data_6VVO
#
_model_server_result.job_id            3TbPl5PEt6rKlJ8qwKAMPQ 
_model_server_result.datetime_utc      '2024-11-04 20:13:24' 
_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          6vvo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":402}' 
#
_entry.id    6VVO 
#
_exptl.entry_id    6VVO 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          8 
_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         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            6VVO 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VVO 
_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 
_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
? 8 J N N 
? 8 L N N 
? 8 N N N 
? 8 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 G SG CYS 135 G CYS 135 1_555 G SG CYS 162 G CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
disulf ? disulf2 H SG CYS 135 H CYS 135 1_555 H SG CYS 162 H CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
metalc ? metalc1 A OG1 THR 105 A THR 658 1_555 I MG MG . A MG 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? 
metalc ? metalc2 I MG MG . A MG 1201 1_555 J O3G AGS . A AGS 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
metalc ? metalc3 I MG MG . A MG 1201 1_555 J O1B AGS . A AGS 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? 
metalc ? metalc4 B OG1 THR 83 B THR 83 1_555 K MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? 
metalc ? metalc5 K MG MG . B MG 401 1_555 L O3G AGS . B AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc6 K MG MG . B MG 401 1_555 L O1B AGS . B AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc7 C OG1 THR 67 C THR 67 1_555 M MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? 
metalc ? metalc8 M MG MG . C MG 401 1_555 N O3G AGS . C AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? 
metalc ? metalc9 M MG MG . C MG 401 1_555 N O1B AGS . C AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? 
metalc ? metalc10 D OG1 THR 85 D THR 85 1_555 O MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc11 O MG MG . D MG 401 1_555 P O3G AGS . D AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc12 O MG MG . D MG 401 1_555 P O2B AGS . D AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? 
#
_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 45 n n 
PG O2G AGS sing 46 n n 
PG O3G AGS sing 47 n n 
PG O3B AGS sing 48 n n 
PB O1B AGS doub 49 n n 
PB O2B AGS sing 50 n n 
PB O3B AGS sing 51 n n 
PB O3A AGS sing 52 n n 
PA O1A AGS doub 53 n n 
PA O2A AGS sing 54 n n 
PA O3A AGS sing 55 n n 
PA O5' AGS sing 56 n n 
O5' C5' AGS sing 57 n n 
C5' C4' AGS sing 58 n n 
C4' O4' AGS sing 59 n n 
C4' C3' AGS sing 60 n n 
O4' C1' AGS sing 61 n n 
C3' O3' AGS sing 62 n n 
C3' C2' AGS sing 63 n n 
C2' O2' AGS sing 64 n n 
C2' C1' AGS sing 65 n n 
C1' N9 AGS sing 66 n n 
N9 C8 AGS sing 67 n y 
N9 C4 AGS sing 68 n y 
C8 N7 AGS doub 69 n y 
N7 C5 AGS sing 70 n y 
C5 C6 AGS sing 71 n y 
C5 C4 AGS doub 72 n y 
C6 N6 AGS sing 73 n n 
C6 N1 AGS doub 74 n y 
N1 C2 AGS sing 75 n y 
C2 N3 AGS doub 76 n y 
N3 C4 AGS sing 77 n y 
O2G HOG2 AGS sing 78 n n 
O3G H21 AGS sing 79 n n 
O2B HOB2 AGS sing 80 n n 
O2A HOA2 AGS sing 81 n n 
C5' "H5'1" AGS sing 82 n n 
C5' "H5'2" AGS sing 83 n n 
C4' H4' AGS sing 84 n n 
C3' H3' AGS sing 85 n n 
O3' HO3' AGS sing 86 n n 
C2' H2' AGS sing 87 n n 
O2' HO2' AGS sing 88 n n 
C1' H1' AGS sing 89 n n 
C8 H8 AGS sing 90 n n 
N6 HN61 AGS sing 91 n n 
N6 HN62 AGS sing 92 n n 
C2 H2 AGS sing 93 n n 
#
_atom_sites.entry_id                     6VVO 
_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
I 7 MG A 1 1201 2010 MG MG . 
J 8 AGS A 1 1202 2000 AGS AGS . 
K 7 MG B 1 401 2010 MG MG . 
L 8 AGS B 1 402 2000 AGS AGS . 
M 7 MG C 1 401 2010 MG MG . 
N 8 AGS C 1 402 2000 AGS AGS . 
O 7 MG D 1 401 2010 MG MG . 
