data_4YMV
#
_model_server_result.job_id            3WtMFN2gDUI7HLV9xbR1mg 
_model_server_result.datetime_utc      '2025-03-30 10:53:59' 
_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          4ymv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":301}' 
#
_entry.id    4YMV 
#
_exptl.entry_id    4YMV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            4YMV 
_cell.length_a            96.527 
_cell.length_b            115.257 
_cell.length_c            301.546 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YMV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_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 
_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
? 3 E N N 
? 3 F N N 
#
_chem_comp.formula           'C10 H16 N5 O13 P3' 
_chem_comp.formula_weight    507.181 
_chem_comp.id                ATP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "ADENOSINE-5'-TRIPHOSPHATE" 
_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
PG O1G ATP doub 70 n n 
PG O2G ATP sing 71 n n 
PG O3G ATP sing 72 n n 
PG O3B ATP sing 73 n n 
O2G HOG2 ATP sing 74 n n 
O3G HOG3 ATP sing 75 n n 
PB O1B ATP doub 76 n n 
PB O2B ATP sing 77 n n 
PB O3B ATP sing 78 n n 
PB O3A ATP sing 79 n n 
O2B HOB2 ATP sing 80 n n 
PA O1A ATP doub 81 n n 
PA O2A ATP sing 82 n n 
PA O3A ATP sing 83 n n 
PA O5' ATP sing 84 n n 
O2A HOA2 ATP sing 85 n n 
O5' C5' ATP sing 86 n n 
C5' C4' ATP sing 87 n n 
C5' "H5'1" ATP sing 88 n n 
C5' "H5'2" ATP sing 89 n n 
C4' O4' ATP sing 90 n n 
C4' C3' ATP sing 91 n n 
C4' H4' ATP sing 92 n n 
O4' C1' ATP sing 93 n n 
C3' O3' ATP sing 94 n n 
C3' C2' ATP sing 95 n n 
C3' H3' ATP sing 96 n n 
O3' HO3' ATP sing 97 n n 
C2' O2' ATP sing 98 n n 
C2' C1' ATP sing 99 n n 
C2' H2' ATP sing 100 n n 
O2' HO2' ATP sing 101 n n 
C1' N9 ATP sing 102 n n 
C1' H1' ATP sing 103 n n 
N9 C8 ATP sing 104 n y 
N9 C4 ATP sing 105 n y 
C8 N7 ATP doub 106 n y 
C8 H8 ATP sing 107 n n 
N7 C5 ATP sing 108 n y 
C5 C6 ATP sing 109 n y 
C5 C4 ATP doub 110 n y 
C6 N6 ATP sing 111 n n 
C6 N1 ATP doub 112 n y 
N6 HN61 ATP sing 113 n n 
N6 HN62 ATP sing 114 n n 
N1 C2 ATP sing 115 n y 
C2 N3 ATP doub 116 n y 
C2 H2 ATP sing 117 n n 
N3 C4 ATP sing 118 n y 
#
_atom_sites.entry_id                     4YMV 
_atom_sites.fract_transf_matrix[1][1]    0.01036 
_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]    0.008676 
_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]    0.003316 
_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 3 ATP J 1 301 1 ATP ATP . 
F 3 ATP A 1 301 2 ATP ATP . 
#
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 PG ATP . . . F 3 -7.784 13.172 20.272 1 148.56 ? PG ATP 301 A 1 
HETATM 2 O O1G ATP . . . F 3 -7.835 13.383 18.76 1 144.07 ? O1G ATP 301 A 1 
HETATM 3 O O2G ATP . . . F 3 -9.158 12.816 20.826 1 148.22 ? O2G ATP 301 A 1 
HETATM 4 O O3G ATP . . . F 3 -7.008 14.153 21.143 1 148.33 ? O3G ATP 301 A 1 
HETATM 5 P PB ATP . . . F 3 -7.237 10.413 20.318 1 119.74 ? PB ATP 301 A 1 
HETATM 6 O O1B ATP . . . F 3 -8.754 10.328 20.236 1 124.55 ? O1B ATP 301 A 1 
