data_6JB1
#
_model_server_result.job_id            VymnynYw_uOccAmXv22Gnw 
_model_server_result.datetime_utc      '2025-08-31 18:23:00' 
_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          6jb1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"TA","auth_seq_id":1602}' 
#
_entry.id    6JB1 
#
_exptl.entry_id    6JB1 
_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    8 
_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            6JB1 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6JB1 
_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    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB 
_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 J N N 
? 4 L N N 
? 4 Z N N 
? 4 CA N N 
? 4 QA N N 
? 4 TA N N 
? 4 HB N N 
? 4 KB 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
disulf ? disulf1 A SG CYS 110 A CYS 110 1_555 A SG CYS 142 A CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf2 B SG CYS 6 B CYS 6 1_555 B SG CYS 26 B CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf3 C SG CYS 110 C CYS 110 1_555 C SG CYS 142 C CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf4 D SG CYS 6 D CYS 6 1_555 D SG CYS 26 D CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf5 E SG CYS 110 E CYS 110 1_555 E SG CYS 142 E CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf6 F SG CYS 6 F CYS 6 1_555 F SG CYS 26 F CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf7 G SG CYS 110 G CYS 110 1_555 G SG CYS 142 G CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf8 H SG CYS 6 H CYS 6 1_555 H SG CYS 26 H CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
#
_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                     6JB1 
_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
I 3 POV A 1 401 4006 POV POV . 
J 4 AGS A 1 402 401 AGS AGS . 
K 5 AJP B 1 1601 2002 AJP AJP . 
L 4 AGS B 1 1602 2501 AGS AGS . 
M 6 BJX B 1 1603 3001 BJX RPG . 
N 3 POV B 1 1604 4001 POV POV . 
O 3 POV B 1 1605 4002 POV POV . 
P 3 POV B 1 1606 4003 POV POV . 
Q 3 POV B 1 1607 4004 POV POV . 
R 3 POV B 1 1608 4005 POV POV . 
S 3 POV B 1 1609 4007 POV POV . 
T 3 POV B 1 1610 4008 POV POV . 
U 3 POV B 1 1611 4009 POV POV . 
V 7 PTY B 1 1612 4011 PTY PTY . 
W 7 PTY B 1 1613 4012 PTY PTY . 
X 7 PTY B 1 1614 4013 PTY PTY . 
Y 7 PTY B 1 1615 4014 PTY PTY . 
Z 4 AGS C 1 401 401 AGS AGS . 
AA 3 POV C 1 402 4006 POV POV . 
BA 5 AJP D 1 1601 2002 AJP AJP . 
CA 4 AGS D 1 1602 2501 AGS AGS . 
DA 6 BJX D 1 1603 3001 BJX RPG . 
EA 3 POV D 1 1604 4001 POV POV . 
FA 3 POV D 1 1605 4002 POV POV . 
GA 3 POV D 1 1606 4003 POV POV . 
HA 3 POV D 1 1607 4004 POV POV . 
IA 3 POV D 1 1608 4005 POV POV . 
JA 3 POV D 1 1609 4007 POV POV . 
KA 3 POV D 1 1610 4008 POV POV . 
LA 3 POV D 1 1611 4009 POV POV . 
MA 7 PTY D 1 1612 4011 PTY PTY . 
NA 7 PTY D 1 1613 4012 PTY PTY . 
OA 7 PTY D 1 1614 4013 PTY PTY . 
PA 7 PTY D 1 1615 4014 PTY PTY . 
QA 4 AGS E 1 401 401 AGS AGS . 
RA 3 POV E 1 402 4006 POV POV . 
SA 5 AJP F 1 1601 2002 AJP AJP . 
TA 4 AGS F 1 1602 2501 AGS AGS . 
UA 6 BJX F 1 1603 3001 BJX RPG . 
VA 3 POV F 1 1604 4001 POV POV . 
WA 3 POV F 1 1605 4002 POV POV . 
XA 3 POV F 1 1606 4003 POV POV . 
YA 3 POV F 1 1607 4004 POV POV . 
ZA 3 POV F 1 1608 4005 POV POV . 
AB 3 POV F 1 1609 4007 POV POV . 
BB 3 POV F 1 1610 4008 POV POV . 
CB 3 POV F 1 1611 4009 POV POV . 
DB 7 PTY F 1 1612 4011 PTY PTY . 
EB 7 PTY F 1 1613 4012 PTY PTY . 
FB 7 PTY F 1 1614 4013 PTY PTY . 
GB 7 PTY F 1 1615 4014 PTY PTY . 
HB 4 AGS G 1 401 401 AGS AGS . 
IB 3 POV G 1 402 4006 POV POV . 
JB 5 AJP H 1 1601 2002 AJP AJP . 
KB 4 AGS H 1 1602 2501 AGS AGS . 
LB 6 BJX H 1 1603 3001 BJX RPG . 
MB 3 POV H 1 1604 4001 POV POV . 
NB 3 POV H 1 1605 4002 POV POV . 
OB 3 POV H 1 1606 4003 POV POV . 
