data_5YA1
#
_model_server_result.job_id            9IjKUJU8vfJfaDFpdEtMwg 
_model_server_result.datetime_utc      '2025-08-01 10:23:09' 
_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          5ya1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":701}' 
#
_entry.id    5YA1 
#
_exptl.entry_id    5YA1 
_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         120 
_cell.entry_id            5YA1 
_cell.length_a            101.016 
_cell.length_b            101.016 
_cell.length_c            344.453 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YA1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 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,C,E,F,G,H,I,J,K,Q,S,U 1 1 
B,D,L,M,N,O,P,R,T,V 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 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                     5YA1 
_atom_sites.fract_transf_matrix[1][1]    0.009899 
_atom_sites.fract_transf_matrix[1][2]    0.005715 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011431 
_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]    0.002903 
_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 4 HEZ A 1 702 802 HEZ HEZ . 
G 4 HEZ A 1 703 803 HEZ HEZ . 
H 5 PO4 A 1 704 1 PO4 PO4 . 
I 5 PO4 A 1 705 2 PO4 PO4 . 
J 5 PO4 A 1 706 4 PO4 PO4 . 
K 5 PO4 A 1 707 8 PO4 PO4 . 
L 3 ATP B 1 601 702 ATP ATP . 
M 4 HEZ B 1 602 801 HEZ HEZ . 
N 4 HEZ B 1 603 804 HEZ HEZ . 
O 5 PO4 B 1 604 3 PO4 PO4 . 
P 5 PO4 B 1 605 7 PO4 PO4 . 
Q 5 PO4 C 1 101 6 PO4 PO4 . 
R 5 PO4 D 1 101 5 PO4 PO4 . 
S 6 HOH A 1 801 11 HOH HOH . 
S 6 HOH A 2 802 7 HOH HOH . 
S 6 HOH A 3 803 27 HOH HOH . 
S 6 HOH A 4 804 21 HOH HOH . 
S 6 HOH A 5 805 20 HOH HOH . 
S 6 HOH A 6 806 69 HOH HOH . 
S 6 HOH A 7 807 34 HOH HOH . 
S 6 HOH A 8 808 25 HOH HOH . 
S 6 HOH A 9 809 35 HOH HOH . 
S 6 HOH A 10 810 13 HOH HOH . 
S 6 HOH A 11 811 57 HOH HOH . 
S 6 HOH A 12 812 48 HOH HOH . 
S 6 HOH A 13 813 2 HOH HOH . 
S 6 HOH A 14 814 38 HOH HOH . 
S 6 HOH A 15 815 70 HOH HOH . 
S 6 HOH A 16 816 65 HOH HOH . 
S 6 HOH A 17 817 29 HOH HOH . 
S 6 HOH A 18 818 36 HOH HOH . 
S 6 HOH A 19 819 43 HOH HOH . 
S 6 HOH A 20 820 63 HOH HOH . 
S 6 HOH A 21 821 51 HOH HOH . 
S 6 HOH A 22 822 60 HOH HOH . 
S 6 HOH A 23 823 4 HOH HOH . 
S 6 HOH A 24 824 44 HOH HOH . 
S 6 HOH A 25 825 32 HOH HOH . 
S 6 HOH A 26 826 53 HOH HOH . 
S 6 HOH A 27 827 10 HOH HOH . 
S 6 HOH A 28 828 64 HOH HOH . 
S 6 HOH A 29 829 18 HOH HOH . 
S 6 HOH A 30 830 71 HOH HOH . 
S 6 HOH A 31 831 41 HOH HOH . 
S 6 HOH A 32 832 56 HOH HOH . 
T 6 HOH B 1 701 22 HOH HOH . 
T 6 HOH B 2 702 19 HOH HOH . 
T 6 HOH B 3 703 28 HOH HOH . 
T 6 HOH B 4 704 68 HOH HOH . 
T 6 HOH B 5 705 39 HOH HOH . 
T 6 HOH B 6 706 14 HOH HOH . 
T 6 HOH B 7 707 33 HOH HOH . 
T 6 HOH B 8 708 31 HOH HOH . 
T 6 HOH B 9 709 1 HOH HOH . 
T 6 HOH B 10 710 26 HOH HOH . 
T 6 HOH B 11 711 6 HOH HOH . 
T 6 HOH B 12 712 58 HOH HOH . 
T 6 HOH B 13 713 59 HOH HOH . 
T 6 HOH B 14 714 67 HOH HOH . 
T 6 HOH B 15 715 49 HOH HOH . 
T 6 HOH B 16 716 52 HOH HOH . 
T 6 HOH B 17 717 12 HOH HOH . 
T 6 HOH B 18 718 46 HOH HOH . 
T 6 HOH B 19 719 16 HOH HOH . 
T 6 HOH B 20 720 66 HOH HOH . 
T 6 HOH B 21 721 30 HOH HOH . 
T 6 HOH B 22 722 37 HOH HOH . 
T 6 HOH B 23 723 5 HOH HOH . 
T 6 HOH B 24 724 3 HOH HOH . 
T 6 HOH B 25 725 45 HOH HOH . 
