data_4DN5
#
_model_server_result.job_id            QJkmwv0ibtLRDbhiQ7hhYA 
_model_server_result.datetime_utc      '2024-10-22 00:36:44' 
_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          4dn5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":1003}' 
#
_entry.id    4DN5 
#
_exptl.entry_id    4DN5 
_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         90 
_cell.entry_id            4DN5 
_cell.length_a            85.06 
_cell.length_b            85.06 
_cell.length_c            115.4 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4DN5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,I,J,N 1 1 
B,K,L,M,O 2 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 3 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 J N N 
? 5 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
metalc ? metalc1 A OD1 ASN 196 A ASN 520 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc2 A OD2 ASP 210 A ASP 534 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
metalc ? metalc3 C MG MG . A MG 1001 1_555 J O1A AGS . A AGS 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.825 ? 
metalc ? metalc4 C MG MG . A MG 1001 1_555 J O2B AGS . A AGS 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc5 C MG MG . A MG 1001 1_555 N O HOH . A HOH 1118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? 
metalc ? metalc6 C MG MG . A MG 1001 1_555 N O HOH . A HOH 1119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? 
metalc ? metalc7 B OD1 ASN 196 B ASN 520 1_555 K MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc8 B OD1 ASP 210 B ASP 534 1_555 K MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? 
metalc ? metalc9 K MG MG . B MG 1001 1_555 M O2A AGS . B AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? 
metalc ? metalc10 K MG MG . B MG 1001 1_555 M O2B AGS . B AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? 
metalc ? metalc11 K MG MG . B MG 1001 1_555 O O HOH . B HOH 1108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc12 K MG MG . B MG 1001 1_555 O O HOH . B HOH 1109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? 
#
_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                     4DN5 
_atom_sites.fract_transf_matrix[1][1]    0.011756 
_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]    0.011756 
_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]    0.008666 
_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
C 2 MG A 1 1001 1001 MG MG . 
D 3 GOL A 1 1002 1 GOL GOL . 
E 4 EDO A 1 1003 2 EDO EDO . 
F 4 EDO A 1 1004 3 EDO EDO . 
G 4 EDO A 1 1005 4 EDO EDO . 
H 4 EDO A 1 1006 5 EDO EDO . 
I 4 EDO A 1 1007 7 EDO EDO . 
J 5 AGS A 1 1008 1 AGS AGS . 
K 2 MG B 1 1001 1001 MG MG . 
L 4 EDO B 1 1002 6 EDO EDO . 
M 5 AGS B 1 1003 1 AGS AGS . 
N 6 HOH A 1 1101 1 HOH HOH . 
N 6 HOH A 2 1102 2 HOH HOH . 
N 6 HOH A 3 1103 7 HOH HOH . 
N 6 HOH A 4 1104 9 HOH HOH . 
N 6 HOH A 5 1105 10 HOH HOH . 
N 6 HOH A 6 1106 11 HOH HOH . 
N 6 HOH A 7 1107 12 HOH HOH . 
N 6 HOH A 8 1108 14 HOH HOH . 
N 6 HOH A 9 1109 15 HOH HOH . 
N 6 HOH A 10 1110 18 HOH HOH . 
N 6 HOH A 11 1111 19 HOH HOH . 
N 6 HOH A 12 1112 20 HOH HOH . 
N 6 HOH A 13 1113 21 HOH HOH . 
N 6 HOH A 14 1114 22 HOH HOH . 
N 6 HOH A 15 1115 23 HOH HOH . 
N 6 HOH A 16 1116 24 HOH HOH . 
N 6 HOH A 17 1117 25 HOH HOH . 
N 6 HOH A 18 1118 28 HOH HOH . 
N 6 HOH A 19 1119 29 HOH HOH . 
N 6 HOH A 20 1120 30 HOH HOH . 
N 6 HOH A 21 1121 31 HOH HOH . 
N 6 HOH A 22 1122 32 HOH HOH . 
N 6 HOH A 23 1123 33 HOH HOH . 
N 6 HOH A 24 1124 34 HOH HOH . 
N 6 HOH A 25 1125 37 HOH HOH . 
N 6 HOH A 26 1126 38 HOH HOH . 
N 6 HOH A 27 1127 39 HOH HOH . 
N 6 HOH A 28 1128 40 HOH HOH . 
N 6 HOH A 29 1129 41 HOH HOH . 
N 6 HOH A 30 1130 42 HOH HOH . 
N 6 HOH A 31 1131 43 HOH HOH . 
N 6 HOH A 32 1132 44 HOH HOH . 
N 6 HOH A 33 1133 45 HOH HOH . 
N 6 HOH A 34 1134 46 HOH HOH . 
N 6 HOH A 35 1135 47 HOH HOH . 
N 6 HOH A 36 1136 48 HOH HOH . 
N 6 HOH A 37 1137 49 HOH HOH . 
N 6 HOH A 38 1138 50 HOH HOH . 
N 6 HOH A 39 1139 51 HOH HOH . 
N 6 HOH A 40 1140 65 HOH HOH . 
N 6 HOH A 41 1141 66 HOH HOH . 
N 6 HOH A 42 1142 67 HOH HOH . 
N 6 HOH A 43 1143 68 HOH HOH . 
N 6 HOH A 44 1144 70 HOH HOH . 
N 6 HOH A 45 1145 71 HOH HOH . 
N 6 HOH A 46 1146 72 HOH HOH . 
O 6 HOH B 1 1101 3 HOH HOH . 
O 6 HOH B 2 1102 4 HOH HOH . 
O 6 HOH B 3 1103 5 HOH HOH . 
O 6 HOH B 4 1104 6 HOH HOH . 
