data_6WRF
#
_model_server_result.job_id            N9JP9TRyHrtQ4o8B8nqK2w 
_model_server_result.datetime_utc      '2024-10-19 13:30:09' 
_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          6wrf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"X","auth_seq_id":501}' 
#
_entry.id    6WRF 
#
_exptl.entry_id    6WRF 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetradecameric 
_pdbx_struct_assembly.oligomeric_count      14 
_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 
_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
? 4 O N N 
? 4 Q N N 
? 4 S N N 
? 4 U N N 
? 4 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 OG1 THR 90 B THR 126 1_555 P MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? 
metalc ? metalc2 O O2G AGS . B AGS 501 1_555 P MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc3 O O2B AGS . B AGS 501 1_555 P MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc4 B OG1 THR 90 C THR 126 1_555 R MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
metalc ? metalc5 B OD2 ASP 148 C ASP 184 1_555 R MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? 
metalc ? metalc6 Q O2G AGS . C AGS 501 1_555 R MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? 
metalc ? metalc7 Q O2B AGS . C AGS 501 1_555 R MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? 
metalc ? metalc8 C OG1 THR 90 D THR 126 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? 
metalc ? metalc9 C OD2 ASP 148 D ASP 184 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? 
metalc ? metalc10 S O2G AGS . D AGS 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc11 S O2B AGS . D AGS 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? 
metalc ? metalc12 D OD1 ASP 148 E ASP 184 1_555 V MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
metalc ? metalc13 D OD2 ASP 148 E ASP 184 1_555 V MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc14 U O2G AGS . E AGS 501 1_555 V MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc15 N OG1 THR 90 A THR 126 1_555 Y MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
metalc ? metalc16 N OD1 ASP 148 A ASP 184 1_555 Y MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
metalc ? metalc17 N OD2 ASP 148 A ASP 184 1_555 Y MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? 
#
_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                     6WRF 
_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
O 4 AGS B 1 501 600 AGS AGS . 
P 5 MG B 1 502 2 MG MG . 
Q 4 AGS C 1 501 600 AGS AGS . 
R 5 MG C 1 502 3 MG MG . 
S 4 AGS D 1 501 600 AGS AGS . 
T 5 MG D 1 502 4 MG MG . 
U 4 AGS E 1 501 600 AGS AGS . 
V 5 MG E 1 502 5 MG MG . 
W 6 ADP F 1 600 600 ADP ADP . 
X 4 AGS A 1 501 600 AGS AGS . 
Y 5 MG A 1 502 1 MG MG . 
Z 7 HOH H 1 301 6 HOH HOH . 
AA 7 HOH I 1 301 5 HOH HOH . 
BA 7 HOH J 1 301 4 HOH HOH . 
CA 7 HOH K 1 301 3 HOH HOH . 
DA 7 HOH L 1 301 2 HOH HOH . 
EA 7 HOH M 1 301 1 HOH HOH . 
FA 7 HOH N 1 301 7 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 . . . X 4 144.839 151.99 117.352 1 43.7 ? PG AGS 501 A 1 
HETATM 2 S S1G AGS . . . X 4 144.394 152.74 115.612 1 43.7 ? S1G AGS 501 A 1 
HETATM 3 O O2G AGS . . . X 4 146.016 150.988 117.207 1 43.7 ? O2G AGS 501 A 1 