PB 3 POV H 1 1607 4004 POV POV . 
QB 3 POV H 1 1608 4005 POV POV . 
RB 3 POV H 1 1609 4007 POV POV . 
SB 3 POV H 1 1610 4008 POV POV . 
TB 3 POV H 1 1611 4009 POV POV . 
UB 7 PTY H 1 1612 4011 PTY PTY . 
VB 7 PTY H 1 1613 4012 PTY PTY . 
WB 7 PTY H 1 1614 4013 PTY PTY . 
XB 7 PTY H 1 1615 4014 PTY PTY . 
#
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 . . . TA 4 146.101 90.815 215.812 1 248.9 ? PG AGS 1602 F 1 
HETATM 2 S S1G AGS . . . TA 4 146.482 91.92 214.096 1 246.75 ? S1G AGS 1602 F 1 
HETATM 3 O O2G AGS . . . TA 4 147.119 91.256 216.98 1 247.42 ? O2G AGS 1602 F 1 
HETATM 4 O O3G AGS . . . TA 4 146.283 89.372 215.526 1 244.92 ? O3G AGS 1602 F 1 
HETATM 5 P PB AGS . . . TA 4 143.474 89.944 216.391 1 242.19 ? PB AGS 1602 F 1 
HETATM 6 O O1B AGS . . . TA 4 144.029 88.8 217.209 1 238.91 ? O1B AGS 1602 F 1 
HETATM 7 O O2B AGS . . . TA 4 142.24 90.507 217.061 1 243.93 ? O2B AGS 1602 F 1 
HETATM 8 O O3B AGS . . . TA 4 144.588 91.107 216.287 1 239.57 ? O3B AGS 1602 F 1 
HETATM 9 P PA AGS . . . TA 4 142.48 90.358 213.77 1 263.33 ? PA AGS 1602 F 1 
HETATM 10 O O1A AGS . . . TA 4 141.378 91.219 214.34 1 259.39 ? O1A AGS 1602 F 1 
HETATM 11 O O2A AGS . . . TA 4 143.576 91.223 213.195 1 260.59 ? O2A AGS 1602 F 1 
HETATM 12 O O3A AGS . . . TA 4 143.084 89.4 214.92 1 251.47 ? O3A AGS 1602 F 1 
HETATM 13 O O5' AGS . . . TA 4 141.872 89.442 212.598 1 265.07 ? O5' AGS 1602 F 1 
HETATM 14 C C5' AGS . . . TA 4 140.779 88.571 212.871 1 265.01 ? C5' AGS 1602 F 1 
HETATM 15 C C4' AGS . . . TA 4 140.335 87.955 211.556 1 261.47 ? C4' AGS 1602 F 1 
HETATM 16 O O4' AGS . . . TA 4 140.066 88.996 210.615 1 268.01 ? O4' AGS 1602 F 1 
HETATM 17 C C3' AGS . . . TA 4 141.433 87.086 210.964 1 263.36 ? C3' AGS 1602 F 1 
HETATM 18 O O3' AGS . . . TA 4 141.075 85.705 211.065 1 270.04 ? O3' AGS 1602 F 1 
HETATM 19 C C2' AGS . . . TA 4 141.545 87.501 209.511 1 273.58 ? C2' AGS 1602 F 1 
HETATM 20 O O2' AGS . . . TA 4 141.203 86.403 208.66 1 281.64 ? O2' AGS 1602 F 1 
HETATM 21 C C1' AGS . . . TA 4 140.553 88.639 209.32 1 281.64 ? C1' AGS 1602 F 1 
HETATM 22 N N9 AGS . . . TA 4 141.231 89.801 208.692 1 302.76 ? N9 AGS 1602 F 1 
HETATM 23 C C8 AGS . . . TA 4 141.975 90.725 209.328 1 305.78 ? C8 AGS 1602 F 1 
HETATM 24 N N7 AGS . . . TA 4 142.451 91.653 208.46 1 312.69 ? N7 AGS 1602 F 1 
HETATM 25 C C5 AGS . . . TA 4 142.005 91.323 207.234 1 312.01 ? C5 AGS 1602 F 1 
HETATM 26 C C6 AGS . . . TA 4 142.135 91.873 205.865 1 317.12 ? C6 AGS 1602 F 1 
HETATM 27 N N6 AGS . . . TA 4 142.856 92.995 205.629 1 323.62 ? N6 AGS 1602 F 1 
HETATM 28 N N1 AGS . . . TA 4 141.508 91.221 204.86 1 323.41 ? N1 AGS 1602 F 1 
HETATM 29 C C2 AGS . . . TA 4 140.788 90.106 205.08 1 317.75 ? C2 AGS 1602 F 1 
HETATM 30 N N3 AGS . . . TA 4 140.629 89.552 206.295 1 311.18 ? N3 AGS 1602 F 1 
HETATM 31 C C4 AGS . . . TA 4 141.202 90.103 207.392 1 308.05 ? C4 AGS 1602 F 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    60 
_model_server_stats.query_time_ms           409 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#