data_7LMY
#
_model_server_result.job_id            COGmGv6f-MsQoQohAEGsVA 
_model_server_result.datetime_utc      '2024-11-14 17:25:18' 
_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          7lmy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"BA","auth_seq_id":902}' 
#
_entry.id    7LMY 
#
_exptl.entry_id    7LMY 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    12 
_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            7LMY 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7LMY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_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,GA,HA,IA,JA 
_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    ? 
_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
? 2 G N N 
? 2 H N N 
? 2 L N N 
? 2 M N N 
? 2 Q N N 
? 2 R N N 
? 2 V N N 
? 2 W N N 
? 2 AA N N 
? 2 BA N N 
? 2 FA N N 
? 2 GA 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 A OG1 THR 252 A THR 252 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
metalc ? metalc2 G O3G ATP . A ATP 901 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc3 G O2B ATP . A ATP 901 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? 
metalc ? metalc4 H O2G ATP . A ATP 902 1_555 K MG MG . A MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc5 H O1A ATP . A ATP 902 1_555 K MG MG . A MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc6 B OG1 THR 252 B THR 252 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? 
metalc ? metalc7 L O3G ATP . B ATP 901 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? 
metalc ? metalc8 L O2B ATP . B ATP 901 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? 
metalc ? metalc9 M O2G ATP . B ATP 902 1_555 P MG MG . B MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc10 M O1A ATP . B ATP 902 1_555 P MG MG . B MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc11 C OG1 THR 252 C THR 252 1_555 T MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc12 Q O3G ATP . C ATP 901 1_555 T MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? 
metalc ? metalc13 Q O2B ATP . C ATP 901 1_555 T MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? 
metalc ? metalc14 R O2G ATP . C ATP 902 1_555 U MG MG . C MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? 
metalc ? metalc15 R O1A ATP . C ATP 902 1_555 U MG MG . C MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc16 D OG1 THR 252 D THR 252 1_555 Y MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
metalc ? metalc17 V O3G ATP . D ATP 901 1_555 Y MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? 
metalc ? metalc18 V O2B ATP . D ATP 901 1_555 Y MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? 
metalc ? metalc19 W O2G ATP . D ATP 902 1_555 Z MG MG . D MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc20 W O1A ATP . D ATP 902 1_555 Z MG MG . D MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc21 E OG1 THR 252 E THR 252 1_555 DA MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? 
metalc ? metalc22 AA O3G ATP . E ATP 901 1_555 DA MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc23 AA O2B ATP . E ATP 901 1_555 DA MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? 
metalc ? metalc24 BA O2G ATP . E ATP 902 1_555 EA MG MG . E MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc25 BA O1A ATP . E ATP 902 1_555 EA MG MG . E MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc26 F OG1 THR 252 F THR 252 1_555 IA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? 
metalc ? metalc27 FA O3G ATP . F ATP 901 1_555 IA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? 
metalc ? metalc28 FA O2B ATP . F ATP 901 1_555 IA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? 
metalc ? metalc29 GA O2G ATP . F ATP 902 1_555 JA MG MG . F MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc30 GA O1A ATP . F ATP 902 1_555 JA MG MG . F MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
#
_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                     7LMY 
_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
G 2 ATP A 1 901 801 ATP ATP . 
H 2 ATP A 1 902 901 ATP ATP . 
I 3 Y6Y A 1 903 1001 Y6Y NM3 . 
J 4 MG A 1 904 1 MG MG . 
K 4 MG A 1 905 7 MG MG . 
L 2 ATP B 1 901 801 ATP ATP . 
M 2 ATP B 1 902 901 ATP ATP . 
N 3 Y6Y B 1 903 1001 Y6Y NM3 . 
O 4 MG B 1 904 8 MG MG . 
P 4 MG B 1 905 9 MG MG . 
Q 2 ATP C 1 901 801 ATP ATP . 
R 2 ATP C 1 902 901 ATP ATP . 
S 3 Y6Y C 1 903 1001 Y6Y NM3 . 
T 4 MG C 1 904 10 MG MG . 
U 4 MG C 1 905 11 MG MG . 
V 2 ATP D 1 901 801 ATP ATP . 
W 2 ATP D 1 902 901 ATP ATP . 
X 3 Y6Y D 1 903 1001 Y6Y NM3 . 
Y 4 MG D 1 904 12 MG MG . 
Z 4 MG D 1 905 13 MG MG . 
AA 2 ATP E 1 901 801 ATP ATP . 
BA 2 ATP E 1 902 901 ATP ATP . 
CA 3 Y6Y E 1 903 1001 Y6Y NM3 . 
DA 4 MG E 1 904 14 MG MG . 
EA 4 MG E 1 905 15 MG MG . 
