data_2ZRA
#
_model_server_result.job_id            zQNQqWcsSukFisnYKBj6yg 
_model_server_result.datetime_utc      '2024-12-05 15:18:27' 
_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          2zra 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":500}' 
#
_entry.id    2ZRA 
#
_exptl.entry_id    2ZRA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    1 
_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            2ZRA 
_cell.length_a            107.089 
_cell.length_b            107.089 
_cell.length_c            72.99 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2ZRA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_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                     2ZRA 
_atom_sites.fract_transf_matrix[1][1]    0.009338 
_atom_sites.fract_transf_matrix[1][2]    0.005391 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010783 
_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]    0.013701 
_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
B 2 AGS A 1 500 500 AGS SAP . 
C 3 GOL A 1 501 501 GOL GOL . 
D 3 GOL A 1 502 502 GOL GOL . 
E 3 GOL A 1 503 503 GOL GOL . 
F 3 GOL A 1 504 504 GOL GOL . 
G 4 CL A 1 505 505 CL CL . 
H 5 HOH A 1 506 1 HOH HOH . 
H 5 HOH A 2 507 2 HOH HOH . 
H 5 HOH A 3 508 3 HOH HOH . 
H 5 HOH A 4 509 6 HOH HOH . 
H 5 HOH A 5 510 8 HOH HOH . 
H 5 HOH A 6 511 9 HOH HOH . 
H 5 HOH A 7 512 10 HOH HOH . 
H 5 HOH A 8 513 11 HOH HOH . 
H 5 HOH A 9 514 14 HOH HOH . 
H 5 HOH A 10 515 18 HOH HOH . 
H 5 HOH A 11 516 19 HOH HOH . 
H 5 HOH A 12 517 26 HOH HOH . 
H 5 HOH A 13 518 27 HOH HOH . 
H 5 HOH A 14 519 29 HOH HOH . 
H 5 HOH A 15 520 31 HOH HOH . 
H 5 HOH A 16 521 33 HOH HOH . 
H 5 HOH A 17 522 38 HOH HOH . 
H 5 HOH A 18 523 39 HOH HOH . 
H 5 HOH A 19 524 41 HOH HOH . 
H 5 HOH A 20 525 48 HOH HOH . 
H 5 HOH A 21 526 58 HOH HOH . 
H 5 HOH A 22 527 59 HOH HOH . 
H 5 HOH A 23 528 60 HOH HOH . 
H 5 HOH A 24 529 61 HOH HOH . 
H 5 HOH A 25 530 62 HOH HOH . 
H 5 HOH A 26 531 63 HOH HOH . 
H 5 HOH A 27 532 64 HOH HOH . 
H 5 HOH A 28 533 65 HOH HOH . 
H 5 HOH A 29 534 66 HOH HOH . 
H 5 HOH A 30 535 67 HOH HOH . 
H 5 HOH A 31 536 68 HOH HOH . 
H 5 HOH A 32 537 69 HOH HOH . 
#
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 . . . B 2 3.864 24.184 8.49 0.8 82.08 ? PG AGS 500 A 1 
HETATM 2 S S1G AGS . . . B 2 2.43 25.33 9.092 0.8 82.08 ? S1G AGS 500 A 1 
HETATM 3 O O2G AGS . . . B 2 3.242 23.771 7.211 0.8 82.08 ? O2G AGS 500 A 1 
HETATM 4 O O3G AGS . . . B 2 3.951 23.345 9.703 0.8 82.08 ? O3G AGS 500 A 1 
HETATM 5 P PB AGS . . . B 2 6.453 25.211 8.749 0.8 82.08 ? PB AGS 500 A 1 
HETATM 6 O O1B AGS . . . B 2 6.948 24.881 7.396 0.8 82.08 ? O1B AGS 500 A 1 
HETATM 7 O O2B AGS . . . B 2 6.239 24.241 9.838 0.8 82.08 ? O2B AGS 500 A 1 
HETATM 8 O O3B AGS . . . B 2 4.904 25.405 8.345 0.8 82.08 ? O3B AGS 500 A 1 
HETATM 9 P PA AGS . . . B 2 5.875 27.267 10.516 0.8 82.08 ? PA AGS 500 A 1 
HETATM 10 O O1A AGS . . . B 2 5.422 28.663 10.348 0.8 82.08 ? O1A AGS 500 A 1 
HETATM 11 O O2A AGS . . . B 2 4.891 26.254 10.954 0.8 82.08 ? O2A AGS 500 A 1 
HETATM 12 O O3A AGS . . . B 2 6.569 26.766 9.154 0.8 82.08 ? O3A AGS 500 A 1 
HETATM 13 O O5' AGS . . . B 2 7.083 27.23 11.576 0.8 82.08 ? O5' AGS 500 A 1 
HETATM 14 C C5' AGS . . . B 2 6.914 26.461 12.772 0.8 82.08 ? C5' AGS 500 A 1 
HETATM 15 C C4' AGS . . . B 2 7.359 27.247 14.007 0.8 82.08 ? C4' AGS 500 A 1 
HETATM 16 O O4' AGS . . . B 2 7.047 28.651 13.873 0.8 82.08 ? O4' AGS 500 A 1 
HETATM 17 C C3' AGS . . . B 2 6.573 26.768 15.22 0.8 82.08 ? C3' AGS 500 A 1 
HETATM 18 O O3' AGS . . . B 2 7.236 25.669 15.861 0.8 82.08 ? O3' AGS 500 A 1 
HETATM 19 C C2' AGS . . . B 2 6.667 28.01 16.104 0.8 82.08 ? C2' AGS 500 A 1 
HETATM 20 O O2' AGS . . . B 2 7.982 28.168 16.633 0.8 82.08 ? O2' AGS 500 A 1 
HETATM 21 C C1' AGS . . . B 2 6.382 29.092 15.067 0.8 82.08 ? C1' AGS 500 A 1 
HETATM 22 N N9 AGS . . . B 2 4.937 29.201 14.75 0.8 82.08 ? N9 AGS 500 A 1 
HETATM 23 C C8 AGS . . . B 2 4.36 28.883 13.585 0.8 82.08 ? C8 AGS 500 A 1 
HETATM 24 N N7 AGS . . . B 2 3.073 29.175 13.63 0.8 82.08 ? N7 AGS 500 A 1 
HETATM 25 C C5 AGS . . . B 2 2.807 29.685 14.828 0.8 82.08 ? C5 AGS 500 A 1 
HETATM 26 C C6 AGS . . . B 2 1.661 30.159 15.44 0.8 82.08 ? C6 AGS 500 A 1 
HETATM 27 N N6 AGS . . . B 2 0.496 30.186 14.795 0.8 82.08 ? N6 AGS 500 A 1 
HETATM 28 N N1 AGS . . . B 2 1.738 30.615 16.708 0.8 82.08 ? N1 AGS 500 A 1 
HETATM 29 C C2 AGS . . . B 2 2.891 30.606 17.356 0.8 82.08 ? C2 AGS 500 A 1 
HETATM 30 N N3 AGS . . . B 2 4 30.163 16.806 0.8 82.08 ? N3 AGS 500 A 1 
HETATM 31 C C4 AGS . . . B 2 3.99 29.686 15.538 0.8 82.08 ? C4 AGS 500 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           507 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           31 
#