data_8KBG
#
_model_server_result.job_id            aYynX-0Im8IZidtw5-b-3A 
_model_server_result.datetime_utc      '2024-10-15 06:16:21' 
_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          8kbg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":401}' 
#
_entry.id    8KBG 
#
_exptl.entry_id    8KBG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              674.411 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            cGAMP 
_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          98.3 
_cell.angle_gamma         90 
_cell.entry_id            8KBG 
_cell.length_a            71.9 
_cell.length_b            66.04 
_cell.length_c            89.37 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8KBG 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_and_software_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 
_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    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 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
#
_chem_comp.formula           'C20 H24 N10 O13 P2' 
_chem_comp.formula_weight    674.411 
_chem_comp.id                1SY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              cGAMP 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "2',3' cGAMP;c-GMP-AMP;c[G(2',5')pA(3',5')p]" 
#
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
O44 P18 1SY doub 1 n n 
O19 P18 1SY sing 2 n n 
P18 O17 1SY sing 3 n n 
P18 O20 1SY sing 4 n n 
O17 C16 1SY sing 5 n n 
O4' C4' 1SY sing 6 n n 
O4' C1' 1SY sing 7 n n 
C16 C4' 1SY sing 8 n n 
C8 N7 1SY doub 9 n y 
C8 N9 1SY sing 10 n y 
N7 C5 1SY sing 11 n y 
O20 C21 1SY sing 12 n n 
N9 C1' 1SY sing 13 n n 
N9 C4 1SY sing 14 n y 
N41 C40 1SY sing 15 n n 
C4' C3' 1SY sing 16 n n 
C1' C2' 1SY sing 17 n n 
C5 C4 1SY doub 18 n y 
C5 C6 1SY sing 19 n y 
N01 C6 1SY sing 20 n n 
C4 N3 1SY sing 21 n y 
C40 N42 1SY sing 22 n n 
C40 N39 1SY doub 23 n n 
C6 N1 1SY doub 24 n y 
N42 C36 1SY sing 25 n n 
N39 C38 1SY sing 26 n n 
C21 C22 1SY sing 27 n n 
C21 C32 1SY sing 28 n n 
O23 C22 1SY sing 29 n n 
N3 C2 1SY doub 30 n y 
C3' C2' 1SY sing 31 n n 
C3' O28 1SY sing 32 n n 
N1 C2 1SY sing 33 n y 
C2' O2' 1SY sing 34 n n 
C36 C37 1SY doub 35 n y 
C36 N33 1SY sing 36 n y 
C38 O43 1SY doub 37 n n 
C38 C37 1SY sing 38 n n 
C22 C24 1SY sing 39 n n 
C32 N33 1SY sing 40 n n 
C32 O31 1SY sing 41 n n 
C37 N35 1SY sing 42 n y 
N33 C34 1SY sing 43 n y 
O28 P27 1SY sing 44 n n 
N35 C34 1SY doub 45 n y 
O31 C24 1SY sing 46 n n 
C24 C25 1SY sing 47 n n 
O26 P27 1SY sing 48 n n 
O26 C25 1SY sing 49 n n 
P27 O29 1SY doub 50 n n 
P27 O30 1SY sing 51 n n 
C2 H1 1SY sing 52 n n 
N01 H2 1SY sing 53 n n 
N01 H3 1SY sing 54 n n 
C8 H4 1SY sing 55 n n 
C1' H5 1SY sing 56 n n 
C2' H6 1SY sing 57 n n 
O2' H7 1SY sing 58 n n 
C3' H8 1SY sing 59 n n 
C4' H9 1SY sing 60 n n 
C16 H10 1SY sing 61 n n 
C16 H11 1SY sing 62 n n 
O19 H12 1SY sing 63 n n 
C21 H13 1SY sing 64 n n 
C22 H14 1SY sing 65 n n 
O23 H15 1SY sing 66 n n 
C24 H16 1SY sing 67 n n 
C25 H17 1SY sing 68 n n 
C25 H18 1SY sing 69 n n 
O30 H19 1SY sing 70 n n 
C32 H20 1SY sing 71 n n 
C34 H21 1SY sing 72 n n 
N41 H22 1SY sing 73 n n 
N41 H23 1SY sing 74 n n 
N42 H24 1SY sing 75 n n 
#
_atom_sites.entry_id                     8KBG 
_atom_sites.fract_transf_matrix[1][1]    0.013908 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002029 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015142 
_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]    0.011308 
_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 1SY D 1 401 401 1SY 1SY . 