P 8 AGS D 1 402 2000 AGS AGS . 
Q 9 ADP E 1 2000 2000 ADP ADP . 
#
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 . . . L 8 135.01 156.514 129.808 1 47.05 ? PG AGS 402 B 1 
HETATM 2 S S1G AGS . . . L 8 135.873 155.265 131.011 1 47.05 ? S1G AGS 402 B 1 
HETATM 3 O O2G AGS . . . L 8 133.506 156.574 130.17 1 47.05 ? O2G AGS 402 B 1 
HETATM 4 O O3G AGS . . . L 8 135.207 156.038 128.345 1 47.05 ? O3G AGS 402 B 1 
HETATM 5 P PB AGS . . . L 8 136.644 158.439 128.874 1 47.05 ? PB AGS 402 B 1 
HETATM 6 O O1B AGS . . . L 8 136.278 157.923 127.549 1 47.05 ? O1B AGS 402 B 1 
HETATM 7 O O2B AGS . . . L 8 138.019 158.075 129.418 1 47.05 ? O2B AGS 402 B 1 
HETATM 8 O O3B AGS . . . L 8 135.595 157.942 129.92 1 47.05 ? O3B AGS 402 B 1 
HETATM 9 P PA AGS . . . L 8 136.155 160.789 127.582 1 47.05 ? PA AGS 402 B 1 
HETATM 10 O O1A AGS . . . L 8 134.98 160.22 126.943 1 47.05 ? O1A AGS 402 B 1 
HETATM 11 O O2A AGS . . . L 8 137.405 161.002 126.74 1 47.05 ? O2A AGS 402 B 1 
HETATM 12 O O3A AGS . . . L 8 136.551 159.998 128.875 1 47.05 ? O3A AGS 402 B 1 
HETATM 13 O O5' AGS . . . L 8 135.635 162.142 128.161 1 47.05 ? O5' AGS 402 B 1 
HETATM 14 C C5' AGS . . . L 8 134.353 162.627 127.736 1 47.05 ? C5' AGS 402 B 1 
HETATM 15 C C4' AGS . . . L 8 134.392 164.128 127.698 1 47.05 ? C4' AGS 402 B 1 
HETATM 16 O O4' AGS . . . L 8 134.889 164.595 128.961 1 47.05 ? O4' AGS 402 B 1 
HETATM 17 C C3' AGS . . . L 8 135.304 164.724 126.635 1 47.05 ? C3' AGS 402 B 1 
HETATM 18 O O3' AGS . . . L 8 134.555 165.053 125.473 1 47.05 ? O3' AGS 402 B 1 
HETATM 19 C C2' AGS . . . L 8 135.861 165.984 127.298 1 47.05 ? C2' AGS 402 B 1 
HETATM 20 O O2' AGS . . . L 8 135.063 167.124 127.015 1 47.05 ? O2' AGS 402 B 1 
HETATM 21 C C1' AGS . . . L 8 135.78 165.673 128.789 1 47.05 ? C1' AGS 402 B 1 
HETATM 22 N N9 AGS . . . L 8 137.048 165.283 129.374 1 47.05 ? N9 AGS 402 B 1 
HETATM 23 C C8 AGS . . . L 8 137.324 164.099 129.994 1 47.05 ? C8 AGS 402 B 1 
HETATM 24 N N7 AGS . . . L 8 138.552 164.004 130.444 1 47.05 ? N7 AGS 402 B 1 
HETATM 25 C C5 AGS . . . L 8 139.115 165.219 130.103 1 47.05 ? C5 AGS 402 B 1 
HETATM 26 C C6 AGS . . . L 8 140.401 165.753 130.303 1 47.05 ? C6 AGS 402 B 1 
HETATM 27 N N6 AGS . . . L 8 141.386 165.098 130.92 1 47.05 ? N6 AGS 402 B 1 
HETATM 28 N N1 AGS . . . L 8 140.642 166.995 129.838 1 47.05 ? N1 AGS 402 B 1 
HETATM 29 C C2 AGS . . . L 8 139.66 167.652 129.218 1 47.05 ? C2 AGS 402 B 1 
HETATM 30 N N3 AGS . . . L 8 138.411 167.253 128.972 1 47.05 ? N3 AGS 402 B 1 
HETATM 31 C C4 AGS . . . L 8 138.205 166.02 129.44 1 47.05 ? C4 AGS 402 B 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    34 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           31 
#