data_6CVL
#
_model_server_result.job_id            E7x1rlnGahAyEbOgYu-VLQ 
_model_server_result.datetime_utc      '2025-08-30 20:10:48' 
_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          6cvl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":404}' 
#
_entry.id    6CVL 
#
_exptl.entry_id    6CVL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    2 
_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         120 
_cell.entry_id            6CVL 
_cell.length_a            107.96 
_cell.length_b            107.96 
_cell.length_c            354.52 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6CVL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_pdbx_struct_assembly.details               author_and_software_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 
_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
? 5 H N N 
? 5 L 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
metalc ? metalc1 A SG CYS 165 C CYS 164 1_555 G HG HG . C HG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.029 ? 
metalc ? metalc2 F HG HG . C HG 401 5_545 D SG CYS 211 D CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.905 ? 
#
_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                     6CVL 
_atom_sites.fract_transf_matrix[1][1]    0.009263 
_atom_sites.fract_transf_matrix[1][2]    0.005348 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010696 
_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]    0.002821 
_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
F 4 HG C 1 401 55 HG HG . 
G 4 HG C 1 402 60 HG HG . 
H 5 AGS C 1 403 1002 AGS AGS . 
I 4 HG D 1 401 58 HG HG . 
J 6 IOD D 1 402 18 IOD IOD . 
K 6 IOD D 1 403 28 IOD IOD . 
L 5 AGS D 1 404 1001 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 . . . L 5 23.825 -43.69 47.522 1 65.7 ? PG AGS 404 D 1 
HETATM 2 S S1G AGS . . . L 5 22.493 -44.001 49.051 1 67.4 ? S1G AGS 404 D 1 
HETATM 3 O O2G AGS . . . L 5 23.497 -44.712 46.326 1 65.06 ? O2G AGS 404 D 1 
HETATM 4 O O3G AGS . . . L 5 23.791 -42.264 47.127 1 64.67 ? O3G AGS 404 D 1 
HETATM 5 P PB AGS . . . L 5 26.615 -43.61 47.58 1 59.38 ? PB AGS 404 D 1 
HETATM 6 O O1B AGS . . . L 5 26.769 -42.139 47.826 1 58.5 ? O1B AGS 404 D 1 
HETATM 7 O O2B AGS . . . L 5 27.753 -44.329 48.234 1 59.25 ? O2B AGS 404 D 1 
HETATM 8 O O3B AGS . . . L 5 25.223 -44.106 48.18 1 61.47 ? O3B AGS 404 D 1 
HETATM 9 P PA AGS . . . L 5 27.826 -43.231 45.179 1 57.68 ? PA AGS 404 D 1 
HETATM 10 O O1A AGS . . . L 5 29.132 -43.552 45.861 1 56.58 ? O1A AGS 404 D 1 
HETATM 11 O O2A AGS . . . L 5 27.786 -43.779 43.777 1 56.82 ? O2A AGS 404 D 1 
HETATM 12 O O3A AGS . . . L 5 26.651 -43.915 46.015 1 57.16 ? O3A AGS 404 D 1 
HETATM 13 O O5' AGS . . . L 5 27.572 -41.646 45.136 1 61.26 ? O5' AGS 404 D 1 
HETATM 14 C C5' AGS . . . L 5 28.663 -40.747 45.241 1 65.17 ? C5' AGS 404 D 1 
HETATM 15 C C4' AGS . . . L 5 28.698 -39.784 44.066 1 65.42 ? C4' AGS 404 D 1 
HETATM 16 O O4' AGS . . . L 5 29.364 -40.394 42.955 1 64.53 ? O4' AGS 404 D 1 
HETATM 17 C C3' AGS . . . L 5 27.331 -39.338 43.557 1 66.58 ? C3' AGS 404 D 1 
HETATM 18 O O3' AGS . . . L 5 27.148 -37.945 43.801 1 67.57 ? O3' AGS 404 D 1 
HETATM 19 C C2' AGS . . . L 5 27.342 -39.603 42.06 1 66.33 ? C2' AGS 404 D 1 
HETATM 20 O O2' AGS . . . L 5 26.894 -38.461 41.338 1 68.43 ? O2' AGS 404 D 1 
HETATM 21 C C1' AGS . . . L 5 28.797 -39.91 41.739 1 65.05 ? C1' AGS 404 D 1 
HETATM 22 N N9 AGS . . . L 5 28.932 -40.931 40.684 1 65.1 ? N9 AGS 404 D 1 
HETATM 23 C C8 AGS . . . L 5 28.86 -42.258 40.879 1 67.85 ? C8 AGS 404 D 1 
HETATM 24 N N7 AGS . . . L 5 29.033 -42.917 39.705 1 70.09 ? N7 AGS 404 D 1 
HETATM 25 C C5 AGS . . . L 5 29.226 -42.001 38.735 1 66.45 ? C5 AGS 404 D 1 
HETATM 26 C C6 AGS . . . L 5 29.469 -42.021 37.27 1 65.09 ? C6 AGS 404 D 1 
HETATM 27 N N6 AGS . . . L 5 29.547 -43.177 36.567 1 64.59 ? N6 AGS 404 D 1 
HETATM 28 N N1 AGS . . . L 5 29.611 -40.837 36.642 1 66.62 ? N1 AGS 404 D 1 
HETATM 29 C C2 AGS . . . L 5 29.543 -39.668 37.304 1 68.12 ? C2 AGS 404 D 1 
HETATM 30 N N3 AGS . . . L 5 29.327 -39.58 38.632 1 65.62 ? N3 AGS 404 D 1 
HETATM 31 C C4 AGS . . . L 5 29.162 -40.689 39.391 1 65.68 ? C4 AGS 404 D 1 
HETATM 32 H HOG2 AGS . . . L 5 22.641 -45.161 46.295 1 78.03 ? HOG2 AGS 404 D 1 
HETATM 33 H "H5'1" AGS . . . L 5 28.578 -40.181 46.171 1 78.14 ? "H5'1" AGS 404 D 1 
HETATM 34 H "H5'2" AGS . . . L 5 29.597 -41.312 45.276 1 78.14 ? "H5'2" AGS 404 D 1 
HETATM 35 H H4' AGS . . . L 5 29.226 -38.9 44.45 1 78.39 ? H4' AGS 404 D 1 
HETATM 36 H H3' AGS . . . L 5 26.514 -39.871 44.063 1 79.55 ? H3' AGS 404 D 1 
HETATM 37 H H2' AGS . . . L 5 26.666 -40.422 41.776 1 79.3 ? H2' AGS 404 D 1 
HETATM 38 H HO2' AGS . . . L 5 25.976 -38.27 41.573 1 81.4 ? HO2' AGS 404 D 1 
HETATM 39 H H1' AGS . . . L 5 29.29 -39.003 41.363 1 78.02 ? H1' AGS 404 D 1 
HETATM 40 H H8 AGS . . . L 5 28.688 -42.735 41.836 1 80.82 ? H8 AGS 404 D 1 
HETATM 41 H HN61 AGS . . . L 5 29.714 -43.153 35.571 1 77.56 ? HN61 AGS 404 D 1 
HETATM 42 H HN62 AGS . . . L 5 29.438 -44.064 37.039 1 77.56 ? HN62 AGS 404 D 1 
HETATM 43 H H2 AGS . . . L 5 29.667 -38.751 36.742 1 81.09 ? H2 AGS 404 D 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    52 
_model_server_stats.query_time_ms           426 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           43 
#