data_6YBB
#
_model_server_result.job_id            ndYGfmlHRm-fTkLBDMFuxA 
_model_server_result.datetime_utc      '2024-11-16 01:23:05' 
_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          6ybb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":601}' 
#
_entry.id    6YBB 
#
_exptl.entry_id    6YBB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              690.411 
_entity.id                          6 
_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    4 
_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            6YBB 
_cell.length_a            61.43 
_cell.length_b            169.59 
_cell.length_c            177.6 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YBB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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,S,T,U 
_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
? 6 K N N 
? 6 L N N 
? 6 N N N 
? 6 O 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 16 A THR 16 1_555 G MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc2 G MG MG . A MG 301 1_555 H O3G ATP . A ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
metalc ? metalc3 G MG MG . A MG 301 1_555 H O2B ATP . A ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? 
metalc ? metalc4 G MG MG . A MG 301 1_555 H O1A ATP . A ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? 
metalc ? metalc5 G MG MG . A MG 301 1_555 Q O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? 
metalc ? metalc6 G MG MG . A MG 301 1_555 Q O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc7 B OG1 THR 16 B THR 16 1_555 I MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc8 I MG MG . B MG 301 1_555 J O2B ATP . B ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? 
metalc ? metalc9 I MG MG . B MG 301 1_555 J O3G ATP . B ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? 
metalc ? metalc10 I MG MG . B MG 301 1_555 R O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
metalc ? metalc11 I MG MG . B MG 301 1_555 R O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? 
#
_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 119 n n 
O1P P1 C2E doub 120 n n 
O5' P1 C2E sing 121 n n 
C5' O5' C2E sing 122 n n 
C4' O4' C2E sing 123 n n 
C4' C5' C2E sing 124 n n 
C3' C4' C2E sing 125 n n 
O3' P11 C2E sing 126 n n 
O3' C3' C2E sing 127 n n 
C2' C3' C2E sing 128 n n 
C2' C1' C2E sing 129 n n 
O2' C2' C2E sing 130 n n 
C1' O4' C2E sing 131 n n 
C1' N9 C2E sing 132 n n 
N9 C4 C2E sing 133 n y 
N9 C8 C2E sing 134 n y 
C8 N7 C2E doub 135 n y 
C5 N7 C2E sing 136 n y 
C5 C6 C2E sing 137 n n 
C6 O6 C2E doub 138 n n 
N1 C6 C2E sing 139 n n 
C2 N1 C2E sing 140 n n 
N2 C2 C2E sing 141 n n 
N3 C2 C2E doub 142 n n 
N3 C4 C2E sing 143 n n 
C4 C5 C2E doub 144 n y 
P11 O21 C2E sing 145 n n 
P11 O5A C2E sing 146 n n 
O11 P11 C2E doub 147 n n 
C5A O5A C2E sing 148 n n 
C5A C4A C2E sing 149 n n 
C4A O4A C2E sing 150 n n 
C4A C3A C2E sing 151 n n 
O4A C1A C2E sing 152 n n 
C3A C2A C2E sing 153 n n 
O3A C3A C2E sing 154 n n 
O3A P1 C2E sing 155 n n 
C2A O2A C2E sing 156 n n 
C1A C2A C2E sing 157 n n 
C1A N91 C2E sing 158 n n 
N91 C41 C2E sing 159 n y 
C81 N71 C2E doub 160 n y 
C81 N91 C2E sing 161 n y 
N71 C51 C2E sing 162 n y 
C51 C41 C2E doub 163 n y 
C51 C61 C2E sing 164 n n 
C61 O61 C2E doub 165 n n 
C61 N11 C2E sing 166 n n 
C21 N11 C2E sing 167 n n 
C21 N21 C2E sing 168 n n 
N31 C21 C2E doub 169 n n 
C41 N31 C2E sing 170 n n 
O2P HO2P C2E sing 171 n n 
C5' "H5'1" C2E sing 172 n n 
C5' "H5'2" C2E sing 173 n n 
C4' H4' C2E sing 174 n n 
C3' H3' C2E sing 175 n n 
C2' H2' C2E sing 176 n n 
O2' HO2' C2E sing 177 n n 
C1' H1' C2E sing 178 n n 
C8 H8 C2E sing 179 n n 
N1 HN1 C2E sing 180 n n 
N2 HN21 C2E sing 181 n n 
N2 HN22 C2E sing 182 n n 
O21 HO21 C2E sing 183 n n 
C5A H511 C2E sing 184 n n 
C5A H512 C2E sing 185 n n 
C4A H4A C2E sing 186 n n 
C3A H3A C2E sing 187 n n 
C2A H2A C2E sing 188 n n 
O2A HO2A C2E sing 189 n n 
C1A H1A C2E sing 190 n n 
C81 H81 C2E sing 191 n n 
N11 HN11 C2E sing 192 n n 
N21 HN24 C2E sing 193 n n 
N21 HN23 C2E sing 194 n n 
#
_atom_sites.entry_id                     6YBB 
_atom_sites.fract_transf_matrix[1][1]    0.016279 
_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]    0.005897 
_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]    0.005631 
_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 4 MG A 1 301 1 MG MG . 
H 5 ATP A 1 302 1 ATP ATP . 
I 4 MG B 1 301 2 MG MG . 
J 5 ATP B 1 302 2 ATP ATP . 
K 6 C2E E 1 601 3 C2E C2E . 