H 2 1SY E 1 401 401 1SY 1SY . 
I 2 1SY F 1 401 401 1SY 1SY . 
J 2 1SY G 1 401 401 1SY 1SY . 
K 2 1SY H 1 401 401 1SY 1SY . 
L 2 1SY I 1 401 401 1SY 1SY . 
M 3 HOH D 1 501 38 HOH HOH . 
M 3 HOH D 2 502 45 HOH HOH . 
M 3 HOH D 3 503 10 HOH HOH . 
M 3 HOH D 4 504 44 HOH HOH . 
M 3 HOH D 5 505 2 HOH HOH . 
M 3 HOH D 6 506 46 HOH HOH . 
M 3 HOH D 7 507 39 HOH HOH . 
M 3 HOH D 8 508 19 HOH HOH . 
M 3 HOH D 9 509 1 HOH HOH . 
M 3 HOH D 10 510 53 HOH HOH . 
M 3 HOH D 11 511 59 HOH HOH . 
M 3 HOH D 12 512 34 HOH HOH . 
M 3 HOH D 13 513 72 HOH HOH . 
M 3 HOH D 14 514 67 HOH HOH . 
M 3 HOH D 15 515 3 HOH HOH . 
M 3 HOH D 16 516 49 HOH HOH . 
M 3 HOH D 17 517 8 HOH HOH . 
M 3 HOH D 18 518 61 HOH HOH . 
M 3 HOH D 19 519 35 HOH HOH . 
M 3 HOH D 20 520 58 HOH HOH . 
M 3 HOH D 21 521 68 HOH HOH . 
M 3 HOH D 22 522 29 HOH HOH . 
M 3 HOH D 23 523 79 HOH HOH . 
M 3 HOH D 24 524 88 HOH HOH . 
M 3 HOH D 25 525 22 HOH HOH . 
M 3 HOH D 26 526 82 HOH HOH . 
M 3 HOH D 27 527 51 HOH HOH . 
M 3 HOH D 28 528 50 HOH HOH . 
M 3 HOH D 29 529 78 HOH HOH . 
N 3 HOH E 1 501 77 HOH HOH . 
N 3 HOH E 2 502 56 HOH HOH . 
N 3 HOH E 3 503 20 HOH HOH . 
N 3 HOH E 4 504 7 HOH HOH . 
N 3 HOH E 5 505 31 HOH HOH . 
N 3 HOH E 6 506 30 HOH HOH . 
N 3 HOH E 7 507 28 HOH HOH . 
N 3 HOH E 8 508 37 HOH HOH . 
N 3 HOH E 9 509 11 HOH HOH . 
N 3 HOH E 10 510 18 HOH HOH . 
N 3 HOH E 11 511 42 HOH HOH . 
N 3 HOH E 12 512 70 HOH HOH . 
N 3 HOH E 13 513 13 HOH HOH . 
N 3 HOH E 14 514 9 HOH HOH . 
N 3 HOH E 15 515 17 HOH HOH . 
N 3 HOH E 16 516 6 HOH HOH . 
N 3 HOH E 17 517 26 HOH HOH . 
N 3 HOH E 18 518 25 HOH HOH . 
N 3 HOH E 19 519 32 HOH HOH . 
N 3 HOH E 20 520 75 HOH HOH . 
N 3 HOH E 21 521 52 HOH HOH . 
N 3 HOH E 22 522 33 HOH HOH . 
N 3 HOH E 23 523 62 HOH HOH . 
N 3 HOH E 24 524 54 HOH HOH . 
N 3 HOH E 25 525 86 HOH HOH . 
N 3 HOH E 26 526 48 HOH HOH . 
N 3 HOH E 27 527 85 HOH HOH . 
N 3 HOH E 28 528 90 HOH HOH . 
N 3 HOH E 29 529 73 HOH HOH . 
O 3 HOH F 1 501 91 HOH HOH . 
O 3 HOH F 2 502 41 HOH HOH . 
O 3 HOH F 3 503 24 HOH HOH . 
