data_7VCX
#
_model_server_result.job_id            '_ht7shpbgjeHqxyth_y3oQ' 
_model_server_result.datetime_utc      '2024-10-18 15:28:53' 
_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          7vcx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":903}' 
#
_entry.id    7VCX 
#
_exptl.entry_id    7VCX 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    12 
_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            7VCX 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7VCX 
_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    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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 
_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
? 2 G N N 
? 2 I N N 
? 2 K N N 
? 2 M N N 
? 2 O N N 
? 2 Q N N 
? 2 S N N 
? 2 U N N 
? 2 W N N 
? 2 Y N N 
? 2 AA N N 
? 2 CA 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 252 A THR 252 1_555 H MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc2 A OG1 THR 525 A THR 525 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? 
metalc ? metalc3 G O2G AGS . A AGS 901 1_555 H MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc4 G O2B AGS . A AGS 901 1_555 H MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc5 I O2G AGS . A AGS 903 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc6 I O1B AGS . A AGS 903 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc7 I O1A AGS . A AGS 903 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc8 B OG1 THR 252 B THR 252 1_555 L MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc9 B OG1 THR 525 B THR 525 1_555 N MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? 
metalc ? metalc10 K O2G AGS . B AGS 901 1_555 L MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc11 K O2B AGS . B AGS 901 1_555 L MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc12 M O2G AGS . B AGS 903 1_555 N MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc13 M O1B AGS . B AGS 903 1_555 N MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc14 M O1A AGS . B AGS 903 1_555 N MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc15 C OG1 THR 252 C THR 252 1_555 P MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? 
metalc ? metalc16 C OG1 THR 525 C THR 525 1_555 R MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? 
metalc ? metalc17 O O2G AGS . C AGS 901 1_555 P MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc18 O O2B AGS . C AGS 901 1_555 P MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc19 Q O2G AGS . C AGS 903 1_555 R MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc20 Q O1B AGS . C AGS 903 1_555 R MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc21 Q O1A AGS . C AGS 903 1_555 R MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc22 D OG1 THR 252 D THR 252 1_555 T MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc23 D OG1 THR 525 D THR 525 1_555 V MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? 
metalc ? metalc24 S O2G AGS . D AGS 901 1_555 T MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc25 S O2B AGS . D AGS 901 1_555 T MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc26 U O2G AGS . D AGS 903 1_555 V MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc27 U O1B AGS . D AGS 903 1_555 V MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc28 U O1A AGS . D AGS 903 1_555 V MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc29 E OG1 THR 252 E THR 252 1_555 X MG MG . E MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc30 E OG1 THR 525 E THR 525 1_555 Z MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? 
metalc ? metalc31 W O2G AGS . E AGS 901 1_555 X MG MG . E MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc32 W O2B AGS . E AGS 901 1_555 X MG MG . E MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc33 Y O2G AGS . E AGS 903 1_555 Z MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc34 Y O1B AGS . E AGS 903 1_555 Z MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc35 Y O1A AGS . E AGS 903 1_555 Z MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc36 F OG1 THR 252 F THR 252 1_555 BA MG MG . F MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? 
metalc ? metalc37 F OG1 THR 525 F THR 525 1_555 DA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? 
metalc ? metalc38 AA O2G AGS . F AGS 901 1_555 BA MG MG . F MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc39 AA O2B AGS . F AGS 901 1_555 BA MG MG . F MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc40 CA O2G AGS . F AGS 903 1_555 DA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc41 CA O1B AGS . F AGS 903 1_555 DA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc42 CA O1A AGS . F AGS 903 1_555 DA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
#
_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                     7VCX 
_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
G 2 AGS A 1 901 807 AGS AGS . 
H 3 MG A 1 902 808 MG MG . 
I 2 AGS A 1 903 809 AGS AGS . 
J 3 MG A 1 904 810 MG MG . 
K 2 AGS B 1 901 807 AGS AGS . 
L 3 MG B 1 902 808 MG MG . 
M 2 AGS B 1 903 809 AGS AGS . 
N 3 MG B 1 904 810 MG MG . 
O 2 AGS C 1 901 807 AGS AGS . 
P 3 MG C 1 902 808 MG MG . 
Q 2 AGS C 1 903 809 AGS AGS . 
R 3 MG C 1 904 810 MG MG . 
S 2 AGS D 1 901 807 AGS AGS . 
T 3 MG D 1 902 808 MG MG . 
U 2 AGS D 1 903 809 AGS AGS . 
V 3 MG D 1 904 810 MG MG . 
W 2 AGS E 1 901 807 AGS AGS . 
X 3 MG E 1 902 808 MG MG . 