T 6 HOH B 26 726 42 HOH HOH . 
T 6 HOH B 27 727 15 HOH HOH . 
T 6 HOH B 28 728 17 HOH HOH . 
T 6 HOH B 29 729 50 HOH HOH . 
T 6 HOH B 30 730 47 HOH HOH . 
T 6 HOH B 31 731 40 HOH HOH . 
T 6 HOH B 32 732 61 HOH HOH . 
U 6 HOH C 1 201 9 HOH HOH . 
U 6 HOH C 2 202 54 HOH HOH . 
U 6 HOH C 3 203 24 HOH HOH . 
V 6 HOH D 1 201 62 HOH HOH . 
V 6 HOH D 2 202 8 HOH HOH . 
V 6 HOH D 3 203 55 HOH HOH . 
V 6 HOH D 4 204 23 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 . . . E 3 28.927 30.692 16.18 1 129 ? PG ATP 701 A 1 
HETATM 2 O O1G ATP . . . E 3 30.174 30.416 15.373 1 127.17 ? O1G ATP 701 A 1 
HETATM 3 O O2G ATP . . . E 3 28.058 31.798 15.631 1 131.63 ? O2G ATP 701 A 1 
HETATM 4 O O3G ATP . . . E 3 29.152 30.757 17.671 1 128.83 ? O3G ATP 701 A 1 
HETATM 5 P PB ATP . . . E 3 26.587 29.184 16.644 1 169.78 ? PB ATP 701 A 1 
HETATM 6 O O1B ATP . . . E 3 25.595 29.931 15.784 1 168.55 ? O1B ATP 701 A 1 
HETATM 7 O O2B ATP . . . E 3 26.659 29.472 18.125 1 169.5 ? O2B ATP 701 A 1 
HETATM 8 O O3B ATP . . . E 3 28.045 29.361 15.977 1 88.38 ? O3B ATP 701 A 1 
HETATM 9 P PA ATP . . . E 3 27.077 26.479 17.294 1 98.82 ? PA ATP 701 A 1 
HETATM 10 O O1A ATP . . . E 3 26.045 25.486 17.777 1 96.93 ? O1A ATP 701 A 1 
HETATM 11 O O2A ATP . . . E 3 28.038 27.143 18.251 1 99.86 ? O2A ATP 701 A 1 
HETATM 12 O O3A ATP . . . E 3 26.346 27.609 16.406 1 175.71 ? O3A ATP 701 A 1 
HETATM 13 O O5' ATP . . . E 3 27.969 25.785 16.147 1 105.17 ? O5' ATP 701 A 1 
HETATM 14 C C5' ATP . . . E 3 29.311 25.371 16.396 1 101.57 ? C5' ATP 701 A 1 
HETATM 15 C C4' ATP . . . E 3 30.044 25.218 15.066 1 96.81 ? C4' ATP 701 A 1 
HETATM 16 O O4' ATP . . . E 3 29.299 24.376 14.181 1 96.88 ? O4' ATP 701 A 1 
HETATM 17 C C3' ATP . . . E 3 30.224 26.549 14.352 1 91.92 ? C3' ATP 701 A 1 
HETATM 18 O O3' ATP . . . E 3 31.542 27.065 14.559 1 87.14 ? O3' ATP 701 A 1 
HETATM 19 C C2' ATP . . . E 3 29.988 26.249 12.885 1 93.03 ? C2' ATP 701 A 1 
HETATM 20 O O2' ATP . . . E 3 31.245 26.177 12.207 1 92.38 ? O2' ATP 701 A 1 
HETATM 21 C C1' ATP . . . E 3 29.303 24.892 12.847 1 96.77 ? C1' ATP 701 A 1 
HETATM 22 N N9 ATP . . . E 3 27.897 25.058 12.396 1 103.18 ? N9 ATP 701 A 1 
HETATM 23 C C8 ATP . . . E 3 26.92 25.639 13.119 1 106.44 ? C8 ATP 701 A 1 
HETATM 24 N N7 ATP . . . E 3 25.741 25.646 12.446 1 105.87 ? N7 ATP 701 A 1 
HETATM 25 C C5 ATP . . . E 3 25.957 25.057 11.256 1 106.87 ? C5 ATP 701 A 1 
HETATM 26 C C6 ATP . . . E 3 25.139 24.736 10.063 1 106.1 ? C6 ATP 701 A 1 
HETATM 27 N N6 ATP . . . E 3 23.823 25.056 10.007 1 106.99 ? N6 ATP 701 A 1 
HETATM 28 N N1 ATP . . . E 3 25.752 24.114 9.032 1 102.1 ? N1 ATP 701 A 1 
HETATM 29 C C2 ATP . . . E 3 27.058 23.791 9.073 1 101.3 ? C2 ATP 701 A 1 
HETATM 30 N N3 ATP . . . E 3 27.859 24.051 10.122 1 102.84 ? N3 ATP 701 A 1 
HETATM 31 C C4 ATP . . . E 3 27.379 24.672 11.226 1 104.83 ? C4 ATP 701 A 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           356 
_model_server_stats.encode_time_ms          19 
_model_server_stats.element_count           31 
#