data_8TKD
#
_model_server_result.job_id            Riy012aKFdoIHB3WQulSRg 
_model_server_result.datetime_utc      '2024-10-19 03:35:44' 
_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          8tkd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":3003}' 
#
_entry.id    8TKD 
#
_exptl.entry_id    8TKD 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          4 
_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         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            8TKD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8TKD 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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
? 4 G N N 
? 4 J N N 
? 4 M N N 
? 4 P 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 2455 A CYS 2455 1_555 A SG CYS 2461 A CYS 2461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 B SG CYS 2455 B CYS 2455 1_555 B SG CYS 2461 B CYS 2461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 C SG CYS 2455 C CYS 2455 1_555 C SG CYS 2461 C CYS 2461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 D SG CYS 2455 D CYS 2455 1_555 D SG CYS 2461 D CYS 2461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc1 A SG CYS 2538 A CYS 2538 1_555 E ZN ZN . A ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc2 A SG CYS 2541 A CYS 2541 1_555 E ZN ZN . A ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc3 A NE2 HIS 2558 A HIS 2558 1_555 E ZN ZN . A ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc4 A ND1 HIS 2563 A HIS 2563 1_555 E ZN ZN . A ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc5 B SG CYS 2538 B CYS 2538 1_555 H ZN ZN . B ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc6 B SG CYS 2541 B CYS 2541 1_555 H ZN ZN . B ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc7 B NE2 HIS 2558 B HIS 2558 1_555 H ZN ZN . B ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc8 B ND1 HIS 2563 B HIS 2563 1_555 H ZN ZN . B ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc9 C SG CYS 2538 C CYS 2538 1_555 K ZN ZN . C ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc10 C SG CYS 2541 C CYS 2541 1_555 K ZN ZN . C ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc11 C NE2 HIS 2558 C HIS 2558 1_555 K ZN ZN . C ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc12 C ND1 HIS 2563 C HIS 2563 1_555 K ZN ZN . C ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc13 D SG CYS 2538 D CYS 2538 1_555 N ZN ZN . D ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc14 D SG CYS 2541 D CYS 2541 1_555 N ZN ZN . D ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc15 D NE2 HIS 2558 D HIS 2558 1_555 N ZN ZN . D ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc16 D ND1 HIS 2563 D HIS 2563 1_555 N ZN ZN . D ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
#
_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                     8TKD 
_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
E 2 ZN A 1 3001 3001 ZN ZN . 
F 3 I3P A 1 3002 3002 I3P I3P . 
G 4 ATP A 1 3003 3005 ATP ATP . 
H 2 ZN B 1 3001 3001 ZN ZN . 
I 3 I3P B 1 3002 3002 I3P I3P . 
J 4 ATP B 1 3003 3005 ATP ATP . 
K 2 ZN C 1 3001 3001 ZN ZN . 
L 3 I3P C 1 3002 3002 I3P I3P . 
M 4 ATP C 1 3003 3005 ATP ATP . 
N 2 ZN D 1 3001 3001 ZN ZN . 
O 3 I3P D 1 3002 3002 I3P I3P . 
P 4 ATP D 1 3003 3005 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 . . . G 4 247 209.737 242.88 1 61.55 ? PG ATP 3003 A 1 
HETATM 2 O O1G ATP . . . G 4 248.317 210.367 243.184 1 61.55 ? O1G ATP 3003 A 1 
HETATM 3 O O2G ATP . . . G 4 246.502 210.009 241.456 1 61.55 ? O2G ATP 3003 A 1 
