data_5YKF
#
_model_server_result.job_id            IuBwYiqSknJXD5ohuhNBkg 
_model_server_result.datetime_utc      '2024-12-23 18:09:29' 
_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          5ykf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":401}' 
#
_entry.id    5YKF 
#
_exptl.entry_id    5YKF 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    8 
_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            5YKF 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YKF 
_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    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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 
_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
? 3 I N N 
? 3 J N N 
? 3 L N N 
? 3 M N N 
? 3 O N N 
? 3 P N N 
? 3 R N N 
? 3 T 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 110 A CYS 110 1_555 A SG CYS 142 A CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf2 C SG CYS 110 C CYS 110 1_555 C SG CYS 142 C CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf3 E SG CYS 110 E CYS 110 1_555 E SG CYS 142 E CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf4 G SG CYS 110 G CYS 110 1_555 G SG CYS 142 G CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
#
_chem_comp.formula           'C10 H16 N5 O12 P3 S' 
_chem_comp.formula_weight    523.247 
_chem_comp.id                AGS 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" 
#
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 S1G AGS doub 1 n n 
PG O2G AGS sing 2 n n 
PG O3G AGS sing 3 n n 
PG O3B AGS sing 4 n n 
PB O1B AGS doub 5 n n 
PB O2B AGS sing 6 n n 
PB O3B AGS sing 7 n n 
PB O3A AGS sing 8 n n 
PA O1A AGS doub 9 n n 
PA O2A AGS sing 10 n n 
PA O3A AGS sing 11 n n 
PA O5' AGS sing 12 n n 
O5' C5' AGS sing 13 n n 
C5' C4' AGS sing 14 n n 
C4' O4' AGS sing 15 n n 
C4' C3' AGS sing 16 n n 
O4' C1' AGS sing 17 n n 
C3' O3' AGS sing 18 n n 
C3' C2' AGS sing 19 n n 
C2' O2' AGS sing 20 n n 
C2' C1' AGS sing 21 n n 
C1' N9 AGS sing 22 n n 
N9 C8 AGS sing 23 n y 
N9 C4 AGS sing 24 n y 
C8 N7 AGS doub 25 n y 
N7 C5 AGS sing 26 n y 
C5 C6 AGS sing 27 n y 
C5 C4 AGS doub 28 n y 
C6 N6 AGS sing 29 n n 
C6 N1 AGS doub 30 n y 
N1 C2 AGS sing 31 n y 
C2 N3 AGS doub 32 n y 
N3 C4 AGS sing 33 n y 
O2G HOG2 AGS sing 34 n n 
O3G H21 AGS sing 35 n n 
O2B HOB2 AGS sing 36 n n 
O2A HOA2 AGS sing 37 n n 
C5' "H5'1" AGS sing 38 n n 
C5' "H5'2" AGS sing 39 n n 
C4' H4' AGS sing 40 n n 
C3' H3' AGS sing 41 n n 
O3' HO3' AGS sing 42 n n 
C2' H2' AGS sing 43 n n 
O2' HO2' AGS sing 44 n n 
C1' H1' AGS sing 45 n n 
C8 H8 AGS sing 46 n n 
N6 HN61 AGS sing 47 n n 
N6 HN62 AGS sing 48 n n 
C2 H2 AGS sing 49 n n 
#
_atom_sites.entry_id                     5YKF 
_atom_sites.fract_transf_matrix[1][1]    0.003038 
_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]    0.003038 
_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]    0.003038 
_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
I 3 AGS A 1 401 401 AGS AGS . 
J 3 AGS A 1 402 401 AGS AGS . 
K 4 GBM B 1 2001 2001 GBM GBM . 
L 3 AGS B 1 2002 2501 AGS AGS . 
M 3 AGS C 1 401 401 AGS AGS . 
N 4 GBM D 1 2001 2001 GBM GBM . 
O 3 AGS D 1 2002 2501 AGS AGS . 
P 3 AGS E 1 401 401 AGS AGS . 
Q 4 GBM F 1 2001 2001 GBM GBM . 
R 3 AGS F 1 2002 2501 AGS AGS . 
S 4 GBM H 1 2001 2001 GBM GBM . 
T 3 AGS H 1 2002 2501 AGS AGS . 
