data_5GRB
#
_model_server_result.job_id            0Bir3oU6scE2cfe7nSV25Q 
_model_server_result.datetime_utc      '2025-03-04 07:42:41' 
_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          5grb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":401}' 
#
_entry.id    5GRB 
#
_exptl.entry_id    5GRB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          89.98 
_cell.angle_gamma         90 
_cell.entry_id            5GRB 
_cell.length_a            73.668 
_cell.length_b            54.912 
_cell.length_c            163.097 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5GRB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? tetrameric 4 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,F,G,H,K,L,O,P,Q,R,S,U 1 1 
B,I,J,T 2 1 
D,M,N,V 3 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
? 2 G N N 
? 2 I N N 
? 2 K N N 
? 2 M N N 
? 2 O N N 
? 2 Q 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 SG CYS 155 A CYS 270 1_555 H ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? 
metalc ? metalc2 A SG CYS 166 A CYS 281 1_555 H ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc3 A SG CYS 171 A CYS 286 1_555 H ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? 
metalc ? metalc4 H ZN ZN . A ZN 402 1_555 S O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc5 B SG CYS 155 B CYS 270 1_555 J ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? 
metalc ? metalc6 B SG CYS 166 B CYS 281 1_555 J ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc7 B SG CYS 171 B CYS 286 1_555 J ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc8 C SG CYS 155 C CYS 270 1_555 L ZN ZN . C ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc9 C SG CYS 166 C CYS 281 1_555 L ZN ZN . C ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc10 D SG CYS 155 D CYS 270 1_555 N ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? 
metalc ? metalc11 D SG CYS 166 D CYS 281 1_555 N ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc12 D SG CYS 171 D CYS 286 1_555 N ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? 
metalc ? metalc13 E SG CYS 155 E CYS 270 1_555 P ZN ZN . E ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
metalc ? metalc14 E SG CYS 166 E CYS 281 1_555 P ZN ZN . E ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? 
metalc ? metalc15 E SG CYS 171 E CYS 286 1_555 P ZN ZN . E ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc16 F SG CYS 155 F CYS 270 1_555 R ZN ZN . F ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc17 F SG CYS 166 F CYS 281 1_555 R ZN ZN . F ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc18 F SG CYS 171 F CYS 286 1_555 R ZN ZN . F ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? 
#
_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                     5GRB 
_atom_sites.fract_transf_matrix[1][1]    0.013574 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    -0.000005 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018211 
_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]    0.006131 
_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 1 401 10 AGS AGS . 
H 3 ZN A 1 402 2 ZN ZN . 
I 2 AGS B 1 401 11 AGS AGS . 
J 3 ZN B 1 402 3 ZN ZN . 
K 2 AGS C 1 401 12 AGS AGS . 
L 3 ZN C 1 402 4 ZN ZN . 
M 2 AGS D 1 401 13 AGS AGS . 
N 3 ZN D 1 402 5 ZN ZN . 
O 2 AGS E 1 401 4 AGS AGS . 
P 3 ZN E 1 402 6 ZN ZN . 
Q 2 AGS F 1 401 9 AGS AGS . 
R 3 ZN F 1 402 1 ZN ZN . 
S 4 HOH A 1 501 13 HOH HOH . 
S 4 HOH A 2 502 3 HOH HOH . 
T 4 HOH B 1 501 4 HOH HOH . 
T 4 HOH B 2 502 7 HOH HOH . 
U 4 HOH C 1 501 5 HOH HOH . 
U 4 HOH C 2 502 6 HOH HOH . 
U 4 HOH C 3 503 8 HOH HOH . 
U 4 HOH C 4 504 1 HOH HOH . 
V 4 HOH D 1 501 10 HOH HOH . 
V 4 HOH D 2 502 2 HOH HOH . 
V 4 HOH D 3 503 12 HOH HOH . 
