data_5YH3
#
_model_server_result.job_id            tnw_IhqFZs42LvKvWwc-EA 
_model_server_result.datetime_utc      '2025-01-30 08:41:29' 
_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          5yh3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":702}' 
#
_entry.id    5YH3 
#
_exptl.entry_id    5YH3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_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            5YH3 
_cell.length_a            78.469 
_cell.length_b            192.747 
_cell.length_c            226.669 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YH3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F 1 1 
C,D,G,H 2 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 
? 3 G N N 
? 3 H 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
disulf ? disulf1 A SG CYS 147 A CYS 209 1_555 A SG CYS 257 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 A SG CYS 149 A CYS 211 1_555 A SG CYS 261 A CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf3 A SG CYS 252 A CYS 314 1_555 A SG CYS 268 A CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf4 A SG CYS 316 A CYS 378 1_555 A SG CYS 390 A CYS 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf5 A SG CYS 391 A CYS 453 1_555 A SG CYS 450 A CYS 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf6 B SG CYS 222 C CYS 362 1_555 B SG CYS 238 C CYS 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
disulf ? disulf7 B SG CYS 227 C CYS 367 1_555 B SG CYS 231 C CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
disulf ? disulf8 B SG CYS 286 C CYS 426 1_555 B SG CYS 360 C CYS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf9 B SG CYS 361 C CYS 501 1_555 B SG CYS 420 C CYS 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf10 C SG CYS 147 B CYS 209 1_555 C SG CYS 257 B CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf11 C SG CYS 149 B CYS 211 1_555 C SG CYS 261 B CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf12 C SG CYS 252 B CYS 314 1_555 C SG CYS 268 B CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf13 C SG CYS 316 B CYS 378 1_555 C SG CYS 390 B CYS 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf14 C SG CYS 391 B CYS 453 1_555 C SG CYS 450 B CYS 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf15 D SG CYS 222 D CYS 362 1_555 D SG CYS 238 D CYS 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf16 D SG CYS 227 D CYS 367 1_555 D SG CYS 231 D CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
disulf ? disulf17 D SG CYS 286 D CYS 426 1_555 D SG CYS 360 D CYS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf18 D SG CYS 361 D CYS 501 1_555 D SG CYS 420 D CYS 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
#
_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                     5YH3 
_atom_sites.fract_transf_matrix[1][1]    0.012744 
_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]    0.005188 
_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]    0.004412 
_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 A 1 701 701 ATP ATP . 
F 3 ATP A 1 702 702 ATP ATP . 
G 3 ATP B 1 701 701 ATP ATP . 
H 3 ATP B 1 702 702 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 -27.062 42.409 -10.491 1 105.07 ? PG ATP 702 A 1 
HETATM 2 O O1G ATP . . . F 3 -27.724 42.202 -11.837 1 89.9 ? O1G ATP 702 A 1 
HETATM 3 O O2G ATP . . . F 3 -27.955 42.185 -9.289 1 77.02 ? O2G ATP 702 A 1 
HETATM 4 O O3G ATP . . . F 3 -25.721 41.728 -10.377 1 76.7 ? O3G ATP 702 A 1 
HETATM 5 P PB ATP . . . F 3 -27.764 45.17 -10.289 1 67.43 ? PB ATP 702 A 1 
HETATM 6 O O1B ATP . . . F 3 -29.03 44.574 -9.726 1 66.86 ? O1B ATP 702 A 1 
HETATM 7 O O2B ATP . . . F 3 -27.082 46.274 -9.523 1 64.61 ? O2B ATP 702 A 1 
HETATM 8 O O3B ATP . . . F 3 -26.686 43.981 -10.477 1 70.7 ? O3B ATP 702 A 1 
HETATM 9 P PA ATP . . . F 3 -28.175 47.127 -12.401 1 56.35 ? PA ATP 702 A 1 
HETATM 10 O O1A ATP . . . F 3 -27.92 47.089 -13.889 1 64.16 ? O1A ATP 702 A 1 
HETATM 11 O O2A ATP . . . F 3 -29.444 47.779 -11.925 1 52.14 ? O2A ATP 702 A 1 
HETATM 12 O O3A ATP . . . F 3 -28.014 45.622 -11.824 1 61.57 ? O3A ATP 702 A 1 
HETATM 13 O O5' ATP . . . F 3 -26.978 47.96 -11.734 1 58.48 ? O5' ATP 702 A 1 
HETATM 14 C C5' ATP . . . F 3 -27.366 48.982 -10.832 1 50.57 ? C5' ATP 702 A 1 
HETATM 15 C C4' ATP . . . F 3 -26.198 49.754 -10.246 1 44.49 ? C4' ATP 702 A 1 
HETATM 16 O O4' ATP . . . F 3 -26.395 51.132 -10.559 1 47.99 ? O4' ATP 702 A 1 
HETATM 17 C C3' ATP . . . F 3 -26.207 49.623 -8.737 1 43.44 ? C3' ATP 702 A 1 
HETATM 18 O O3' ATP . . . F 3 -24.953 49.105 -8.288 1 44.89 ? O3' ATP 702 A 1 
HETATM 19 C C2' ATP . . . F 3 -26.424 51.02 -8.2 1 47.52 ? C2' ATP 702 A 1 
HETATM 20 O O2' ATP . . . F 3 -25.202 51.473 -7.615 1 46.14 ? O2' ATP 702 A 1 
HETATM 21 C C1' ATP . . . F 3 -26.755 51.887 -9.402 1 48.39 ? C1' ATP 702 A 1 
HETATM 22 N N9 ATP . . . F 3 -28.214 52.206 -9.485 1 54.1 ? N9 ATP 702 A 1 
HETATM 23 C C8 ATP . . . F 3 -29.193 51.335 -9.802 1 53.48 ? C8 ATP 702 A 1 
HETATM 24 N N7 ATP . . . F 3 -30.418 51.911 -9.81 1 51.7 ? N7 ATP 702 A 1 
HETATM 25 C C5 ATP . . . F 3 -30.241 53.2 -9.489 1 52.54 ? C5 ATP 702 A 1 
HETATM 26 C C6 ATP . . . F 3 -31.129 54.372 -9.315 1 50.06 ? C6 ATP 702 A 1 
HETATM 27 N N6 ATP . . . F 3 -32.467 54.264 -9.491 1 49.4 ? N6 ATP 702 A 1 
HETATM 28 N N1 ATP . . . F 3 -30.555 55.547 -8.974 1 55.38 ? N1 ATP 702 A 1 
HETATM 29 C C2 ATP . . . F 3 -29.223 55.656 -8.798 1 58.82 ? C2 ATP 702 A 1 
HETATM 30 N N3 ATP . . . F 3 -28.358 54.633 -8.94 1 59.38 ? N3 ATP 702 A 1 
HETATM 31 C C4 ATP . . . F 3 -28.794 53.395 -9.277 1 56.56 ? C4 ATP 702 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           31 
#