data_1KMN
#
_model_server_result.job_id            aMMnjqIf5XWIzb-w51Ghag 
_model_server_result.datetime_utc      '2025-03-21 11:18:17' 
_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          1kmn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":452}' 
#
_entry.id    1KMN 
#
_exptl.entry_id    1KMN 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         114.1 
_cell.angle_beta          97.4 
_cell.angle_gamma         90 
_cell.entry_id            1KMN 
_cell.length_a            60.9 
_cell.length_b            107.3 
_cell.length_c            107.2 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1KMN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1' 
#
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,G,H,M,N 1 1 
C,D,I,J,K,L,O,P 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 F N N 
? 3 H N N 
? 3 J N N 
? 3 L 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                     1KMN 
_atom_sites.fract_transf_matrix[1][1]    0.01642 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00234 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00932 
_atom_sites.fract_transf_matrix[2][3]    0.004211 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.010322 
_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 HSO A 1 451 451 HSO HSO . 
F 3 ATP A 1 452 452 ATP ATP . 
G 2 HSO B 1 451 451 HSO HSO . 
H 3 ATP B 1 452 452 ATP ATP . 
I 2 HSO C 1 451 451 HSO HSO . 
J 3 ATP C 1 452 452 ATP ATP . 
K 2 HSO D 1 451 451 HSO HSO . 
L 3 ATP D 1 452 452 ATP ATP . 
M 4 HOH A 1 508 508 HOH HOH . 
M 4 HOH A 2 511 511 HOH HOH . 
M 4 HOH A 3 513 513 HOH HOH . 
M 4 HOH A 4 514 514 HOH HOH . 
M 4 HOH A 5 515 515 HOH HOH . 
M 4 HOH A 6 516 516 HOH HOH . 
M 4 HOH A 7 517 517 HOH HOH . 
M 4 HOH A 8 518 518 HOH HOH . 
M 4 HOH A 9 519 519 HOH HOH . 
M 4 HOH A 10 520 520 HOH HOH . 
M 4 HOH A 11 521 521 HOH HOH . 
M 4 HOH A 12 523 523 HOH HOH . 
M 4 HOH A 13 524 524 HOH HOH . 
N 4 HOH B 1 504 504 HOH HOH . 
N 4 HOH B 2 506 506 HOH HOH . 
N 4 HOH B 3 507 507 HOH HOH . 
N 4 HOH B 4 512 512 HOH HOH . 
N 4 HOH B 5 522 522 HOH HOH . 
O 4 HOH C 1 501 501 HOH HOH . 
O 4 HOH C 2 502 502 HOH HOH . 
O 4 HOH C 3 509 509 HOH HOH . 
O 4 HOH C 4 510 510 HOH HOH . 
P 4 HOH D 1 503 503 HOH HOH . 
P 4 HOH D 2 505 505 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 PG ATP . . . H 3 -16.846 -13.922 10.989 1 78.63 ? PG ATP 452 B 1 
HETATM 2 O O1G ATP . . . H 3 -16.67 -14.125 9.494 1 79.81 ? O1G ATP 452 B 1 
HETATM 3 O O2G ATP . . . H 3 -17.407 -12.543 11.324 1 78.17 ? O2G ATP 452 B 1 
HETATM 4 O O3G ATP . . . H 3 -17.727 -15.035 11.555 1 77.98 ? O3G ATP 452 B 1 
HETATM 5 P PB ATP . . . H 3 -14.186 -13.004 11.942 1 69.34 ? PB ATP 452 B 1 
HETATM 6 O O1B ATP . . . H 3 -13.032 -13.365 11.083 1 72.77 ? O1B ATP 452 B 1 
HETATM 7 O O2B ATP . . . H 3 -14.718 -11.619 11.882 1 69.22 ? O2B ATP 452 B 1 
HETATM 8 O O3B ATP . . . H 3 -15.368 -14.073 11.659 1 73.64 ? O3B ATP 452 B 1 
HETATM 9 P PA ATP . . . H 3 -13.369 -12.442 14.735 1 68.27 ? PA ATP 452 B 1 
HETATM 10 O O1A ATP . . . H 3 -13.322 -13.385 15.894 1 68.08 ? O1A ATP 452 B 1 
HETATM 11 O O2A ATP . . . H 3 -12.187 -11.555 14.503 1 70.11 ? O2A ATP 452 B 1 
HETATM 12 O O3A ATP . . . H 3 -13.685 -13.366 13.437 1 68 ? O3A ATP 452 B 1 
HETATM 13 O O5' ATP . . . H 3 -14.653 -11.474 14.826 1 63.24 ? O5' ATP 452 B 1 
HETATM 14 C C5' ATP . . . H 3 -15.548 -11.499 15.946 1 53.46 ? C5' ATP 452 B 1 
HETATM 15 C C4' ATP . . . H 3 -16.932 -11.082 15.521 1 45.49 ? C4' ATP 452 B 1 
HETATM 16 O O4' ATP . . . H 3 -16.838 -9.739 14.988 1 45.11 ? O4' ATP 452 B 1 
HETATM 17 C C3' ATP . . . H 3 -17.587 -11.859 14.39 1 43.45 ? C3' ATP 452 B 1 
HETATM 18 O O3' ATP . . . H 3 -18.172 -13.108 14.795 1 39.52 ? O3' ATP 452 B 1 
HETATM 19 C C2' ATP . . . H 3 -18.623 -10.86 13.896 1 43.7 ? C2' ATP 452 B 1 
HETATM 20 O O2' ATP . . . H 3 -19.791 -10.814 14.682 1 40.11 ? O2' ATP 452 B 1 
HETATM 21 C C1' ATP . . . H 3 -17.879 -9.532 14.039 1 45.72 ? C1' ATP 452 B 1 
HETATM 22 N N9 ATP . . . H 3 -17.298 -9.01 12.795 1 45.91 ? N9 ATP 452 B 1 
HETATM 23 C C8 ATP . . . H 3 -16.093 -9.361 12.226 1 47.63 ? C8 ATP 452 B 1 
HETATM 24 N N7 ATP . . . H 3 -15.814 -8.711 11.116 1 46.75 ? N7 ATP 452 B 1 
HETATM 25 C C5 ATP . . . H 3 -16.909 -7.873 10.938 1 45.23 ? C5 ATP 452 B 1 
HETATM 26 C C6 ATP . . . H 3 -17.214 -6.906 9.946 1 43.63 ? C6 ATP 452 B 1 
HETATM 27 N N6 ATP . . . H 3 -16.401 -6.615 8.945 1 40.72 ? N6 ATP 452 B 1 
HETATM 28 N N1 ATP . . . H 3 -18.389 -6.24 10.043 1 44.72 ? N1 ATP 452 B 1 
HETATM 29 C C2 ATP . . . H 3 -19.193 -6.521 11.088 1 45.24 ? C2 ATP 452 B 1 
HETATM 30 N N3 ATP . . . H 3 -19.008 -7.399 12.098 1 44.85 ? N3 ATP 452 B 1 
HETATM 31 C C4 ATP . . . H 3 -17.836 -8.051 11.96 1 44.76 ? C4 ATP 452 B 1 
HETATM 32 H HO2' ATP . . . H 3 -20.35 -10.156 14.295 1 0 ? HO2' ATP 452 B 1 
HETATM 33 H HN61 ATP . . . H 3 -15.517 -7.093 8.861 1 0 ? HN61 ATP 452 B 1 
HETATM 34 H HN62 ATP . . . H 3 -16.661 -5.917 8.263 1 0 ? HN62 ATP 452 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           34 
#