data_8RC5
#
_model_server_result.job_id            u_RN1fEHeKOjLdyOMtAVlA 
_model_server_result.datetime_utc      '2025-03-23 17:45:42' 
_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          8rc5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"ZA","auth_seq_id":301}' 
#
_entry.id    8RC5 
#
_exptl.entry_id    8RC5 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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    16 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    36-meric 
_pdbx_struct_assembly.oligomeric_count      36 
_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,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA 
_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
? 3 KA N N 
? 3 LA N N 
? 3 MA N N 
? 3 NA N N 
? 3 OA N N 
? 3 PA N N 
? 3 QA N N 
? 3 RA N N 
? 3 SA N N 
? 3 TA N N 
? 3 UA N N 
? 3 VA N N 
? 3 WA N N 
? 3 XA N N 
? 3 YA N N 
? 3 ZA N 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                     8RC5 
_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
KA 3 AGS 4A 1 301 523 AGS AGS . 
LA 3 AGS 1B 1 301 515 AGS AGS . 
MA 3 AGS 4B 1 301 524 AGS AGS . 
NA 3 AGS 1C 1 301 515 AGS AGS . 
OA 3 AGS 4C 1 301 525 AGS AGS . 
PA 3 AGS 1D 1 301 521 AGS AGS . 
QA 3 AGS 4D 1 301 526 AGS AGS . 
RA 3 AGS 1E 1 301 520 AGS AGS . 
SA 3 AGS 4E 1 301 527 AGS AGS . 
TA 3 AGS 1F 1 301 519 AGS AGS . 
UA 3 AGS 4F 1 301 528 AGS AGS . 
VA 3 AGS 1G 1 301 518 AGS AGS . 
WA 3 AGS 4G 1 301 522 AGS AGS . 
XA 3 AGS 1H 1 301 517 AGS AGS . 
YA 3 AGS 4H 1 301 522 AGS AGS . 
ZA 3 AGS 1I 1 301 516 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 . . . ZA 3 198.686 249.838 145.233 1 105.05 ? PG AGS 301 1I 1 
HETATM 2 S S1G AGS . . . ZA 3 198.114 249.411 147.046 1 98.74 ? S1G AGS 301 1I 1 
HETATM 3 O O2G AGS . . . ZA 3 197.829 249.262 144.134 1 92.14 ? O2G AGS 301 1I 1 
HETATM 4 O O3G AGS . . . ZA 3 200.141 249.585 144.935 1 103.27 ? O3G AGS 301 1I 1 
HETATM 5 P PB AGS . . . ZA 3 197.27 252.382 144.887 1 99.08 ? PB AGS 301 1I 1 
HETATM 6 O O1B AGS . . . ZA 3 197.705 253.779 145.167 1 100.7 ? O1B AGS 301 1I 1 
HETATM 7 O O2B AGS . . . ZA 3 196.152 251.782 145.674 1 90.01 ? O2B AGS 301 1I 1 
HETATM 8 O O3B AGS . . . ZA 3 198.545 251.424 144.985 1 96.27 ? O3B AGS 301 1I 1 
HETATM 9 P PA AGS . . . ZA 3 197.655 252.939 142.06 1 94.53 ? PA AGS 301 1I 1 
HETATM 10 O O1A AGS . . . ZA 3 197.687 254.421 142.237 1 92.5 ? O1A AGS 301 1I 1 
HETATM 11 O O2A AGS . . . ZA 3 198.945 252.222 141.841 1 89.25 ? O2A AGS 301 1I 1 
HETATM 12 O O3A AGS . . . ZA 3 196.919 252.287 143.328 1 89.73 ? O3A AGS 301 1I 1 
HETATM 13 O O5' AGS . . . ZA 3 196.637 252.583 140.876 1 96.43 ? O5' AGS 301 1I 1 
HETATM 14 C C5' AGS . . . ZA 3 196.764 253.375 139.675 1 92.31 ? C5' AGS 301 1I 1 
HETATM 15 C C4' AGS . . . ZA 3 195.735 252.942 138.663 1 87.06 ? C4' AGS 301 1I 1 
HETATM 16 O O4' AGS . . . ZA 3 194.426 252.909 139.285 1 89.82 ? O4' AGS 301 1I 1 
HETATM 17 C C3' AGS . . . ZA 3 195.568 253.857 137.444 1 91.95 ? C3' AGS 301 1I 1 
HETATM 18 O O3' AGS . . . ZA 3 196.481 253.533 136.401 1 102.21 ? O3' AGS 301 1I 1 
HETATM 19 C C2' AGS . . . ZA 3 194.121 253.572 137.054 1 87.67 ? C2' AGS 301 1I 1 
HETATM 20 O O2' AGS . . . ZA 3 193.984 252.341 136.385 1 91.73 ? O2' AGS 301 1I 1 
HETATM 21 C C1' AGS . . . ZA 3 193.479 253.52 138.437 1 89.03 ? C1' AGS 301 1I 1 
HETATM 22 N N9 AGS . . . ZA 3 193.134 254.826 138.984 1 96.47 ? N9 AGS 301 1I 1 
HETATM 23 C C8 AGS . . . ZA 3 193.722 255.451 140.056 1 96.78 ? C8 AGS 301 1I 1 
HETATM 24 N N7 AGS . . . ZA 3 193.205 256.621 140.326 1 95.6 ? N7 AGS 301 1I 1 
HETATM 25 C C5 AGS . . . ZA 3 192.22 256.787 139.365 1 95.64 ? C5 AGS 301 1I 1 
HETATM 26 C C6 AGS . . . ZA 3 191.308 257.835 139.113 1 94.3 ? C6 AGS 301 1I 1 
HETATM 27 N N6 AGS . . . ZA 3 191.248 258.95 139.834 1 92.13 ? N6 AGS 301 1I 1 
HETATM 28 N N1 AGS . . . ZA 3 190.455 257.682 138.074 1 95.66 ? N1 AGS 301 1I 1 
HETATM 29 C C2 AGS . . . ZA 3 190.52 256.558 137.352 1 93.77 ? C2 AGS 301 1I 1 
HETATM 30 N N3 AGS . . . ZA 3 191.328 255.51 137.497 1 96.32 ? N3 AGS 301 1I 1 
HETATM 31 C C4 AGS . . . ZA 3 192.166 255.689 138.531 1 96.22 ? C4 AGS 301 1I 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    108 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           31 
#