data_4JSP
#
_model_server_result.job_id            TLmdKBkSEsig09uGk4HvVg 
_model_server_result.datetime_utc      '2024-11-20 04:25:12' 
_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          4jsp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":3000}' 
#
_entry.id    4JSP 
#
_exptl.entry_id    4JSP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    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         90 
_cell.entry_id            4JSP 
_cell.length_a            139.4 
_cell.length_b            163.2 
_cell.length_c            207.8 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4JSP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
? dimeric 2 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,F,G 1 1 
C,D,H,I,J 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
? 3 E N N 
? 3 H 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 OD1 ASN 968 B ASN 2343 1_555 F MG MG . B MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? 
metalc ? metalc2 E O2G AGS . B AGS 3000 1_555 F MG MG . B MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? 
metalc ? metalc3 E O1A AGS . B AGS 3000 1_555 F MG MG . B MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? 
metalc ? metalc4 E O3G AGS . B AGS 3000 1_555 G MG MG . B MG 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? 
metalc ? metalc5 H O2G AGS . A AGS 3000 1_555 I MG MG . A MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.848 ? 
metalc ? metalc6 H O1A AGS . A AGS 3000 1_555 I MG MG . A MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? 
metalc ? metalc7 H O3G AGS . A AGS 3000 1_555 J MG MG . A MG 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? 
metalc ? metalc8 H O1B AGS . A AGS 3000 1_555 J MG MG . A MG 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? 
#
_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                     4JSP 
_atom_sites.fract_transf_matrix[1][1]    0.007174 
_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]    0.006127 
_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]    0.004812 
_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
E 3 AGS B 1 3000 3000 AGS AGS . 
F 4 MG B 1 3001 3001 MG MG . 
G 4 MG B 1 3002 3002 MG MG . 
H 3 AGS A 1 3000 3000 AGS AGS . 
I 4 MG A 1 3001 3001 MG MG . 
J 4 MG A 1 3002 3002 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 . . . H 3 49.914 -3.534 -40.037 1 85.86 ? PG AGS 3000 A 1 
HETATM 2 S S1G AGS . . . H 3 48.423 -4.506 -38.932 1 84.64 ? S1G AGS 3000 A 1 
HETATM 3 O O2G AGS . . . H 3 50.994 -4.6 -40.622 1 78.31 ? O2G AGS 3000 A 1 
HETATM 4 O O3G AGS . . . H 3 50.631 -2.568 -39.141 1 80.89 ? O3G AGS 3000 A 1 
HETATM 5 P PB AGS . . . H 3 49.155 -1.136 -41.325 1 80.84 ? PB AGS 3000 A 1 
HETATM 6 O O1B AGS . . . H 3 50.555 -0.568 -41.176 1 81.03 ? O1B AGS 3000 A 1 
HETATM 7 O O2B AGS . . . H 3 48.052 -0.728 -40.362 1 81.68 ? O2B AGS 3000 A 1 
HETATM 8 O O3B AGS . . . H 3 49.244 -2.756 -41.301 1 79 ? O3B AGS 3000 A 1 
HETATM 9 P PA AGS . . . H 3 49.485 -1.519 -44.044 1 72.67 ? PA AGS 3000 A 1 
HETATM 10 O O1A AGS . . . H 3 50.629 -2.335 -43.479 1 71.54 ? O1A AGS 3000 A 1 
HETATM 11 O O2A AGS . . . H 3 49.764 -0.498 -45.111 1 72.12 ? O2A AGS 3000 A 1 
HETATM 12 O O3A AGS . . . H 3 48.705 -0.81 -42.832 1 75.78 ? O3A AGS 3000 A 1 
HETATM 13 O O5' AGS . . . H 3 48.359 -2.529 -44.586 1 69.57 ? O5' AGS 3000 A 1 
HETATM 14 C C5' AGS . . . H 3 47.045 -2.067 -44.897 1 64.86 ? C5' AGS 3000 A 1 
HETATM 15 C C4' AGS . . . H 3 46.742 -2.419 -46.341 1 61.23 ? C4' AGS 3000 A 1 
HETATM 16 O O4' AGS . . . H 3 47.266 -1.398 -47.178 1 59.08 ? O4' AGS 3000 A 1 
HETATM 17 C C3' AGS . . . H 3 47.43 -3.715 -46.741 1 60.66 ? C3' AGS 3000 A 1 
HETATM 18 O O3' AGS . . . H 3 46.448 -4.726 -46.978 1 62.29 ? O3' AGS 3000 A 1 
HETATM 19 C C2' AGS . . . H 3 48.204 -3.417 -48.003 1 58.82 ? C2' AGS 3000 A 1 
HETATM 20 O O2' AGS . . . H 3 47.702 -4.192 -49.092 1 59.14 ? O2' AGS 3000 A 1 
HETATM 21 C C1' AGS . . . H 3 47.913 -1.969 -48.316 1 57.46 ? C1' AGS 3000 A 1 
HETATM 22 N N9 AGS . . . H 3 49.154 -1.235 -48.665 1 54.77 ? N9 AGS 3000 A 1 
HETATM 23 C C8 AGS . . . H 3 50.139 -0.866 -47.83 1 53.86 ? C8 AGS 3000 A 1 
HETATM 24 N N7 AGS . . . H 3 51.108 -0.188 -48.496 1 53.19 ? N7 AGS 3000 A 1 
HETATM 25 C C5 AGS . . . H 3 50.744 -0.121 -49.787 1 52.94 ? C5 AGS 3000 A 1 
HETATM 26 C C6 AGS . . . H 3 51.308 0.44 -51.041 1 53.19 ? C6 AGS 3000 A 1 
HETATM 27 N N6 AGS . . . H 3 52.501 1.088 -51.039 1 53.5 ? N6 AGS 3000 A 1 
HETATM 28 N N1 AGS . . . H 3 50.596 0.28 -52.187 1 52.17 ? N1 AGS 3000 A 1 
HETATM 29 C C2 AGS . . . H 3 49.412 -0.362 -52.206 1 51.84 ? C2 AGS 3000 A 1 
HETATM 30 N N3 AGS . . . H 3 48.853 -0.897 -51.107 1 52.36 ? N3 AGS 3000 A 1 
HETATM 31 C C4 AGS . . . H 3 49.454 -0.812 -49.894 1 53.14 ? C4 AGS 3000 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    34 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           31 
#