HETATM 7 O O2B ATP . . . F 3 -6.39 9.85 19.201 1 110.48 ? O2B ATP 301 A 1 
HETATM 8 O O3B ATP . . . F 3 -6.777 11.932 20.523 1 95.19 ? O3B ATP 301 A 1 
HETATM 9 P PA ATP . . . F 3 -7.401 10.375 23.138 1 111.02 ? PA ATP 301 A 1 
HETATM 10 O O1A ATP . . . F 3 -7.843 11.821 23.095 1 109.92 ? O1A ATP 301 A 1 
HETATM 11 O O2A ATP . . . F 3 -6.405 9.929 24.181 1 116.15 ? O2A ATP 301 A 1 
HETATM 12 O O3A ATP . . . F 3 -6.791 9.819 21.748 1 131.24 ? O3A ATP 301 A 1 
HETATM 13 O O5' ATP . . . F 3 -8.746 9.528 23.285 1 123.78 ? O5' ATP 301 A 1 
HETATM 14 C C5' ATP . . . F 3 -8.705 8.119 23.457 1 122.81 ? C5' ATP 301 A 1 
HETATM 15 C C4' ATP . . . F 3 -9.838 7.7 24.382 1 118.1 ? C4' ATP 301 A 1 
HETATM 16 O O4' ATP . . . F 3 -9.531 8.098 25.721 1 112.48 ? O4' ATP 301 A 1 
HETATM 17 C C3' ATP . . . F 3 -11.166 8.339 23.99 1 116.5 ? C3' ATP 301 A 1 
HETATM 18 O O3' ATP . . . F 3 -12.137 7.298 23.811 1 114.3 ? O3' ATP 301 A 1 
HETATM 19 C C2' ATP . . . F 3 -11.472 9.296 25.133 1 115.06 ? C2' ATP 301 A 1 
HETATM 20 O O2' ATP . . . F 3 -12.862 9.412 25.443 1 116.43 ? O2' ATP 301 A 1 
HETATM 21 C C1' ATP . . . F 3 -10.695 8.691 26.288 1 116.99 ? C1' ATP 301 A 1 
HETATM 22 N N9 ATP . . . F 3 -10.268 9.672 27.298 1 124.13 ? N9 ATP 301 A 1 
HETATM 23 C C8 ATP . . . F 3 -9.652 10.847 27.069 1 129.49 ? C8 ATP 301 A 1 
HETATM 24 N N7 ATP . . . F 3 -9.397 11.481 28.247 1 131.17 ? N7 ATP 301 A 1 
HETATM 25 C C5 ATP . . . F 3 -9.852 10.696 29.236 1 129.46 ? C5 ATP 301 A 1 
HETATM 26 C C6 ATP . . . F 3 -9.905 10.772 30.704 1 130.8 ? C6 ATP 301 A 1 
HETATM 27 N N6 ATP . . . F 3 -9.393 11.852 31.336 1 132.89 ? N6 ATP 301 A 1 
HETATM 28 N N1 ATP . . . F 3 -10.478 9.742 31.368 1 129.36 ? N1 ATP 301 A 1 
HETATM 29 C C2 ATP . . . F 3 -10.994 8.676 30.726 1 128.37 ? C2 ATP 301 A 1 
HETATM 30 N N3 ATP . . . F 3 -10.969 8.538 29.386 1 127.87 ? N3 ATP 301 A 1 
HETATM 31 C C4 ATP . . . F 3 -10.428 9.502 28.606 1 127.27 ? C4 ATP 301 A 1 
HETATM 32 H "H5'1" ATP . . . F 3 -7.746 7.825 23.888 1 147.87 ? "H5'1" ATP 301 A 1 
HETATM 33 H "H5'2" ATP . . . F 3 -8.813 7.624 22.49 1 147.87 ? "H5'2" ATP 301 A 1 
HETATM 34 H H4' ATP . . . F 3 -9.946 6.607 24.334 1 137.36 ? H4' ATP 301 A 1 
HETATM 35 H H3' ATP . . . F 3 -11.035 8.91 23.06 1 134.04 ? H3' ATP 301 A 1 
HETATM 36 H HO3' ATP . . . F 3 -12.986 7.688 23.562 1 128.58 ? HO3' ATP 301 A 1 
HETATM 37 H H2' ATP . . . F 3 -11.051 10.283 24.896 1 131.54 ? H2' ATP 301 A 1 
HETATM 38 H HO2' ATP . . . F 3 -13.336 9.757 24.674 1 134.31 ? HO2' ATP 301 A 1 
HETATM 39 H H1' ATP . . . F 3 -11.314 7.916 26.761 1 135.42 ? H1' ATP 301 A 1 
HETATM 40 H H8 ATP . . . F 3 -9.39 11.229 26.09 1 163.55 ? H8 ATP 301 A 1 
HETATM 41 H HN61 ATP . . . F 3 -9.427 11.911 32.344 1 170.91 ? HN61 ATP 301 A 1 
HETATM 42 H HN62 ATP . . . F 3 -8.978 12.601 30.8 1 170.91 ? HN62 ATP 301 A 1 
HETATM 43 H H2 ATP . . . F 3 -11.429 7.88 31.317 1 159.43 ? H2 ATP 301 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           29 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#