V 4 HOH D 4 504 9 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 . . . Q 2 -50.587 9.421 -5.994 1 108.15 ? PG AGS 401 F 1 
HETATM 2 S S1G AGS . . . Q 2 -49.2 10.784 -5.806 1 94.52 ? S1G AGS 401 F 1 
HETATM 3 O O2G AGS . . . Q 2 -50.471 8.692 -7.373 1 101.16 ? O2G AGS 401 F 1 
HETATM 4 O O3G AGS . . . Q 2 -51.999 10.083 -5.911 1 101.45 ? O3G AGS 401 F 1 
HETATM 5 P PB AGS . . . Q 2 -49.103 7.713 -4.412 1 81.77 ? PB AGS 401 F 1 
HETATM 6 O O1B AGS . . . Q 2 -48.007 8.021 -5.363 1 101.75 ? O1B AGS 401 F 1 
HETATM 7 O O2B AGS . . . Q 2 -48.757 8.135 -2.978 1 87.21 ? O2B AGS 401 F 1 
HETATM 8 O O3B AGS . . . Q 2 -50.476 8.383 -4.833 1 97.87 ? O3B AGS 401 F 1 
HETATM 9 P PA AGS . . . Q 2 -48.991 5.612 -5.869 1 86.7 ? PA AGS 401 F 1 
HETATM 10 O O1A AGS . . . Q 2 -49.719 6.372 -6.914 1 93.45 ? O1A AGS 401 F 1 
HETATM 11 O O2A AGS . . . Q 2 -47.477 5.841 -5.858 1 99.45 ? O2A AGS 401 F 1 
HETATM 12 O O3A AGS . . . Q 2 -49.359 6.167 -4.453 1 81.61 ? O3A AGS 401 F 1 
HETATM 13 O O5' AGS . . . Q 2 -49.375 4.076 -6.006 1 86.18 ? O5' AGS 401 F 1 
HETATM 14 C C5' AGS . . . Q 2 -49.24 3.414 -7.293 1 92.03 ? C5' AGS 401 F 1 
HETATM 15 C C4' AGS . . . Q 2 -47.902 2.713 -7.395 1 90.37 ? C4' AGS 401 F 1 
HETATM 16 O O4' AGS . . . Q 2 -47.912 1.823 -8.531 1 87.8 ? O4' AGS 401 F 1 
HETATM 17 C C3' AGS . . . Q 2 -46.685 3.604 -7.612 1 81.86 ? C3' AGS 401 F 1 
HETATM 18 O O3' AGS . . . Q 2 -45.495 2.995 -7.125 1 81.21 ? O3' AGS 401 F 1 
HETATM 19 C C2' AGS . . . Q 2 -46.657 3.749 -9.131 1 83.85 ? C2' AGS 401 F 1 
HETATM 20 O O2' AGS . . . Q 2 -45.337 4.021 -9.581 1 87.27 ? O2' AGS 401 F 1 
HETATM 21 C C1' AGS . . . Q 2 -47.147 2.372 -9.591 1 91.26 ? C1' AGS 401 F 1 
HETATM 22 N N9 AGS . . . Q 2 -47.999 2.407 -10.778 1 112.38 ? N9 AGS 401 F 1 
HETATM 23 C C8 AGS . . . Q 2 -48.09 3.423 -11.702 1 106.84 ? C8 AGS 401 F 1 
HETATM 24 N N7 AGS . . . Q 2 -48.951 3.181 -12.67 1 95.12 ? N7 AGS 401 F 1 
HETATM 25 C C5 AGS . . . Q 2 -49.454 1.932 -12.356 1 110.73 ? C5 AGS 401 F 1 
HETATM 26 C C6 AGS . . . Q 2 -50.408 1.104 -12.989 1 111.56 ? C6 AGS 401 F 1 
HETATM 27 N N6 AGS . . . Q 2 -51.051 1.44 -14.118 1 94.11 ? N6 AGS 401 F 1 
HETATM 28 N N1 AGS . . . Q 2 -50.688 -0.092 -12.42 1 109.42 ? N1 AGS 401 F 1 
HETATM 29 C C2 AGS . . . Q 2 -50.048 -0.426 -11.29 1 95.23 ? C2 AGS 401 F 1 
HETATM 30 N N3 AGS . . . Q 2 -49.137 0.263 -10.604 1 88.06 ? N3 AGS 401 F 1 
HETATM 31 C C4 AGS . . . Q 2 -48.881 1.445 -11.196 1 107.49 ? C4 AGS 401 F 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           230 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           31 
#