Y 2 AGS E 1 903 809 AGS AGS . 
Z 3 MG E 1 904 810 MG MG . 
AA 2 AGS F 1 901 807 AGS AGS . 
BA 3 MG F 1 902 808 MG MG . 
CA 2 AGS F 1 903 809 AGS AGS . 
DA 3 MG F 1 904 810 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 . . . M 2 192.856 154.07 141.65 1 19.95 ? PG AGS 903 B 1 
HETATM 2 S S1G AGS . . . M 2 193.461 152.322 141.097 1 19.95 ? S1G AGS 903 B 1 
HETATM 3 O O2G AGS . . . M 2 193.065 154.323 143.156 1 19.95 ? O2G AGS 903 B 1 
HETATM 4 O O3G AGS . . . M 2 191.36 154.19 141.344 1 19.95 ? O3G AGS 903 B 1 
HETATM 5 P PB AGS . . . M 2 194.792 155.858 141.598 1 19.95 ? PB AGS 903 B 1 
HETATM 6 O O1B AGS . . . M 2 194.418 156.155 142.975 1 19.95 ? O1B AGS 903 B 1 
HETATM 7 O O2B AGS . . . M 2 195.032 157.07 140.725 1 19.95 ? O2B AGS 903 B 1 
HETATM 8 O O3B AGS . . . M 2 193.632 155.143 140.873 1 19.95 ? O3B AGS 903 B 1 
HETATM 9 P PA AGS . . . M 2 197.006 154.653 142.661 1 19.95 ? PA AGS 903 B 1 
HETATM 10 O O1A AGS . . . M 2 196.347 154.302 143.864 1 19.95 ? O1A AGS 903 B 1 
HETATM 11 O O2A AGS . . . M 2 198.014 155.762 142.825 1 19.95 ? O2A AGS 903 B 1 
HETATM 12 O O3A AGS . . . M 2 196.087 155.024 141.489 1 19.95 ? O3A AGS 903 B 1 
HETATM 13 O O5' AGS . . . M 2 197.736 153.425 142.119 1 19.95 ? O5' AGS 903 B 1 
HETATM 14 C C5' AGS . . . M 2 197.174 152.123 141.992 1 19.95 ? C5' AGS 903 B 1 
HETATM 15 C C4' AGS . . . M 2 198.336 151.169 142.055 1 19.95 ? C4' AGS 903 B 1 
HETATM 16 O O4' AGS . . . M 2 198.926 151.053 140.749 1 19.95 ? O4' AGS 903 B 1 
HETATM 17 C C3' AGS . . . M 2 199.45 151.644 142.972 1 19.95 ? C3' AGS 903 B 1 
HETATM 18 O O3' AGS . . . M 2 199.303 151.044 144.249 1 19.95 ? O3' AGS 903 B 1 
HETATM 19 C C2' AGS . . . M 2 200.707 151.122 142.296 1 19.95 ? C2' AGS 903 B 1 
HETATM 20 O O2' AGS . . . M 2 200.93 149.795 142.732 1 19.95 ? O2' AGS 903 B 1 
HETATM 21 C C1' AGS . . . M 2 200.331 151.151 140.821 1 19.95 ? C1' AGS 903 B 1 
HETATM 22 N N9 AGS . . . M 2 200.727 152.351 140.105 1 19.95 ? N9 AGS 903 B 1 
HETATM 23 C C8 AGS . . . M 2 199.878 153.225 139.496 1 19.95 ? C8 AGS 903 B 1 
HETATM 24 N N7 AGS . . . M 2 200.479 154.222 138.903 1 19.95 ? N7 AGS 903 B 1 
HETATM 25 C C5 AGS . . . M 2 201.817 153.983 139.131 1 19.95 ? C5 AGS 903 B 1 
HETATM 26 C C6 AGS . . . M 2 202.978 154.677 138.761 1 19.95 ? C6 AGS 903 B 1 
HETATM 27 N N6 AGS . . . M 2 202.968 155.804 138.05 1 19.95 ? N6 AGS 903 B 1 
HETATM 28 N N1 AGS . . . M 2 204.16 154.172 139.149 1 19.95 ? N1 AGS 903 B 1 
HETATM 29 C C2 AGS . . . M 2 204.175 153.045 139.858 1 19.95 ? C2 AGS 903 B 1 
HETATM 30 N N3 AGS . . . M 2 203.148 152.301 140.264 1 19.95 ? N3 AGS 903 B 1 
HETATM 31 C C4 AGS . . . M 2 201.99 152.829 139.869 1 19.95 ? C4 AGS 903 B 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    52 
_model_server_stats.query_time_ms           263 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#