data_8Y40
#
_model_server_result.job_id            8DrF_CvoUIyfYshqwAA98w 
_model_server_result.datetime_utc      '2025-03-05 03:32:18' 
_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          8y40 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":5104}' 
#
_entry.id    8Y40 
#
_exptl.entry_id    8Y40 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          7 
_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                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    12-meric 
_pdbx_struct_assembly.oligomeric_count      12 
_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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA 
_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
? 7 P N N 
? 7 U N N 
? 7 Z N N 
? 7 EA 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
metalc ? metalc1 I OE1 GLU 3967 A GLU 3967 1_555 O CA CA . A CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc2 I OE2 GLU 3967 A GLU 3967 1_555 O CA CA . A CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.118 ? 
metalc ? metalc3 I SG CYS 4961 A CYS 4961 1_555 N ZN ZN . A ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? 
metalc ? metalc4 I ND1 HIS 4978 A HIS 4978 1_555 N ZN ZN . A ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? 
metalc ? metalc5 I O THR 5001 A THR 5001 1_555 O CA CA . A CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? 
metalc ? metalc6 J OE1 GLU 3967 B GLU 3967 1_555 T CA CA . B CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc7 J OE2 GLU 3967 B GLU 3967 1_555 T CA CA . B CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.113 ? 
metalc ? metalc8 J SG CYS 4961 B CYS 4961 1_555 S ZN ZN . B ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? 
metalc ? metalc9 J ND1 HIS 4978 B HIS 4978 1_555 S ZN ZN . B ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? 
metalc ? metalc10 J O THR 5001 B THR 5001 1_555 T CA CA . B CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? 
metalc ? metalc11 K OE1 GLU 3967 C GLU 3967 1_555 Y CA CA . C CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc12 K OE2 GLU 3967 C GLU 3967 1_555 Y CA CA . C CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.112 ? 
metalc ? metalc13 K SG CYS 4961 C CYS 4961 1_555 X ZN ZN . C ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? 
metalc ? metalc14 K ND1 HIS 4978 C HIS 4978 1_555 X ZN ZN . C ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? 
metalc ? metalc15 K O THR 5001 C THR 5001 1_555 Y CA CA . C CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? 
metalc ? metalc16 L OE1 GLU 3967 D GLU 3967 1_555 DA CA CA . D CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc17 L OE2 GLU 3967 D GLU 3967 1_555 DA CA CA . D CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.117 ? 
metalc ? metalc18 L SG CYS 4961 D CYS 4961 1_555 CA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? 
metalc ? metalc19 L ND1 HIS 4978 D HIS 4978 1_555 CA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? 
metalc ? metalc20 L O THR 5001 D THR 5001 1_555 DA CA CA . D CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? 
#
_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                     8Y40 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
M 4 F0U A 1 5101 1 F0U CHL . 
N 5 ZN A 1 5102 1 ZN ZN . 
O 6 CA A 1 5103 1 CA CA . 
P 7 ATP A 1 5104 1 ATP ATP . 
Q 8 CFF A 1 5105 1 CFF CFF . 
R 4 F0U B 1 5101 2 F0U CHL . 
S 5 ZN B 1 5102 2 ZN ZN . 
T 6 CA B 1 5103 2 CA CA . 
U 7 ATP B 1 5104 2 ATP ATP . 
V 8 CFF B 1 5105 2 CFF CFF . 
W 4 F0U C 1 5101 3 F0U CHL . 
X 5 ZN C 1 5102 3 ZN ZN . 
Y 6 CA C 1 5103 3 CA CA . 
Z 7 ATP C 1 5104 3 ATP ATP . 
AA 8 CFF C 1 5105 3 CFF CFF . 
BA 4 F0U D 1 5101 4 F0U CHL . 
CA 5 ZN D 1 5102 4 ZN ZN . 
DA 6 CA D 1 5103 4 CA CA . 
EA 7 ATP D 1 5104 4 ATP ATP . 
FA 8 CFF D 1 5105 4 CFF CFF . 
