data_5EXX
#
_model_server_result.job_id            N2e91IytTJqR598MAcHfnw 
_model_server_result.datetime_utc      '2024-11-28 05:36:09' 
_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          5exx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":502}' 
#
_entry.id    5EXX 
#
_exptl.entry_id    5EXX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              690.411 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" 
_entity.pdbx_number_of_molecules    2 
_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         120 
_cell.entry_id            5EXX 
_cell.length_a            137.836 
_cell.length_b            137.836 
_cell.length_c            172.773 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5EXX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        182 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63 2 2' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4,5,6 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 137.836 0 0 
3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 68.918 119.369478 0 
4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 68.918 119.369478 86.3865 
5 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 137.836 0 86.3865 
6 'crystal symmetry operation' 12_555 x,x-y,-z+1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 86.3865 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 D N N 
#
_chem_comp.formula           'C20 H24 N10 O14 P2' 
_chem_comp.formula_weight    690.411 
_chem_comp.id                C2E 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'c-di-GMP;Cyclic diguanosine monophosphate' 
#
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
P1 O2P C2E sing 70 n n 
O1P P1 C2E doub 71 n n 
O5' P1 C2E sing 72 n n 
C5' O5' C2E sing 73 n n 
C4' O4' C2E sing 74 n n 
C4' C5' C2E sing 75 n n 
C3' C4' C2E sing 76 n n 
O3' P11 C2E sing 77 n n 
O3' C3' C2E sing 78 n n 
C2' C3' C2E sing 79 n n 
C2' C1' C2E sing 80 n n 
O2' C2' C2E sing 81 n n 
C1' O4' C2E sing 82 n n 
C1' N9 C2E sing 83 n n 
N9 C4 C2E sing 84 n y 
N9 C8 C2E sing 85 n y 
C8 N7 C2E doub 86 n y 
C5 N7 C2E sing 87 n y 
C5 C6 C2E sing 88 n n 
C6 O6 C2E doub 89 n n 
N1 C6 C2E sing 90 n n 
C2 N1 C2E sing 91 n n 
N2 C2 C2E sing 92 n n 
N3 C2 C2E doub 93 n n 
N3 C4 C2E sing 94 n n 
C4 C5 C2E doub 95 n y 
P11 O21 C2E sing 96 n n 
P11 O5A C2E sing 97 n n 
O11 P11 C2E doub 98 n n 
C5A O5A C2E sing 99 n n 
C5A C4A C2E sing 100 n n 
C4A O4A C2E sing 101 n n 
C4A C3A C2E sing 102 n n 
O4A C1A C2E sing 103 n n 
C3A C2A C2E sing 104 n n 
O3A C3A C2E sing 105 n n 
O3A P1 C2E sing 106 n n 
C2A O2A C2E sing 107 n n 
C1A C2A C2E sing 108 n n 
C1A N91 C2E sing 109 n n 
N91 C41 C2E sing 110 n y 
C81 N71 C2E doub 111 n y 
C81 N91 C2E sing 112 n y 
N71 C51 C2E sing 113 n y 
C51 C41 C2E doub 114 n y 
C51 C61 C2E sing 115 n n 
C61 O61 C2E doub 116 n n 
C61 N11 C2E sing 117 n n 
C21 N11 C2E sing 118 n n 
C21 N21 C2E sing 119 n n 
N31 C21 C2E doub 120 n n 
C41 N31 C2E sing 121 n n 
O2P HO2P C2E sing 122 n n 
C5' "H5'1" C2E sing 123 n n 
C5' "H5'2" C2E sing 124 n n 
C4' H4' C2E sing 125 n n 
C3' H3' C2E sing 126 n n 
C2' H2' C2E sing 127 n n 
O2' HO2' C2E sing 128 n n 
C1' H1' C2E sing 129 n n 
C8 H8 C2E sing 130 n n 
N1 HN1 C2E sing 131 n n 
N2 HN21 C2E sing 132 n n 
N2 HN22 C2E sing 133 n n 
O21 HO21 C2E sing 134 n n 
C5A H511 C2E sing 135 n n 
C5A H512 C2E sing 136 n n 
C4A H4A C2E sing 137 n n 
C3A H3A C2E sing 138 n n 
C2A H2A C2E sing 139 n n 
O2A HO2A C2E sing 140 n n 
C1A H1A C2E sing 141 n n 
C81 H81 C2E sing 142 n n 
N11 HN11 C2E sing 143 n n 
N21 HN24 C2E sing 144 n n 
N21 HN23 C2E sing 145 n n 
#
_atom_sites.entry_id                     5EXX 
_atom_sites.fract_transf_matrix[1][1]    0.007255 
_atom_sites.fract_transf_matrix[1][2]    0.004189 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008377 
_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]    0.005788 
_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
B 2 SO4 A 1 501 1 SO4 SO4 . 
C 3 C2E A 1 502 360 C2E C2E . 
D 3 C2E A 1 503 361 C2E C2E . 