O 3 HOH F 4 504 71 HOH HOH . 
O 3 HOH F 5 505 64 HOH HOH . 
O 3 HOH F 6 506 15 HOH HOH . 
O 3 HOH F 7 507 57 HOH HOH . 
P 3 HOH G 1 501 93 HOH HOH . 
P 3 HOH G 2 502 60 HOH HOH . 
P 3 HOH G 3 503 23 HOH HOH . 
P 3 HOH G 4 504 63 HOH HOH . 
P 3 HOH G 5 505 84 HOH HOH . 
P 3 HOH G 6 506 66 HOH HOH . 
P 3 HOH G 7 507 43 HOH HOH . 
P 3 HOH G 8 508 92 HOH HOH . 
P 3 HOH G 9 509 83 HOH HOH . 
Q 3 HOH H 1 501 16 HOH HOH . 
Q 3 HOH H 2 502 4 HOH HOH . 
Q 3 HOH H 3 503 74 HOH HOH . 
Q 3 HOH H 4 504 36 HOH HOH . 
Q 3 HOH H 5 505 69 HOH HOH . 
Q 3 HOH H 6 506 80 HOH HOH . 
Q 3 HOH H 7 507 27 HOH HOH . 
Q 3 HOH H 8 508 21 HOH HOH . 
Q 3 HOH H 9 509 47 HOH HOH . 
Q 3 HOH H 10 510 12 HOH HOH . 
Q 3 HOH H 11 511 55 HOH HOH . 
Q 3 HOH H 12 512 89 HOH HOH . 
R 3 HOH I 1 501 81 HOH HOH . 
R 3 HOH I 2 502 76 HOH HOH . 
R 3 HOH I 3 503 65 HOH HOH . 
R 3 HOH I 4 504 5 HOH HOH . 
R 3 HOH I 5 505 14 HOH HOH . 
R 3 HOH I 6 506 40 HOH HOH . 
R 3 HOH I 7 507 94 HOH HOH . 
R 3 HOH I 8 508 87 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 C C2 1SY . . . J 2 -2.128 -2.747 -5.285 1 55.57 ? C2 1SY 401 G 1 
HETATM 2 N N01 1SY . . . J 2 -3.987 -4.188 -7.935 1 49.55 ? N01 1SY 401 G 1 
HETATM 3 C C6 1SY . . . J 2 -3.074 -4.035 -6.973 1 59.99 ? C6 1SY 401 G 1 
HETATM 4 N N1 1SY . . . J 2 -3.049 -2.879 -6.252 1 55.59 ? N1 1SY 401 G 1 
HETATM 5 N N3 1SY . . . J 2 -1.184 -3.612 -4.894 1 54.94 ? N3 1SY 401 G 1 
HETATM 6 C C4 1SY . . . J 2 -1.235 -4.74 -5.62 1 51.71 ? C4 1SY 401 G 1 
HETATM 7 C C5 1SY . . . J 2 -2.116 -5.026 -6.646 1 58.18 ? C5 1SY 401 G 1 
HETATM 8 N N7 1SY . . . J 2 -1.877 -6.289 -7.148 1 58.36 ? N7 1SY 401 G 1 
HETATM 9 C C8 1SY . . . J 2 -0.852 -6.745 -6.453 1 59.72 ? C8 1SY 401 G 1 
HETATM 10 N N9 1SY . . . J 2 -0.399 -5.837 -5.514 1 59.75 ? N9 1SY 401 G 1 
HETATM 11 C C1' 1SY . . . J 2 0.702 -6.109 -4.566 1 61.86 ? C1' 1SY 401 G 1 
HETATM 12 C C2' 1SY . . . J 2 1.42 -4.889 -3.964 1 56.22 ? C2' 1SY 401 G 1 
HETATM 13 O O2' 1SY . . . J 2 2.816 -5.115 -3.885 1 60.49 ? O2' 1SY 401 G 1 
HETATM 14 C C3' 1SY . . . J 2 0.815 -4.839 -2.567 1 58.36 ? C3' 1SY 401 G 1 
HETATM 15 C C4' 1SY . . . J 2 0.593 -6.31 -2.252 1 60.46 ? C4' 1SY 401 G 1 
HETATM 16 C C16 1SY . . . J 2 -0.46 -6.557 -1.201 1 65.19 ? C16 1SY 401 G 1 
