data_6WJD
#
_model_server_result.job_id            3EY9kvi-lSNp8LfKsV6KDA 
_model_server_result.datetime_utc      '2025-07-30 11:45:57' 
_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          6wjd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"DB","auth_seq_id":401}' 
#
_entry.id    6WJD 
#
_exptl.entry_id    6WJD 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          35 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    4 
_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            6WJD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6WJD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    47-meric 
_pdbx_struct_assembly.oligomeric_count      47 
_pdbx_struct_assembly.details               author_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,AB,BB,CB,DB,EB,FB,GB 
_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
? 35 WA N N 
? 35 YA N N 
? 35 BB N N 
? 35 DB 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 I OE2 GLU 51 c GLU 52 1_555 VA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc2 I ND1 HIS 112 c HIS 113 1_555 VA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? 
metalc ? metalc3 I OD2 ASP 125 c ASP 126 1_555 VA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? 
metalc ? metalc4 WA O2G AGS . A AGS 501 1_555 XA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc5 WA O3G AGS . A AGS 501 1_555 XA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc6 WA O2B AGS . A AGS 501 1_555 XA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? 
metalc ? metalc7 YA O2G AGS . B AGS 501 1_555 ZA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc8 YA O1B AGS . B AGS 501 1_555 ZA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? 
metalc ? metalc9 YA O3B AGS . B AGS 501 1_555 ZA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc10 YA O2A AGS . B AGS 501 1_555 ZA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? 
metalc ? metalc11 P OG1 THR 213 D THR 213 1_555 CB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? 
metalc ? metalc12 BB O2G AGS . D AGS 501 1_555 CB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? 
metalc ? metalc13 BB O3G AGS . D AGS 501 1_555 CB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? 
metalc ? metalc14 BB O1B AGS . D AGS 501 1_555 CB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? 
metalc ? metalc15 Q OG1 THR 195 E THR 181 1_555 EB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc16 DB O2G AGS . E AGS 401 1_555 EB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc17 DB O3G AGS . E AGS 401 1_555 EB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? 
metalc ? metalc18 DB O1B AGS . E AGS 401 1_555 EB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc19 R OG1 THR 234 F THR 234 1_555 GB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? 
metalc ? metalc20 R OD2 ASP 286 F ASP 286 1_555 GB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? 
metalc ? metalc21 FB O1B ADP . F ADP 501 1_555 GB MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? 
#
_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                     6WJD 
_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
VA 34 ZN c 1 401 401 ZN ZN . 
WA 35 AGS A 1 501 501 AGS AGS . 
XA 36 MG A 1 502 502 MG MG . 
YA 35 AGS B 1 501 501 AGS AGS . 
ZA 36 MG B 1 502 502 MG MG . 
AB 37 ADP C 1 501 501 ADP ADP . 
BB 35 AGS D 1 501 501 AGS AGS . 
CB 36 MG D 1 502 502 MG MG . 
DB 35 AGS E 1 401 401 AGS AGS . 
EB 36 MG E 1 402 402 MG MG . 
FB 37 ADP F 1 501 501 ADP ADP . 
GB 36 MG F 1 502 502 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 . . . DB 35 389.461 320.089 274.16 1 108 ? PG AGS 401 E 1 
HETATM 2 S S1G AGS . . . DB 35 388.259 318.783 274.951 1 108 ? S1G AGS 401 E 1 
HETATM 3 O O2G AGS . . . DB 35 390.71 319.329 273.486 1 108 ? O2G AGS 401 E 1 
HETATM 4 O O3G AGS . . . DB 35 389.951 321.008 275.211 1 108 ? O3G AGS 401 E 1 
HETATM 5 P PB AGS . . . DB 35 388.974 322.333 272.317 1 108 ? PB AGS 401 E 1 
HETATM 6 O O1B AGS . . . DB 35 390.288 322.863 272.838 1 108 ? O1B AGS 401 E 1 
HETATM 7 O O2B AGS . . . DB 35 387.729 323.185 272.386 1 108 ? O2B AGS 401 E 1 
HETATM 8 O O3B AGS . . . DB 35 388.672 320.933 273.032 1 108 ? O3B AGS 401 E 1 
HETATM 9 P PA AGS . . . DB 35 390.398 322.029 269.771 1 108 ? PA AGS 401 E 1 
HETATM 10 O O1A AGS . . . DB 35 391.356 320.878 269.967 1 108 ? O1A AGS 401 E 1 
HETATM 11 O O2A AGS . . . DB 35 390.895 323.453 269.848 1 108 ? O2A AGS 401 E 1 
HETATM 12 O O3A AGS . . . DB 35 389.182 321.859 270.802 1 108 ? O3A AGS 401 E 1 
HETATM 13 O O5' AGS . . . DB 35 389.643 321.829 268.371 1 108 ? O5' AGS 401 E 1 
HETATM 14 C C5' AGS . . . DB 35 388.94 320.583 268.135 1 108 ? C5' AGS 401 E 1 
HETATM 15 C C4' AGS . . . DB 35 388.865 320.326 266.65 1 108 ? C4' AGS 401 E 1 
HETATM 16 O O4' AGS . . . DB 35 387.477 320.382 266.227 1 108 ? O4' AGS 401 E 1 
HETATM 17 C C3' AGS . . . DB 35 389.606 321.327 265.754 1 108 ? C3' AGS 401 E 1 
HETATM 18 O O3' AGS . . . DB 35 390.927 320.867 265.467 1 108 ? O3' AGS 401 E 1 
HETATM 19 C C2' AGS . . . DB 35 388.746 321.33 264.488 1 108 ? C2' AGS 401 E 1 
HETATM 20 O O2' AGS . . . DB 35 389.084 320.22 263.655 1 108 ? O2' AGS 401 E 1 
HETATM 21 C C1' AGS . . . DB 35 387.344 321.167 265.05 1 108 ? C1' AGS 401 E 1 
HETATM 22 N N9 AGS . . . DB 35 386.748 322.459 265.481 1 108 ? N9 AGS 401 E 1 
HETATM 23 C C8 AGS . . . DB 35 386.484 322.845 266.735 1 108 ? C8 AGS 401 E 1 
HETATM 24 N N7 AGS . . . DB 35 385.927 324.075 266.76 1 108 ? N7 AGS 401 E 1 
HETATM 25 C C5 AGS . . . DB 35 385.838 324.485 265.435 1 108 ? C5 AGS 401 E 1 
HETATM 26 C C6 AGS . . . DB 35 385.356 325.652 264.815 1 108 ? C6 AGS 401 E 1 
HETATM 27 N N6 AGS . . . DB 35 384.847 326.664 265.559 1 108 ? N6 AGS 401 E 1 
HETATM 28 N N1 AGS . . . DB 35 385.409 325.75 263.469 1 108 ? N1 AGS 401 E 1 
HETATM 29 C C2 AGS . . . DB 35 385.912 324.751 262.732 1 108 ? C2 AGS 401 E 1 
HETATM 30 N N3 AGS . . . DB 35 386.376 323.63 263.3 1 108 ? N3 AGS 401 E 1 
HETATM 31 C C4 AGS . . . DB 35 386.348 323.478 264.646 1 108 ? C4 AGS 401 E 1 
#
_model_server_stats.io_time_ms              41 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    139 
_model_server_stats.query_time_ms           360 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#