HETATM 4 O O3G ATP . . . G 4 246.965 208.228 243.143 1 61.55 ? O3G ATP 3003 A 1 
HETATM 5 P PB ATP . . . G 4 244.758 209.846 244.865 1 61.55 ? PB ATP 3003 A 1 
HETATM 6 O O1B ATP . . . G 4 245.102 210.222 246.251 1 61.55 ? O1B ATP 3003 A 1 
HETATM 7 O O2B ATP . . . G 4 244.534 208.354 244.618 1 61.55 ? O2B ATP 3003 A 1 
HETATM 8 O O3B ATP . . . G 4 245.858 210.337 243.826 1 61.55 ? O3B ATP 3003 A 1 
HETATM 9 P PA ATP . . . G 4 243.141 211.866 243.427 1 61.55 ? PA ATP 3003 A 1 
HETATM 10 O O1A ATP . . . G 4 243.481 211.599 242.014 1 61.55 ? O1A ATP 3003 A 1 
HETATM 11 O O2A ATP . . . G 4 243.856 213.069 244.043 1 61.55 ? O2A ATP 3003 A 1 
HETATM 12 O O3A ATP . . . G 4 243.459 210.61 244.351 1 61.55 ? O3A ATP 3003 A 1 
HETATM 13 O O5' ATP . . . G 4 241.585 212.054 243.616 1 61.55 ? O5' ATP 3003 A 1 
HETATM 14 C C5' ATP . . . G 4 241.052 212.939 244.624 1 61.55 ? C5' ATP 3003 A 1 
HETATM 15 C C4' ATP . . . G 4 239.949 212.248 245.383 1 61.55 ? C4' ATP 3003 A 1 
HETATM 16 O O4' ATP . . . G 4 238.734 212.979 245.101 1 61.55 ? O4' ATP 3003 A 1 
HETATM 17 C C3' ATP . . . G 4 239.67 210.86 244.821 1 61.55 ? C3' ATP 3003 A 1 
HETATM 18 O O3' ATP . . . G 4 238.788 210.239 245.746 1 61.55 ? O3' ATP 3003 A 1 
HETATM 19 C C2' ATP . . . G 4 238.819 211.19 243.601 1 61.55 ? C2' ATP 3003 A 1 
HETATM 20 O O2' ATP . . . G 4 237.963 210.075 243.401 1 61.55 ? O2' ATP 3003 A 1 
HETATM 21 C C1' ATP . . . G 4 237.911 212.261 244.199 1 61.55 ? C1' ATP 3003 A 1 
HETATM 22 N N9 ATP . . . G 4 237.471 213.212 243.188 1 61.55 ? N9 ATP 3003 A 1 
HETATM 23 C C8 ATP . . . G 4 238.249 214.096 242.487 1 61.55 ? C8 ATP 3003 A 1 
HETATM 24 N N7 ATP . . . G 4 237.583 214.837 241.634 1 61.55 ? N7 ATP 3003 A 1 
HETATM 25 C C5 ATP . . . G 4 236.272 214.41 241.784 1 61.55 ? C5 ATP 3003 A 1 
HETATM 26 C C6 ATP . . . G 4 235.069 214.8 241.165 1 61.55 ? C6 ATP 3003 A 1 
HETATM 27 N N6 ATP . . . G 4 234.988 215.749 240.227 1 61.55 ? N6 ATP 3003 A 1 
HETATM 28 N N1 ATP . . . G 4 233.934 214.173 241.545 1 61.55 ? N1 ATP 3003 A 1 
HETATM 29 C C2 ATP . . . G 4 234.008 213.223 242.481 1 61.55 ? C2 ATP 3003 A 1 
HETATM 30 N N3 ATP . . . G 4 235.081 212.773 243.134 1 61.55 ? N3 ATP 3003 A 1 
HETATM 31 C C4 ATP . . . G 4 236.188 213.409 242.738 1 61.55 ? C4 ATP 3003 A 1 
HETATM 32 H "H5'1" ATP . . . G 4 240.699 213.736 244.199 1 61.55 ? "H5'1" ATP 3003 A 1 
HETATM 33 H "H5'2" ATP . . . G 4 241.758 213.188 245.241 1 61.55 ? "H5'2" ATP 3003 A 1 
HETATM 34 H H4' ATP . . . G 4 240.149 212.215 246.332 1 61.55 ? H4' ATP 3003 A 1 
HETATM 35 H H3' ATP . . . G 4 240.46 210.331 244.63 1 61.55 ? H3' ATP 3003 A 1 
HETATM 36 H HO3' ATP . . . G 4 238.511 210.848 246.271 1 61.55 ? HO3' ATP 3003 A 1 
HETATM 37 H H2' ATP . . . G 4 239.316 211.462 242.814 1 61.55 ? H2' ATP 3003 A 1 
HETATM 38 H HO2' ATP . . . G 4 237.686 209.838 244.169 1 61.55 ? HO2' ATP 3003 A 1 
HETATM 39 H H1' ATP . . . G 4 237.151 211.86 244.649 1 61.55 ? H1' ATP 3003 A 1 
HETATM 40 H H8 ATP . . . G 4 239.169 214.164 242.605 1 61.55 ? H8 ATP 3003 A 1 
HETATM 41 H HN61 ATP . . . G 4 235.692 216.186 239.996 1 61.55 ? HN61 ATP 3003 A 1 
HETATM 42 H HN62 ATP . . . G 4 234.232 215.922 239.855 1 61.55 ? HN62 ATP 3003 A 1 
HETATM 43 H H2 ATP . . . G 4 233.201 212.821 242.709 1 61.55 ? H2 ATP 3003 A 1 
#
_model_server_stats.io_time_ms              383 
_model_server_stats.parse_time_ms           41 
_model_server_stats.create_model_time_ms    465 
_model_server_stats.query_time_ms           314 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#