#
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 AGS . . . P 3 164.81 131.173 164.532 1 156.43 ? PG AGS 401 E 1 
HETATM 2 S S1G AGS . . . P 3 165.947 129.382 164.584 1 181.41 ? S1G AGS 401 E 1 
HETATM 3 O O2G AGS . . . P 3 163.21 130.811 164.704 1 142.52 ? O2G AGS 401 E 1 
HETATM 4 O O3G AGS . . . P 3 165.244 132.046 165.719 1 153.52 ? O3G AGS 401 E 1 
HETATM 5 P PB AGS . . . P 3 164.379 131.273 161.844 1 137.47 ? PB AGS 401 E 1 
HETATM 6 O O1B AGS . . . P 3 165.549 130.821 161.017 1 131.3 ? O1B AGS 401 E 1 
HETATM 7 O O2B AGS . . . P 3 163.664 129.966 162.079 1 148.76 ? O2B AGS 401 E 1 
HETATM 8 O O3B AGS . . . P 3 164.974 131.861 163.17 1 137.51 ? O3B AGS 401 E 1 
HETATM 9 P PA AGS . . . P 3 162.58 133.261 161.775 1 130.12 ? PA AGS 401 E 1 
HETATM 10 O O1A AGS . . . P 3 161.218 133.394 161.011 1 126.75 ? O1A AGS 401 E 1 
HETATM 11 O O2A AGS . . . P 3 162.356 132.61 163.176 1 127.04 ? O2A AGS 401 E 1 
HETATM 12 O O3A AGS . . . P 3 163.556 132.31 161.087 1 136.47 ? O3A AGS 401 E 1 
HETATM 13 O O5' AGS . . . P 3 163.292 134.739 161.977 1 115.85 ? O5' AGS 401 E 1 
HETATM 14 C C5' AGS . . . P 3 162.486 135.787 162.503 1 111.41 ? C5' AGS 401 E 1 
HETATM 15 C C4' AGS . . . P 3 163.266 136.354 163.661 1 108.19 ? C4' AGS 401 E 1 
HETATM 16 O O4' AGS . . . P 3 162.375 136.967 164.59 1 108.91 ? O4' AGS 401 E 1 
HETATM 17 C C3' AGS . . . P 3 164.002 135.258 164.392 1 112.34 ? C3' AGS 401 E 1 
HETATM 18 O O3' AGS . . . P 3 165.388 135.605 164.441 1 119.48 ? O3' AGS 401 E 1 
HETATM 19 C C2' AGS . . . P 3 163.361 135.187 165.768 1 112.77 ? C2' AGS 401 E 1 
HETATM 20 O O2' AGS . . . P 3 164.255 135.619 166.789 1 126.1 ? O2' AGS 401 E 1 
HETATM 21 C C1' AGS . . . P 3 162.2 136.155 165.748 1 103.91 ? C1' AGS 401 E 1 
HETATM 22 N N9 AGS . . . P 3 160.941 135.39 165.614 1 112.59 ? N9 AGS 401 E 1 
HETATM 23 C C8 AGS . . . P 3 160.79 134.239 164.937 1 119.01 ? C8 AGS 401 E 1 
HETATM 24 N N7 AGS . . . P 3 159.515 133.791 164.993 1 117.58 ? N7 AGS 401 E 1 
HETATM 25 C C5 AGS . . . P 3 158.827 134.674 165.726 1 110.19 ? C5 AGS 401 E 1 
HETATM 26 C C6 AGS . . . P 3 157.431 134.792 166.163 1 102.57 ? C6 AGS 401 E 1 
HETATM 27 N N6 AGS . . . P 3 156.521 133.848 165.823 1 106.13 ? N6 AGS 401 E 1 
HETATM 28 N N1 AGS . . . P 3 157.12 135.86 166.918 1 100.04 ? N1 AGS 401 E 1 
HETATM 29 C C2 AGS . . . P 3 158.031 136.79 167.253 1 95.79 ? C2 AGS 401 E 1 
HETATM 30 N N3 AGS . . . P 3 159.318 136.746 166.886 1 100.27 ? N3 AGS 401 E 1 
HETATM 31 C C4 AGS . . . P 3 159.765 135.726 166.133 1 106.14 ? C4 AGS 401 E 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    48 
_model_server_stats.query_time_ms           222 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#