HETATM 4 O O3G AGS . . . X 4 145.251 153.132 118.32 1 43.7 ? O3G AGS 501 A 1 
HETATM 5 P PB AGS . . . X 4 142.165 151.611 117.452 1 43.7 ? PB AGS 501 A 1 
HETATM 6 O O1B AGS . . . X 4 141.726 152.852 118.114 1 43.7 -1 O1B AGS 501 A 1 
HETATM 7 O O2B AGS . . . X 4 142.215 151.703 115.929 1 43.7 ? O2B AGS 501 A 1 
HETATM 8 O O3B AGS . . . X 4 143.614 151.236 117.928 1 43.7 ? O3B AGS 501 A 1 
HETATM 9 P PA AGS . . . X 4 140.319 149.906 116.539 1 43.7 ? PA AGS 501 A 1 
HETATM 10 O O1A AGS . . . X 4 141.171 149.762 115.361 1 43.7 -1 O1A AGS 501 A 1 
HETATM 11 O O2A AGS . . . X 4 139.152 150.88 116.386 1 43.7 ? O2A AGS 501 A 1 
HETATM 12 O O3A AGS . . . X 4 141.173 150.431 117.746 1 43.7 ? O3A AGS 501 A 1 
HETATM 13 O O5' AGS . . . X 4 139.816 148.478 116.948 1 43.7 ? O5' AGS 501 A 1 
HETATM 14 C C5' AGS . . . X 4 140.508 147.325 116.473 1 43.7 ? C5' AGS 501 A 1 
HETATM 15 C C4' AGS . . . X 4 139.715 146.086 116.787 1 43.7 ? C4' AGS 501 A 1 
HETATM 16 O O4' AGS . . . X 4 139.312 146.101 118.171 1 43.7 ? O4' AGS 501 A 1 
HETATM 17 C C3' AGS . . . X 4 138.425 145.946 115.993 1 43.7 ? C3' AGS 501 A 1 
HETATM 18 O O3' AGS . . . X 4 138.64 145.281 114.755 1 43.7 ? O3' AGS 501 A 1 
HETATM 19 C C2' AGS . . . X 4 137.559 145.106 116.923 1 43.7 ? C2' AGS 501 A 1 
HETATM 20 O O2' AGS . . . X 4 137.866 143.726 116.793 1 43.7 ? O2' AGS 501 A 1 
HETATM 21 C C1' AGS . . . X 4 137.988 145.616 118.302 1 43.7 ? C1' AGS 501 A 1 
HETATM 22 N N9 AGS . . . X 4 137.176 146.686 118.869 1 43.7 ? N9 AGS 501 A 1 
HETATM 23 C C8 AGS . . . X 4 137.66 147.8 119.499 1 43.7 ? C8 AGS 501 A 1 
HETATM 24 N N7 AGS . . . X 4 136.732 148.613 119.936 1 43.7 ? N7 AGS 501 A 1 
HETATM 25 C C5 AGS . . . X 4 135.551 147.985 119.576 1 43.7 ? C5 AGS 501 A 1 
HETATM 26 C C6 AGS . . . X 4 134.202 148.335 119.754 1 43.7 ? C6 AGS 501 A 1 
HETATM 27 N N6 AGS . . . X 4 133.804 149.45 120.366 1 43.7 ? N6 AGS 501 A 1 
HETATM 28 N N1 AGS . . . X 4 133.266 147.488 119.276 1 43.7 ? N1 AGS 501 A 1 
HETATM 29 C C2 AGS . . . X 4 133.663 146.371 118.663 1 43.7 ? C2 AGS 501 A 1 
HETATM 30 N N3 AGS . . . X 4 134.903 145.934 118.442 1 43.7 ? N3 AGS 501 A 1 
HETATM 31 C C4 AGS . . . X 4 135.809 146.794 118.923 1 43.7 ? C4 AGS 501 A 1 
HETATM 32 H "H5'1" AGS . . . X 4 141.38 147.274 116.896 1 43.7 ? "H5'1" AGS 501 A 1 
HETATM 33 H "H5'2" AGS . . . X 4 140.606 147.393 115.509 1 43.7 ? "H5'2" AGS 501 A 1 
HETATM 34 H H4' AGS . . . X 4 140.263 145.302 116.629 1 43.7 ? H4' AGS 501 A 1 
HETATM 35 H H3' AGS . . . X 4 138.024 146.817 115.854 1 43.7 ? H3' AGS 501 A 1 
HETATM 36 H HO3' AGS . . . X 4 137.991 144.689 114.634 1 43.7 ? HO3' AGS 501 A 1 
HETATM 37 H H2' AGS . . . X 4 136.627 145.262 116.719 1 43.7 ? H2' AGS 501 A 1 
HETATM 38 H HO2' AGS . . . X 4 138.722 143.646 116.58 1 43.7 ? HO2' AGS 501 A 1 
HETATM 39 H H1' AGS . . . X 4 137.986 144.866 118.919 1 43.7 ? H1' AGS 501 A 1 
HETATM 40 H H8 AGS . . . X 4 138.606 147.969 119.606 1 43.7 ? H8 AGS 501 A 1 
HETATM 41 H HN61 AGS . . . X 4 133.454 150.134 119.883 1 43.7 ? HN61 AGS 501 A 1 
HETATM 42 H HN62 AGS . . . X 4 133.888 149.525 121.267 1 43.7 ? HN62 AGS 501 A 1 
HETATM 43 H H2 AGS . . . X 4 132.954 145.793 118.335 1 43.7 ? H2 AGS 501 A 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    60 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#