data_6QV2
#
_model_server_result.job_id            l1Y51b_IlYncze_kFbRtxQ 
_model_server_result.datetime_utc      '2024-11-08 03:54:45' 
_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          6qv2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":600}' 
#
_entry.id    6QV2 
#
_exptl.entry_id    6QV2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         83.18 
_cell.angle_beta          73 
_cell.angle_gamma         67.37 
_cell.entry_id            6QV2 
_cell.length_a            88.6 
_cell.length_b            113.07 
_cell.length_c            126.89 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6QV2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? trimeric 3 author_defined_assembly 1 
? trimeric 3 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,G,H,I,J 1 1 
C,D,F,K,L,M,N 2 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
? 4 G N N 
? 4 I N N 
? 4 K N N 
? 4 M 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 E SG CYS 25 E CYS 22 1_555 E SG CYS 99 E CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf2 E SG CYS 53 E CYS 50 1_555 E SG CYS 112 E CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf3 F SG CYS 25 F CYS 22 1_555 F SG CYS 99 F CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf4 F SG CYS 53 F CYS 50 1_555 F SG CYS 112 F CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc1 A OG SER 383 A SER 373 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
metalc ? metalc2 A OE1 GLN 424 A GLN 414 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? 
metalc ? metalc3 G O2G AGS . A AGS 600 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? 
metalc ? metalc4 G O2B AGS . A AGS 600 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc5 B OG1 THR 395 B THR 395 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? 
metalc ? metalc6 I O3G AGS . B AGS 600 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? 
metalc ? metalc7 I O2B AGS . B AGS 600 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? 
metalc ? metalc8 I O3A AGS . B AGS 600 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? 
metalc ? metalc9 C OG SER 383 C SER 373 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc10 C OE1 GLN 424 C GLN 414 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? 
metalc ? metalc11 K O2G AGS . C AGS 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? 
metalc ? metalc12 K O2B AGS . C AGS 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? 
metalc ? metalc13 D OG1 THR 395 D THR 395 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
metalc ? metalc14 M O1B AGS . D AGS 600 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? 
metalc ? metalc15 M O2B AGS . D AGS 600 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc16 M O1A AGS . D AGS 600 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc17 M O3A AGS . D AGS 600 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? 
#
_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                     6QV2 
_atom_sites.fract_transf_matrix[1][1]    0.011287 
_atom_sites.fract_transf_matrix[1][2]    -0.004705 
_atom_sites.fract_transf_matrix[1][3]    -0.003417 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009582 
_atom_sites.fract_transf_matrix[2][3]    -0.000068 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.008241 
_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 4 AGS A 1 600 600 AGS AGS . 
H 5 MG A 1 601 601 MG MG . 
I 4 AGS B 1 600 600 AGS AGS . 
J 5 MG B 1 601 601 MG MG . 
K 4 AGS C 1 600 600 AGS AGS . 
L 5 MG C 1 601 601 MG MG . 
M 4 AGS D 1 600 600 AGS AGS . 
N 5 MG D 1 601 601 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 AGS . . . K 4 9.508 10.334 30.956 1 210.71 ? PG AGS 600 C 1 
HETATM 2 S S1G AGS . . . K 4 9.621 8.823 32.102 1 211.76 ? S1G AGS 600 C 1 
HETATM 3 O O2G AGS . . . K 4 10.151 11.649 31.526 1 212.17 ? O2G AGS 600 C 1 
HETATM 4 O O3G AGS . . . K 4 10.208 10.329 29.564 1 206.03 ? O3G AGS 600 C 1 
HETATM 5 P PB AGS . . . K 4 6.867 11.36 31.57 1 218.41 ? PB AGS 600 C 1 
HETATM 6 O O1B AGS . . . K 4 5.92 10.375 32.134 1 221.05 ? O1B AGS 600 C 1 
HETATM 7 O O2B AGS . . . K 4 7.58 12.257 32.578 1 219.9 ? O2B AGS 600 C 1 
HETATM 8 O O3B AGS . . . K 4 7.991 10.659 30.689 1 213.36 ? O3B AGS 600 C 1 
HETATM 9 P PA AGS . . . K 4 5.475 13.742 30.61 1 221.3 ? PA AGS 600 C 1 
HETATM 10 O O1A AGS . . . K 4 4.759 13.91 31.891 1 225.52 ? O1A AGS 600 C 1 
HETATM 11 O O2A AGS . . . K 4 6.557 14.779 30.333 1 219.55 ? O2A AGS 600 C 1 
HETATM 12 O O3A AGS . . . K 4 6.163 12.31 30.506 1 218.2 ? O3A AGS 600 C 1 
HETATM 13 O O5' AGS . . . K 4 4.477 13.799 29.364 1 220.74 ? O5' AGS 600 C 1 
HETATM 14 C C5' AGS . . . K 4 3.334 12.932 29.214 1 222.88 ? C5' AGS 600 C 1 
HETATM 15 C C4' AGS . . . K 4 2.657 13.223 27.896 1 219.93 ? C4' AGS 600 C 1 
HETATM 16 O O4' AGS . . . K 4 2.512 14.65 27.714 1 219.39 ? O4' AGS 600 C 1 
HETATM 17 C C3' AGS . . . K 4 3.346 12.687 26.638 1 206.75 ? C3' AGS 600 C 1 
HETATM 18 O O3' AGS . . . K 4 2.41 12.082 25.751 1 203.52 ? O3' AGS 600 C 1 
HETATM 19 C C2' AGS . . . K 4 4.023 13.931 26.048 1 197.74 ? C2' AGS 600 C 1 
HETATM 20 O O2' AGS . . . K 4 4.15 13.88 24.631 1 187.03 ? O2' AGS 600 C 1 
HETATM 21 C C1' AGS . . . K 4 3.061 15.043 26.471 1 205.81 ? C1' AGS 600 C 1 
HETATM 22 N N9 AGS . . . K 4 3.692 16.351 26.635 1 203.88 ? N9 AGS 600 C 1 
HETATM 23 C C8 AGS . . . K 4 4.574 16.731 27.614 1 208.98 ? C8 AGS 600 C 1 
HETATM 24 N N7 AGS . . . K 4 5.024 17.956 27.485 1 205.55 ? N7 AGS 600 C 1 
HETATM 25 C C5 AGS . . . K 4 4.391 18.419 26.342 1 198.05 ? C5 AGS 600 C 1 
HETATM 26 C C6 AGS . . . K 4 4.443 19.652 25.658 1 194.64 ? C6 AGS 600 C 1 
HETATM 27 N N6 AGS . . . K 4 5.196 20.686 26.048 1 194.15 ? N6 AGS 600 C 1 
HETATM 28 N N1 AGS . . . K 4 3.683 19.789 24.547 1 195.71 ? N1 AGS 600 C 1 
HETATM 29 C C2 AGS . . . K 4 2.924 18.76 24.153 1 196.26 ? C2 AGS 600 C 1 
HETATM 30 N N3 AGS . . . K 4 2.796 17.552 24.714 1 195.87 ? N3 AGS 600 C 1 
HETATM 31 C C4 AGS . . . K 4 3.56 17.443 25.811 1 197.04 ? C4 AGS 600 C 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    59 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          51 
_model_server_stats.element_count           31 
#