FA 2 ATP F 1 901 801 ATP ATP . 
GA 2 ATP F 1 902 901 ATP ATP . 
HA 3 Y6Y F 1 903 1001 Y6Y NM3 . 
IA 4 MG F 1 904 16 MG MG . 
JA 4 MG F 1 905 17 MG MG . 
#
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 . . . BA 2 194.33 191.773 136.744 1 14.83 ? PG ATP 902 E 1 
HETATM 2 O O1G ATP . . . BA 2 193.033 191.043 136.692 1 14.83 ? O1G ATP 902 E 1 
HETATM 3 O O2G ATP . . . BA 2 194.913 191.891 138.155 1 14.83 ? O2G ATP 902 E 1 
HETATM 4 O O3G ATP . . . BA 2 195.399 191.198 135.812 1 14.83 ? O3G ATP 902 E 1 
HETATM 5 P PB ATP . . . BA 2 194.16 194.759 136.846 1 14.83 ? PB ATP 902 E 1 
HETATM 6 O O1B ATP . . . BA 2 193.408 194.851 138.11 1 14.83 ? O1B ATP 902 E 1 
HETATM 7 O O2B ATP . . . BA 2 193.697 195.694 135.734 1 14.83 ? O2B ATP 902 E 1 
HETATM 8 O O3B ATP . . . BA 2 194.143 193.285 136.258 1 14.83 ? O3B ATP 902 E 1 
HETATM 9 P PA ATP . . . BA 2 196.702 195.218 138.281 1 14.83 ? PA ATP 902 E 1 
HETATM 10 O O1A ATP . . . BA 2 196.459 194.223 139.344 1 14.83 ? O1A ATP 902 E 1 
HETATM 11 O O2A ATP . . . BA 2 196.572 196.671 138.723 1 14.83 ? O2A ATP 902 E 1 
HETATM 12 O O3A ATP . . . BA 2 195.718 195.01 137.055 1 14.83 ? O3A ATP 902 E 1 
HETATM 13 O O5' ATP . . . BA 2 198.127 195.025 137.629 1 14.83 ? O5' ATP 902 E 1 
HETATM 14 C C5' ATP . . . BA 2 198.8 193.749 137.667 1 14.83 ? C5' ATP 902 E 1 
HETATM 15 C C4' ATP . . . BA 2 200.272 193.936 137.388 1 14.83 ? C4' ATP 902 E 1 
HETATM 16 O O4' ATP . . . BA 2 200.451 194.825 136.262 1 14.83 ? O4' ATP 902 E 1 
HETATM 17 C C3' ATP . . . BA 2 201.091 194.53 138.533 1 14.83 ? C3' ATP 902 E 1 
HETATM 18 O O3' ATP . . . BA 2 202.39 193.952 138.58 1 14.83 ? O3' ATP 902 E 1 
HETATM 19 C C2' ATP . . . BA 2 201.154 196.014 138.17 1 14.83 ? C2' ATP 902 E 1 
HETATM 20 O O2' ATP . . . BA 2 202.325 196.631 138.692 1 14.83 ? O2' ATP 902 E 1 
HETATM 21 C C1' ATP . . . BA 2 201.218 195.95 136.645 1 14.83 ? C1' ATP 902 E 1 
HETATM 22 N N9 ATP . . . BA 2 200.665 197.123 135.978 1 14.83 ? N9 ATP 902 E 1 
HETATM 23 C C8 ATP . . . BA 2 199.547 197.168 135.187 1 14.83 ? C8 ATP 902 E 1 
HETATM 24 N N7 ATP . . . BA 2 199.274 198.359 134.714 1 14.83 ? N7 ATP 902 E 1 
HETATM 25 C C5 ATP . . . BA 2 200.282 199.157 135.232 1 14.83 ? C5 ATP 902 E 1 
HETATM 26 C C6 ATP . . . BA 2 200.565 200.53 135.106 1 14.83 ? C6 ATP 902 E 1 
HETATM 27 N N6 ATP . . . BA 2 199.824 201.38 134.388 1 14.83 ? N6 ATP 902 E 1 
HETATM 28 N N1 ATP . . . BA 2 201.65 201.009 135.752 1 14.83 ? N1 ATP 902 E 1 
HETATM 29 C C2 ATP . . . BA 2 202.395 200.166 136.471 1 14.83 ? C2 ATP 902 E 1 
HETATM 30 N N3 ATP . . . BA 2 202.226 198.856 136.662 1 14.83 ? N3 ATP 902 E 1 
HETATM 31 C C4 ATP . . . BA 2 201.148 198.409 136.012 1 14.83 ? C4 ATP 902 E 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    42 
_model_server_stats.query_time_ms           215 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#