#
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 . . . U 7 296.746 288.171 319.251 1 20 ? PG ATP 5104 B 1 
HETATM 2 O O1G ATP . . . U 7 298.026 288.211 318.453 1 20 ? O1G ATP 5104 B 1 
HETATM 3 O O2G ATP . . . U 7 296.324 286.788 319.685 1 20 ? O2G ATP 5104 B 1 
HETATM 4 O O3G ATP . . . U 7 296.643 289.227 320.323 1 20 ? O3G ATP 5104 B 1 
HETATM 5 P PB ATP . . . U 7 294.179 289.09 318.733 1 20 ? PB ATP 5104 B 1 
HETATM 6 O O1B ATP . . . U 7 293.782 288.206 319.89 1 20 ? O1B ATP 5104 B 1 
HETATM 7 O O2B ATP . . . U 7 294.24 290.586 318.917 1 20 ? O2B ATP 5104 B 1 
HETATM 8 O O3B ATP . . . U 7 295.612 288.599 318.195 1 20 ? O3B ATP 5104 B 1 
HETATM 9 P PA ATP . . . U 7 293.542 287.476 316.563 1 20 ? PA ATP 5104 B 1 
HETATM 10 O O1A ATP . . . U 7 293.837 286.305 317.468 1 20 ? O1A ATP 5104 B 1 
HETATM 11 O O2A ATP . . . U 7 294.55 287.894 315.521 1 20 ? O2A ATP 5104 B 1 
HETATM 12 O O3A ATP . . . U 7 293.217 288.752 317.489 1 20 ? O3A ATP 5104 B 1 
HETATM 13 O O5' ATP . . . U 7 292.143 287.196 315.822 1 20 ? O5' ATP 5104 B 1 
HETATM 14 C C5' ATP . . . U 7 292.118 286.416 314.632 1 20 ? C5' ATP 5104 B 1 
HETATM 15 C C4' ATP . . . U 7 290.912 285.493 314.653 1 20 ? C4' ATP 5104 B 1 
HETATM 16 O O4' ATP . . . U 7 289.719 286.273 314.689 1 20 ? O4' ATP 5104 B 1 
HETATM 17 C C3' ATP . . . U 7 290.863 284.623 313.412 1 20 ? C3' ATP 5104 B 1 
HETATM 18 O O3' ATP . . . U 7 290.715 283.248 313.761 1 20 ? O3' ATP 5104 B 1 
HETATM 19 C C2' ATP . . . U 7 289.675 285.104 312.61 1 20 ? C2' ATP 5104 B 1 
HETATM 20 O O2' ATP . . . U 7 288.757 284.046 312.329 1 20 ? O2' ATP 5104 B 1 
HETATM 21 C C1' ATP . . . U 7 289.005 286.167 313.458 1 20 ? C1' ATP 5104 B 1 
HETATM 22 N N9 ATP . . . U 7 289.047 287.441 312.709 1 20 ? N9 ATP 5104 B 1 
HETATM 23 C C8 ATP . . . U 7 289.763 288.536 313.023 1 20 ? C8 ATP 5104 B 1 
HETATM 24 N N7 ATP . . . U 7 289.558 289.516 312.104 1 20 ? N7 ATP 5104 B 1 
HETATM 25 C C5 ATP . . . U 7 288.7 289.039 311.189 1 20 ? C5 ATP 5104 B 1 
HETATM 26 C C6 ATP . . . U 7 288.061 289.542 309.959 1 20 ? C6 ATP 5104 B 1 
HETATM 27 N N6 ATP . . . U 7 288.317 290.793 309.527 1 20 ? N6 ATP 5104 B 1 
HETATM 28 N N1 ATP . . . U 7 287.224 288.72 309.296 1 20 ? N1 ATP 5104 B 1 
HETATM 29 C C2 ATP . . . U 7 286.965 287.473 309.726 1 20 ? C2 ATP 5104 B 1 
HETATM 30 N N3 ATP . . . U 7 287.513 286.952 310.836 1 20 ? N3 ATP 5104 B 1 
HETATM 31 C C4 ATP . . . U 7 288.368 287.672 311.591 1 20 ? C4 ATP 5104 B 1 
HETATM 32 H "H5'1" ATP . . . U 7 293.033 285.825 314.557 1 20 ? "H5'1" ATP 5104 B 1 
HETATM 33 H "H5'2" ATP . . . U 7 292.06 287.069 313.76 1 20 ? "H5'2" ATP 5104 B 1 
HETATM 34 H H4' ATP . . . U 7 290.972 284.846 315.538 1 20 ? H4' ATP 5104 B 1 
HETATM 35 H H3' ATP . . . U 7 291.78 284.778 312.828 1 20 ? H3' ATP 5104 B 1 
HETATM 36 H HO3' ATP . . . U 7 289.778 283.059 313.906 1 20 ? HO3' ATP 5104 B 1 
HETATM 37 H H2' ATP . . . U 7 290.03 285.559 311.674 1 20 ? H2' ATP 5104 B 1 
HETATM 38 H HO2' ATP . . . U 7 287.914 284.429 312.048 1 20 ? HO2' ATP 5104 B 1 
HETATM 39 H H1' ATP . . . U 7 287.963 285.874 313.648 1 20 ? H1' ATP 5104 B 1 
HETATM 40 H H8 ATP . . . U 7 290.41 288.625 313.886 1 20 ? H8 ATP 5104 B 1 
HETATM 41 H HN61 ATP . . . U 7 287.884 291.143 308.686 1 20 ? HN61 ATP 5104 B 1 
HETATM 42 H HN62 ATP . . . U 7 288.95 291.376 310.051 1 20 ? HN62 ATP 5104 B 1 
HETATM 43 H H2 ATP . . . U 7 286.289 286.858 309.152 1 20 ? H2 ATP 5104 B 1 
#
_model_server_stats.io_time_ms              50 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    220 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#