HETATM 17 O O17 1SY . . . J 2 -1.688 -5.932 -1.66 1 71.86 ? O17 1SY 401 G 1 
HETATM 18 P P18 1SY . . . J 2 -2.956 -5.771 -0.703 1 114.86 ? P18 1SY 401 G 1 
HETATM 19 O O19 1SY . . . J 2 -4.027 -4.999 -1.389 1 73.61 ? O19 1SY 401 G 1 
HETATM 20 O O20 1SY . . . J 2 -2.3 -4.819 0.401 1 60.18 ? O20 1SY 401 G 1 
HETATM 21 C C21 1SY . . . J 2 -1.756 -3.56 0.06 1 61.46 ? C21 1SY 401 G 1 
HETATM 22 C C22 1SY . . . J 2 -0.446 -3.329 0.806 1 66.28 ? C22 1SY 401 G 1 
HETATM 23 O O23 1SY . . . J 2 -0.616 -3.744 2.157 1 71.65 ? O23 1SY 401 G 1 
HETATM 24 C C24 1SY . . . J 2 -0.338 -1.798 0.791 1 66.22 ? C24 1SY 401 G 1 
HETATM 25 C C25 1SY . . . J 2 0.608 -1.213 -0.23 1 63.27 ? C25 1SY 401 G 1 
HETATM 26 O O26 1SY . . . J 2 0.669 -2.086 -1.365 1 63.08 ? O26 1SY 401 G 1 
HETATM 27 P P27 1SY . . . J 2 2.101 -2.724 -1.669 1 59.01 ? P27 1SY 401 G 1 
HETATM 28 O O28 1SY . . . J 2 1.695 -4.272 -1.619 1 54.06 ? O28 1SY 401 G 1 
HETATM 29 O O29 1SY . . . J 2 2.512 -2.244 -3.02 1 68.35 ? O29 1SY 401 G 1 
HETATM 30 O O30 1SY . . . J 2 3.007 -2.445 -0.52 1 65.82 ? O30 1SY 401 G 1 
HETATM 31 O O31 1SY . . . J 2 -1.672 -1.299 0.543 1 66.32 ? O31 1SY 401 G 1 
HETATM 32 C C32 1SY . . . J 2 -2.548 -2.412 0.658 1 67.53 ? C32 1SY 401 G 1 
HETATM 33 N N33 1SY . . . J 2 -3.794 -2.064 -0.021 1 72.6 ? N33 1SY 401 G 1 
HETATM 34 C C34 1SY . . . J 2 -4.016 -1.944 -1.37 1 72.6 ? C34 1SY 401 G 1 
HETATM 35 N N35 1SY . . . J 2 -5.246 -1.594 -1.675 1 70.43 ? N35 1SY 401 G 1 
HETATM 36 C C36 1SY . . . J 2 -4.99 -1.752 0.588 1 70.98 ? C36 1SY 401 G 1 
HETATM 37 C C37 1SY . . . J 2 -5.885 -1.468 -0.446 1 69.37 ? C37 1SY 401 G 1 
HETATM 38 C C38 1SY . . . J 2 -7.238 -1.112 -0.067 1 64.94 ? C38 1SY 401 G 1 
HETATM 39 N N39 1SY . . . J 2 -7.591 -1.073 1.246 1 63.17 ? N39 1SY 401 G 1 
HETATM 40 C C40 1SY . . . J 2 -6.7 -1.35 2.188 1 61.76 ? C40 1SY 401 G 1 
HETATM 41 N N41 1SY . . . J 2 -7.053 -1.307 3.473 1 66.83 ? N41 1SY 401 G 1 
HETATM 42 N N42 1SY . . . J 2 -5.416 -1.682 1.896 1 67.07 ? N42 1SY 401 G 1 
HETATM 43 O O43 1SY . . . J 2 -8.094 -0.843 -0.88 1 60.14 ? O43 1SY 401 G 1 
HETATM 44 O O44 1SY . . . J 2 -3.3 -7.094 -0.119 1 64.4 ? O44 1SY 401 G 1 
HETATM 45 O O4' 1SY . . . J 2 0.176 -6.887 -3.498 1 57.33 ? O4' 1SY 401 G 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           45 
#