147 HOH HOH . 
F 3 HOH B 73 473 75 HOH HOH . 
F 3 HOH B 74 474 81 HOH HOH . 
F 3 HOH B 75 475 102 HOH HOH . 
F 3 HOH B 76 476 108 HOH HOH . 
F 3 HOH B 77 477 68 HOH HOH . 
F 3 HOH B 78 478 41 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 . . . D 2 10.91 13.98 18.413 1 39.33 ? P AMP 301 B 1 
HETATM 2 O O1P AMP . . . D 2 11.774 14.061 17.177 1 34.63 ? O1P AMP 301 B 1 
HETATM 3 O O2P AMP . . . D 2 10.287 15.293 18.83 1 40.14 ? O2P AMP 301 B 1 
HETATM 4 O O3P AMP . . . D 2 9.95 12.817 18.451 1 41.41 ? O3P AMP 301 B 1 
HETATM 5 O O5' AMP . . . D 2 11.96 13.674 19.565 1 40.13 ? O5' AMP 301 B 1 
HETATM 6 C C5' AMP . . . D 2 12.803 14.693 20.078 1 36.96 ? C5' AMP 301 B 1 
HETATM 7 C C4' AMP . . . D 2 12.827 14.672 21.581 1 38.27 ? C4' AMP 301 B 1 
HETATM 8 O O4' AMP . . . D 2 11.588 15.214 22.101 1 34.03 ? O4' AMP 301 B 1 
HETATM 9 C C3' AMP . . . D 2 12.94 13.294 22.213 1 39.36 ? C3' AMP 301 B 1 
HETATM 10 O O3' AMP . . . D 2 14.282 12.856 22.265 1 51.02 ? O3' AMP 301 B 1 
HETATM 11 C C2' AMP . . . D 2 12.301 13.492 23.577 1 33.22 ? C2' AMP 301 B 1 
HETATM 12 O O2' AMP . . . D 2 13.216 14.077 24.482 1 39.74 ? O2' AMP 301 B 1 
HETATM 13 C C1' AMP . . . D 2 11.205 14.511 23.259 1 32.23 ? C1' AMP 301 B 1 
HETATM 14 N N9 AMP . . . D 2 9.91 13.87 22.992 1 31.33 ? N9 AMP 301 B 1 
HETATM 15 C C8 AMP . . . D 2 9.59 13.019 21.991 1 28.68 ? C8 AMP 301 B 1 
HETATM 16 N N7 AMP . . . D 2 8.29 12.655 22.087 1 25.45 ? N7 AMP 301 B 1 
HETATM 17 C C5 AMP . . . D 2 7.789 13.293 23.16 1 25.38 ? C5 AMP 301 B 1 
HETATM 18 C C6 AMP . . . D 2 6.487 13.361 23.833 1 27.73 ? C6 AMP 301 B 1 
HETATM 19 N N6 AMP . . . D 2 5.49 12.637 23.312 1 26.84 ? N6 AMP 301 B 1 
HETATM 20 N N1 AMP . . . D 2 6.366 14.143 24.933 1 24.99 ? N1 AMP 301 B 1 
HETATM 21 C C2 AMP . . . D 2 7.398 14.854 25.42 1 26.54 ? C2 AMP 301 B 1 
HETATM 22 N N3 AMP . . . D 2 8.617 14.838 24.855 1 28.34 ? N3 AMP 301 B 1 
HETATM 23 C C4 AMP . . . D 2 8.852 14.088 23.753 1 28.67 ? C4 AMP 301 B 1 
HETATM 24 H "H5'1" AMP . . . D 2 12.447 15.667 19.734 1 44.21 ? "H5'1" AMP 301 B 1 
HETATM 25 H "H5'2" AMP . . . D 2 13.816 14.553 19.696 1 44.21 ? "H5'2" AMP 301 B 1 
HETATM 26 H H4' AMP . . . D 2 13.672 15.285 21.926 1 45.79 ? H4' AMP 301 B 1 
HETATM 27 H H3' AMP . . . D 2 12.332 12.585 21.634 1 47.09 ? H3' AMP 301 B 1 
HETATM 28 H HO3' AMP . . . D 2 14.319 11.979 22.671 1 61.09 ? HO3' AMP 301 B 1 
HETATM 29 H H2' AMP . . . D 2 11.872 12.554 23.956 1 39.73 ? H2' AMP 301 B 1 
HETATM 30 H HO2' AMP . . . D 2 13.975 13.49 24.597 1 47.55 ? HO2' AMP 301 B 1 
HETATM 31 H H1' AMP . . . D 2 11.112 15.206 24.105 1 38.54 ? H1' AMP 301 B 1 
HETATM 32 H H8 AMP . . . D 2 10.275 12.675 21.227 1 34.29 ? H8 AMP 301 B 1 
HETATM 33 H HN61 AMP . . . D 2 4.576 12.654 23.742 1 32.07 ? HN61 AMP 301 B 1 
HETATM 34 H HN62 AMP . . . D 2 5.65 12.074 22.489 1 32.07 ? HN62 AMP 301 B 1 
HETATM 35 H H2 AMP . . . D 2 7.24 15.461 26.303 1 31.71 ? H2 AMP 301 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           35 
#