data_6XTX
#
_model_server_result.job_id            5R_4okJif9WtqCYYK0H1hQ 
_model_server_result.datetime_utc      '2024-11-26 21:45:49' 
_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          6xtx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"X","auth_seq_id":1001}' 
#
_entry.id    6XTX 
#
_exptl.entry_id    6XTX 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          15 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_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,M,N,O,P,Q,R,S,T,U,V,W,X,Y 
_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
? 15 Q N N 
? 15 S N N 
? 15 X 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 329 2 CYS 329 1_555 M ZN ZN . 2 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc2 A SG CYS 332 2 CYS 332 1_555 M ZN ZN . 2 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc3 A SG CYS 352 2 CYS 352 1_555 M ZN ZN . 2 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc4 A SG CYS 355 2 CYS 355 1_555 M ZN ZN . 2 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? 
metalc ? metalc5 C SG CYS 326 4 CYS 306 1_555 P ZN ZN . 4 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc6 C SG CYS 329 4 CYS 309 1_555 P ZN ZN . 4 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
metalc ? metalc7 C SG CYS 348 4 CYS 328 1_555 P ZN ZN . 4 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc8 C SG CYS 351 4 CYS 331 1_555 P ZN ZN . 4 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc9 C OG SER 537 4 SER 517 1_555 R MG MG . 4 MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
metalc ? metalc10 Q O2G AGS . 4 AGS 902 1_555 R MG MG . 4 MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc11 Q O2B AGS . 4 AGS 902 1_555 R MG MG . 4 MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? 
metalc ? metalc12 S O2G AGS . 4 AGS 904 1_555 V MG MG . 6 MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc13 S O2B AGS . 4 AGS 904 1_555 V MG MG . 6 MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc14 D SG CYS 172 5 CYS 172 1_555 T ZN ZN . 5 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc15 D SG CYS 175 5 CYS 175 1_555 T ZN ZN . 5 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc16 D SG CYS 197 5 CYS 197 1_555 T ZN ZN . 5 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc17 D SG CYS 207 5 CYS 207 1_555 T ZN ZN . 5 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc18 E SG CYS 158 6 CYS 158 1_555 U ZN ZN . 6 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc19 E SG CYS 161 6 CYS 161 1_555 U ZN ZN . 6 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc20 E SG CYS 180 6 CYS 180 1_555 U ZN ZN . 6 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc21 E SG CYS 185 6 CYS 185 1_555 U ZN ZN . 6 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc22 E OG SER 403 6 SER 403 1_555 V MG MG . 6 MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc23 F SG CYS 184 7 CYS 184 1_555 W ZN ZN . 7 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc24 F SG CYS 187 7 CYS 187 1_555 W ZN ZN . 7 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc25 F SG CYS 206 7 CYS 206 1_555 W ZN ZN . 7 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc26 F SG CYS 211 7 CYS 211 1_555 W ZN ZN . 7 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? 
metalc ? metalc27 F OG SER 388 7 SER 388 1_555 Y MG MG . 7 MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc28 X O2G AGS . 7 AGS 1001 1_555 Y MG MG . 7 MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc29 X O2B AGS . 7 AGS 1001 1_555 Y MG MG . 7 MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? 
#
_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                     6XTX 
_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
M 13 ZN 2 1 1000 1000 ZN ZN . 
N 14 ADP 2 1 1001 1001 ADP ADP . 
O 14 ADP 3 1 1001 1001 ADP ADP . 
P 13 ZN 4 1 901 1000 ZN ZN . 
Q 15 AGS 4 1 902 1001 AGS AGS . 
R 16 MG 4 1 903 1002 MG MG . 
S 15 AGS 4 1 904 1001 AGS AGS . 
T 13 ZN 5 1 1000 1000 ZN ZN . 
U 13 ZN 6 1 901 1000 ZN ZN . 
V 16 MG 6 1 902 1002 MG MG . 
W 13 ZN 7 1 1000 1000 ZN ZN . 
X 15 AGS 7 1 1001 1001 AGS AGS . 