#
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 P1 C2E . . . C 3 64.768 43.927 56.618 1 46.42 ? P1 C2E 502 A 1 
HETATM 2 O O2P C2E . . . C 3 65.054 42.505 56.705 1 47.39 ? O2P C2E 502 A 1 
HETATM 3 O O1P C2E . . . C 3 63.981 44.521 57.675 1 48.17 ? O1P C2E 502 A 1 
HETATM 4 O O5' C2E . . . C 3 64.23 44.273 55.201 1 45.46 ? O5' C2E 502 A 1 
HETATM 5 C C5' C2E . . . C 3 65.171 44.172 54.179 1 44.42 ? C5' C2E 502 A 1 
HETATM 6 C C4' C2E . . . C 3 64.633 44.554 52.829 1 44.45 ? C4' C2E 502 A 1 
HETATM 7 O O4' C2E . . . C 3 63.294 44.211 52.827 1 45.49 ? O4' C2E 502 A 1 
HETATM 8 C C3' C2E . . . C 3 64.573 46.031 52.685 1 44.43 ? C3' C2E 502 A 1 
HETATM 9 O O3' C2E . . . C 3 65.718 46.609 52.142 1 45.91 ? O3' C2E 502 A 1 
HETATM 10 C C2' C2E . . . C 3 63.415 46.239 51.778 1 46.46 ? C2' C2E 502 A 1 
HETATM 11 O O2' C2E . . . C 3 63.806 45.738 50.544 1 44.66 ? O2' C2E 502 A 1 
HETATM 12 C C1' C2E . . . C 3 62.501 45.168 52.177 1 46.58 ? C1' C2E 502 A 1 
HETATM 13 N N9 C2E . . . C 3 61.459 45.632 53.073 1 46.54 ? N9 C2E 502 A 1 
HETATM 14 C C8 C2E . . . C 3 61.328 45.292 54.332 1 47.16 ? C8 C2E 502 A 1 
HETATM 15 N N7 C2E . . . C 3 60.24 45.84 54.878 1 45.48 ? N7 C2E 502 A 1 
HETATM 16 C C5 C2E . . . C 3 59.65 46.55 53.939 1 45.7 ? C5 C2E 502 A 1 
HETATM 17 C C6 C2E . . . C 3 58.451 47.376 53.842 1 45.92 ? C6 C2E 502 A 1 
HETATM 18 O O6 C2E . . . C 3 57.716 47.536 54.82 1 44.57 ? O6 C2E 502 A 1 
HETATM 19 N N1 C2E . . . C 3 58.192 47.943 52.693 1 47.33 ? N1 C2E 502 A 1 
HETATM 20 C C2 C2E . . . C 3 58.952 47.759 51.654 1 48.48 ? C2 C2E 502 A 1 
HETATM 21 N N2 C2E . . . C 3 58.631 48.345 50.524 1 48.36 ? N2 C2E 502 A 1 
HETATM 22 N N3 C2E . . . C 3 60.05 47.03 51.664 1 47.24 ? N3 C2E 502 A 1 
HETATM 23 C C4 C2E . . . C 3 60.458 46.405 52.76 1 46.85 ? C4 C2E 502 A 1 
HETATM 24 P P11 C2E . . . C 3 65.882 48.04 52.647 1 47.72 ? P11 C2E 502 A 1 
HETATM 25 O O21 C2E . . . C 3 64.676 48.699 52.248 1 45.05 ? O21 C2E 502 A 1 
HETATM 26 O O11 C2E . . . C 3 67.175 48.586 52.327 1 42.94 ? O11 C2E 502 A 1 
HETATM 27 O O5A C2E . . . C 3 65.907 47.852 54.169 1 47.57 ? O5A C2E 502 A 1 
HETATM 28 C C5A C2E . . . C 3 66.888 46.954 54.556 1 44.67 ? C5A C2E 502 A 1 
HETATM 29 C C4A C2E . . . C 3 67.076 46.792 56.05 1 43.56 ? C4A C2E 502 A 1 
HETATM 30 O O4A C2E . . . C 3 67.24 48.005 56.736 1 42.29 ? O4A C2E 502 A 1 
HETATM 31 C C3A C2E . . . C 3 65.929 46.128 56.713 1 43.49 ? C3A C2E 502 A 1 
HETATM 32 O O3A C2E . . . C 3 66.091 44.742 56.686 1 45.2 ? O3A C2E 502 A 1 
HETATM 33 C C2A C2E . . . C 3 66.103 46.596 58.101 1 39.36 ? C2A C2E 502 A 1 
HETATM 34 O O2A C2E . . . C 3 67.189 45.85 58.577 1 37.02 ? O2A C2E 502 A 1 
HETATM 35 C C1A C2E . . . C 3 66.563 48.005 57.967 1 39.72 ? C1A C2E 502 A 1 
HETATM 36 N N91 C2E . . . C 3 65.459 48.997 57.892 1 37.8 ? N91 C2E 502 A 1 
HETATM 37 C C81 C2E . . . C 3 65.078 49.619 56.793 1 37.55 ? C81 C2E 502 A 1 
HETATM 38 N N71 C2E . . . C 3 64.098 50.486 56.996 1 36.7 ? N71 C2E 502 A 1 
HETATM 39 C C51 C2E . . . C 3 63.806 50.447 58.274 1 36.08 ? C51 C2E 502 A 1 
HETATM 40 C C61 C2E . . . C 3 62.83 51.122 59.126 1 35.15 ? C61 C2E 502 A 1 
HETATM 41 O O61 C2E . . . C 3 62.041 51.955 58.68 1 37.16 ? O61 C2E 502 A 1 
HETATM 42 N N11 C2E . . . C 3 62.832 50.814 60.391 1 35.03 ? N11 C2E 502 A 1 
HETATM 43 C C21 C2E . . . C 3 63.681 49.928 60.872 1 34.94 ? C21 C2E 502 A 1 
HETATM 44 N N21 C2E . . . C 3 63.642 49.653 62.171 1 32.06 ? N21 C2E 502 A 1 
HETATM 45 N N31 C2E . . . C 3 64.584 49.278 60.155 1 36.36 ? N31 C2E 502 A 1 
HETATM 46 C C41 C2E . . . C 3 64.702 49.482 58.857 1 37.4 ? C41 C2E 502 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           46 
#