data_5YKG
#
_model_server_result.job_id            icaxS5pwvUrnTs4gxIOLBA 
_model_server_result.datetime_utc      '2024-11-27 04:34:24' 
_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          5ykg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":2002}' 
#
_entry.id    5YKG 
#
_exptl.entry_id    5YKG 
_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            5YKG 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YKG 
_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 K N N 
? 3 L N N 
? 3 N N N 
? 3 O N N 
? 3 Q 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 C SG CYS 110 C CYS 110 1_555 C SG CYS 142 C CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf3 E SG CYS 110 E CYS 110 1_555 E SG CYS 142 E CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf4 G SG CYS 110 G CYS 110 1_555 G SG CYS 142 G CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
#
_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                     5YKG 
_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 4 GBM B 1 2001 2001 GBM GBM . 
K 3 AGS B 1 2002 2501 AGS AGS . 
L 3 AGS C 1 401 401 AGS AGS . 
M 4 GBM D 1 2001 2001 GBM GBM . 
N 3 AGS D 1 2002 2501 AGS AGS . 
O 3 AGS E 1 401 401 AGS AGS . 
P 4 GBM F 1 2001 2001 GBM GBM . 
Q 3 AGS F 1 2002 2501 AGS AGS . 
R 3 AGS G 1 401 401 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 . . . Q 3 128.209 90.667 130.847 1 179.67 ? PG AGS 2002 F 1 
HETATM 2 S S1G AGS . . . Q 3 128.564 91.533 132.699 1 177.52 ? S1G AGS 2002 F 1 
HETATM 3 O O2G AGS . . . Q 3 127.867 91.814 129.769 1 178.19 ? O2G AGS 2002 F 1 
HETATM 4 O O3G AGS . . . Q 3 127.063 89.734 130.941 1 175.69 ? O3G AGS 2002 F 1 
HETATM 5 P PB AGS . . . Q 3 129.552 88.272 130.275 1 172.96 ? PB AGS 2002 F 1 
HETATM 6 O O1B AGS . . . Q 3 128.421 87.835 129.375 1 169.68 ? O1B AGS 2002 F 1 
HETATM 7 O O2B AGS . . . Q 3 130.876 87.838 129.692 1 174.7 ? O2B AGS 2002 F 1 
HETATM 8 O O3B AGS . . . Q 3 129.533 89.879 130.381 1 170.34 ? O3B AGS 2002 F 1 
HETATM 9 P PA AGS . . . Q 3 130.316 87.982 132.973 1 194.1 ? PA AGS 2002 F 1 
HETATM 10 O O1A AGS . . . Q 3 131.753 88.008 132.508 1 190.16 ? O1A AGS 2002 F 1 
HETATM 11 O O2A AGS . . . Q 3 129.92 89.34 133.504 1 191.36 ? O2A AGS 2002 F 1 
HETATM 12 O O3A AGS . . . Q 3 129.358 87.604 131.732 1 182.24 ? O3A AGS 2002 F 1 
HETATM 13 O O5' AGS . . . Q 3 130.149 86.892 134.151 1 195.84 ? O5' AGS 2002 F 1 
HETATM 14 C C5' AGS . . . Q 3 130.506 85.522 133.951 1 195.78 ? C5' AGS 2002 F 1 
HETATM 15 C C4' AGS . . . Q 3 130.272 84.729 135.232 1 192.24 ? C4' AGS 2002 F 1 
HETATM 16 O O4' AGS . . . Q 3 131.087 85.244 136.288 1 198.78 ? O4' AGS 2002 F 1 
HETATM 17 C C3' AGS . . . Q 3 128.826 84.817 135.691 1 194.13 ? C3' AGS 2002 F 1 
HETATM 18 O O3' AGS . . . Q 3 128.199 83.536 135.587 1 200.81 ? O3' AGS 2002 F 1 
HETATM 19 C C2' AGS . . . Q 3 128.876 85.252 137.142 1 204.35 ? C2' AGS 2002 F 1 
HETATM 20 O O2' AGS . . . Q 3 128.218 84.285 137.964 1 212.41 ? O2' AGS 2002 F 1 
HETATM 21 C C1' AGS . . . Q 3 130.348 85.336 137.508 1 212.41 ? C1' AGS 2002 F 1 
HETATM 22 N N9 AGS . . . Q 3 130.625 86.648 138.14 1 233.53 ? N9 AGS 2002 F 1 
HETATM 23 C C8 AGS . . . Q 3 130.558 87.837 137.514 1 236.55 ? C8 AGS 2002 F 1 
HETATM 24 N N7 AGS . . . Q 3 130.868 88.854 138.356 1 243.46 ? N7 AGS 2002 F 1 
HETATM 25 C C5 AGS . . . Q 3 131.148 88.311 139.555 1 242.78 ? C5 AGS 2002 F 1 
HETATM 26 C C6 AGS . . . Q 3 131.549 88.821 140.887 1 247.89 ? C6 AGS 2002 F 1 
HETATM 27 N N6 AGS . . . Q 3 131.719 90.147 141.105 1 254.39 ? N6 AGS 2002 F 1 
HETATM 28 N N1 AGS . . . Q 3 131.741 87.919 141.875 1 254.18 ? N1 AGS 2002 F 1 
HETATM 29 C C2 AGS . . . Q 3 131.576 86.599 141.668 1 248.52 ? C2 AGS 2002 F 1 
HETATM 30 N N3 AGS . . . Q 3 131.212 86.068 140.486 1 241.95 ? N3 AGS 2002 F 1 
HETATM 31 C C4 AGS . . . Q 3 130.987 86.857 139.408 1 238.82 ? C4 AGS 2002 F 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    61 
_model_server_stats.query_time_ms           242 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#