O 6 HOH B 5 1105 8 HOH HOH . 
O 6 HOH B 6 1106 13 HOH HOH . 
O 6 HOH B 7 1107 16 HOH HOH . 
O 6 HOH B 8 1108 26 HOH HOH . 
O 6 HOH B 9 1109 27 HOH HOH . 
O 6 HOH B 10 1110 35 HOH HOH . 
O 6 HOH B 11 1111 52 HOH HOH . 
O 6 HOH B 12 1112 53 HOH HOH . 
O 6 HOH B 13 1113 54 HOH HOH . 
O 6 HOH B 14 1114 55 HOH HOH . 
O 6 HOH B 15 1115 56 HOH HOH . 
O 6 HOH B 16 1116 57 HOH HOH . 
O 6 HOH B 17 1117 58 HOH HOH . 
O 6 HOH B 18 1118 59 HOH HOH . 
O 6 HOH B 19 1119 60 HOH HOH . 
O 6 HOH B 20 1120 61 HOH HOH . 
O 6 HOH B 21 1121 62 HOH HOH . 
O 6 HOH B 22 1122 63 HOH HOH . 
O 6 HOH B 23 1123 64 HOH HOH . 
O 6 HOH B 24 1124 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 . . . M 5 -13.858 51.952 -18.698 1 46.78 ? PG AGS 1003 B 1 
HETATM 2 S S1G AGS . . . M 5 -14.426 53.295 -19.996 1 47.63 ? S1G AGS 1003 B 1 
HETATM 3 O O2G AGS . . . M 5 -13.749 52.666 -17.365 1 44.16 ? O2G AGS 1003 B 1 
HETATM 4 O O3G AGS . . . M 5 -14.866 50.833 -18.874 1 45.38 ? O3G AGS 1003 B 1 
HETATM 5 P PB AGS . . . M 5 -11.156 51.265 -18.011 1 39.03 ? PB AGS 1003 B 1 
HETATM 6 O O1B AGS . . . M 5 -11.483 50.32 -16.888 1 39.79 ? O1B AGS 1003 B 1 
HETATM 7 O O2B AGS . . . M 5 -10.79 52.685 -17.65 1 40.53 ? O2B AGS 1003 B 1 
HETATM 8 O O3B AGS . . . M 5 -12.405 51.3 -19.04 1 42.4 ? O3B AGS 1003 B 1 
HETATM 9 P PA AGS . . . M 5 -9.017 51.441 -19.923 1 36.9 ? PA AGS 1003 B 1 
HETATM 10 O O1A AGS . . . M 5 -9.314 50.906 -21.299 1 36.69 ? O1A AGS 1003 B 1 
HETATM 11 O O2A AGS . . . M 5 -9.124 52.919 -19.673 1 36.51 ? O2A AGS 1003 B 1 
HETATM 12 O O3A AGS . . . M 5 -9.938 50.626 -18.865 1 38.47 ? O3A AGS 1003 B 1 
HETATM 13 O O5' AGS . . . M 5 -7.515 50.997 -19.536 1 36.5 ? O5' AGS 1003 B 1 
HETATM 14 C C5' AGS . . . M 5 -7.008 51.295 -18.237 1 37.67 ? C5' AGS 1003 B 1 
HETATM 15 C C4' AGS . . . M 5 -5.655 52.002 -18.284 1 38.39 ? C4' AGS 1003 B 1 
HETATM 16 O O4' AGS . . . M 5 -4.637 51.121 -18.772 1 38.9 ? O4' AGS 1003 B 1 
HETATM 17 C C3' AGS . . . M 5 -5.618 53.226 -19.189 1 37.91 ? C3' AGS 1003 B 1 
HETATM 18 O O3' AGS . . . M 5 -5.981 54.42 -18.493 1 38.77 ? O3' AGS 1003 B 1 
HETATM 19 C C2' AGS . . . M 5 -4.179 53.269 -19.656 1 37.6 ? C2' AGS 1003 B 1 
HETATM 20 O O2' AGS . . . M 5 -3.371 53.977 -18.712 1 37.49 ? O2' AGS 1003 B 1 
HETATM 21 C C1' AGS . . . M 5 -3.75 51.813 -19.657 1 38.14 ? C1' AGS 1003 B 1 
HETATM 22 N N9 AGS . . . M 5 -3.865 51.248 -21.029 1 38.61 ? N9 AGS 1003 B 1 
HETATM 23 C C8 AGS . . . M 5 -4.999 50.835 -21.621 1 37.87 ? C8 AGS 1003 B 1 
HETATM 24 N N7 AGS . . . M 5 -4.714 50.394 -22.863 1 37.8 ? N7 AGS 1003 B 1 
HETATM 25 C C5 AGS . . . M 5 -3.386 50.526 -23.05 1 38.48 ? C5 AGS 1003 B 1 
HETATM 26 C C6 AGS . . . M 5 -2.535 50.238 -24.113 1 38.37 ? C6 AGS 1003 B 1 
HETATM 27 N N6 AGS . . . M 5 -3.028 49.708 -25.258 1 37.94 ? N6 AGS 1003 B 1 
HETATM 28 N N1 AGS . . . M 5 -1.211 50.501 -23.994 1 38.44 ? N1 AGS 1003 B 1 
HETATM 29 C C2 AGS . . . M 5 -0.716 51.028 -22.861 1 37.96 ? C2 AGS 1003 B 1 
HETATM 30 N N3 AGS . . . M 5 -1.517 51.313 -21.821 1 37.99 ? N3 AGS 1003 B 1 
HETATM 31 C C4 AGS . . . M 5 -2.854 51.071 -21.89 1 38.36 ? C4 AGS 1003 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           224 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           31 
#