Y 16 MG 7 1 1002 1002 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 . . . X 15 214.383 225.12 166.554 1 62.68 ? PG AGS 1001 7 1 
HETATM 2 S S1G AGS . . . X 15 215.863 225.28 167.735 1 62.68 ? S1G AGS 1001 7 1 
HETATM 3 O O2G AGS . . . X 15 213.036 224.7 167.236 1 62.68 ? O2G AGS 1001 7 1 
HETATM 4 O O3G AGS . . . X 15 214.361 224.086 165.407 1 62.68 ? O3G AGS 1001 7 1 
HETATM 5 P PB AGS . . . X 15 212.863 226.987 165.036 1 62.68 ? PB AGS 1001 7 1 
HETATM 6 O O1B AGS . . . X 15 213.161 227.125 163.617 1 62.68 ? O1B AGS 1001 7 1 
HETATM 7 O O2B AGS . . . X 15 211.716 226.088 165.422 1 62.68 ? O2B AGS 1001 7 1 
HETATM 8 O O3B AGS . . . X 15 214.124 226.486 165.858 1 62.68 ? O3B AGS 1001 7 1 
HETATM 9 P PA AGS . . . X 15 211.193 228.98 166.233 1 62.68 ? PA AGS 1001 7 1 
HETATM 10 O O1A AGS . . . X 15 210.313 229.33 165.129 1 62.68 ? O1A AGS 1001 7 1 
HETATM 11 O O2A AGS . . . X 15 210.663 228.01 167.257 1 62.68 ? O2A AGS 1001 7 1 
HETATM 12 O O3A AGS . . . X 15 212.572 228.395 165.707 1 62.68 ? O3A AGS 1001 7 1 
HETATM 13 O O5' AGS . . . X 15 211.608 230.28 167.004 1 62.68 ? O5' AGS 1001 7 1 
HETATM 14 C C5' AGS . . . X 15 212.245 231.349 166.286 1 62.68 ? C5' AGS 1001 7 1 
HETATM 15 C C4' AGS . . . X 15 211.742 232.66 166.823 1 62.68 ? C4' AGS 1001 7 1 
HETATM 16 O O4' AGS . . . X 15 212.395 233.735 166.12 1 62.68 ? O4' AGS 1001 7 1 
HETATM 17 C C3' AGS . . . X 15 210.256 232.91 166.626 1 62.68 ? C3' AGS 1001 7 1 
HETATM 18 O O3' AGS . . . X 15 209.771 233.836 167.586 1 62.68 ? O3' AGS 1001 7 1 
HETATM 19 C C2' AGS . . . X 15 210.215 233.513 165.227 1 62.68 ? C2' AGS 1001 7 1 
HETATM 20 O O2' AGS . . . X 15 209.092 234.37 165.093 1 62.68 ? O2' AGS 1001 7 1 
HETATM 21 C C1' AGS . . . X 15 211.49 234.351 165.224 1 62.68 ? C1' AGS 1001 7 1 
HETATM 22 N N9 AGS . . . X 15 212.142 234.451 163.928 1 62.68 ? N9 AGS 1001 7 1 
HETATM 23 C C8 AGS . . . X 15 213.389 233.996 163.598 1 62.68 ? C8 AGS 1001 7 1 
HETATM 24 N N7 AGS . . . X 15 213.737 234.243 162.359 1 62.68 ? N7 AGS 1001 7 1 
HETATM 25 C C5 AGS . . . X 15 212.639 234.905 161.838 1 62.68 ? C5 AGS 1001 7 1 
HETATM 26 C C6 AGS . . . X 15 212.373 235.442 160.568 1 62.68 ? C6 AGS 1001 7 1 
HETATM 27 N N6 AGS . . . X 15 213.221 235.369 159.54 1 62.68 ? N6 AGS 1001 7 1 
HETATM 28 N N1 AGS . . . X 15 211.189 236.058 160.383 1 62.68 ? N1 AGS 1001 7 1 
HETATM 29 C C2 AGS . . . X 15 210.334 236.123 161.405 1 62.68 ? C2 AGS 1001 7 1 
HETATM 30 N N3 AGS . . . X 15 210.471 235.644 162.64 1 62.68 ? N3 AGS 1001 7 1 
HETATM 31 C C4 AGS . . . X 15 211.65 235.044 162.793 1 62.68 ? C4 AGS 1001 7 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    56 
_model_server_stats.query_time_ms           250 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           31 
#