L 6 C2E E 1 602 4 C2E C2E . 
M 7 GOL E 1 603 1 GOL GOL . 
N 6 C2E F 1 601 1 C2E C2E . 
O 6 C2E F 1 602 2 C2E C2E . 
P 7 GOL F 1 603 2 GOL GOL . 
Q 8 HOH A 1 401 52 HOH HOH . 
Q 8 HOH A 2 402 31 HOH HOH . 
Q 8 HOH A 3 403 41 HOH HOH . 
Q 8 HOH A 4 404 7 HOH HOH . 
Q 8 HOH A 5 405 40 HOH HOH . 
Q 8 HOH A 6 406 2 HOH HOH . 
R 8 HOH B 1 401 11 HOH HOH . 
R 8 HOH B 2 402 9 HOH HOH . 
R 8 HOH B 3 403 23 HOH HOH . 
S 8 HOH D 1 101 19 HOH HOH . 
S 8 HOH D 2 102 26 HOH HOH . 
T 8 HOH E 1 701 66 HOH HOH . 
T 8 HOH E 2 702 56 HOH HOH . 
T 8 HOH E 3 703 6 HOH HOH . 
T 8 HOH E 4 704 4 HOH HOH . 
T 8 HOH E 5 705 16 HOH HOH . 
T 8 HOH E 6 706 5 HOH HOH . 
T 8 HOH E 7 707 47 HOH HOH . 
U 8 HOH F 1 701 51 HOH HOH . 
U 8 HOH F 2 702 65 HOH HOH . 
U 8 HOH F 3 703 60 HOH HOH . 
U 8 HOH F 4 704 27 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 P1 C2E . . . N 6 100.495 169.783 9.838 1 94.97 ? P1 C2E 601 F 1 
HETATM 2 O O2P C2E . . . N 6 99.081 169.885 10.395 1 95.65 ? O2P C2E 601 F 1 
HETATM 3 O O1P C2E . . . N 6 101.578 170.2 10.754 1 92.57 -1 O1P C2E 601 F 1 
HETATM 4 O O5' C2E . . . N 6 100.688 168.299 9.257 1 88.79 ? O5' C2E 601 F 1 
HETATM 5 C C5' C2E . . . N 6 101.877 167.851 8.572 1 93.7 ? C5' C2E 601 F 1 
HETATM 6 C C4' C2E . . . N 6 101.618 166.541 7.867 1 98.85 ? C4' C2E 601 F 1 
HETATM 7 O O4' C2E . . . N 6 101.174 165.546 8.814 1 98.03 ? O4' C2E 601 F 1 
HETATM 8 C C3' C2E . . . N 6 100.514 166.558 6.82 1 100.9 ? C3' C2E 601 F 1 
HETATM 9 O O3' C2E . . . N 6 101.042 167.017 5.556 1 102.63 ? O3' C2E 601 F 1 
HETATM 10 C C2' C2E . . . N 6 100.146 165.081 6.716 1 97.87 ? C2' C2E 601 F 1 
HETATM 11 O O2' C2E . . . N 6 101.081 164.37 5.911 1 95.53 ? O2' C2E 601 F 1 
HETATM 12 C C1' C2E . . . N 6 100.265 164.653 8.186 1 98.78 ? C1' C2E 601 F 1 
HETATM 13 N N9 C2E . . . N 6 98.983 164.705 8.913 1 98.82 ? N9 C2E 601 F 1 
HETATM 14 C C8 C2E . . . N 6 98.612 165.606 9.879 1 96.79 ? C8 C2E 601 F 1 
HETATM 15 N N7 C2E . . . N 6 97.39 165.417 10.324 1 94.13 ? N7 C2E 601 F 1 
HETATM 16 C C5 C2E . . . N 6 96.931 164.323 9.608 1 96.17 ? C5 C2E 601 F 1 
HETATM 17 C C6 C2E . . . N 6 95.673 163.639 9.637 1 99.38 ? C6 C2E 601 F 1 
HETATM 18 O O6 C2E . . . N 6 94.701 163.89 10.349 1 105.18 ? O6 C2E 601 F 1 
HETATM 19 N N1 C2E . . . N 6 95.633 162.589 8.742 1 93.41 ? N1 C2E 601 F 1 
HETATM 20 C C2 C2E . . . N 6 96.659 162.215 7.917 1 87.88 ? C2 C2E 601 F 1 
HETATM 21 N N2 C2E . . . N 6 96.445 161.162 7.126 1 83.69 ? N2 C2E 601 F 1 
HETATM 22 N N3 C2E . . . N 6 97.834 162.838 7.879 1 91.87 ? N3 C2E 601 F 1 
HETATM 23 C C4 C2E . . . N 6 97.903 163.873 8.738 1 96.03 ? C4 C2E 601 F 1 
HETATM 24 P P11 C2E . . . N 6 100.368 167.805 4.358 1 101.9 ? P11 C2E 601 F 1 
HETATM 25 O O21 C2E . . . N 6 99.118 167.025 3.959 1 101.95 ? O21 C2E 601 F 1 
HETATM 26 O O11 C2E . . . N 6 101.331 168.047 3.262 1 104.43 -1 O11 C2E 601 F 1 
HETATM 27 O O5A C2E . . . N 6 99.889 169.195 5.031 1 96.29 ? O5A C2E 601 F 1 
HETATM 28 C C5A C2E . . . N 6 100.758 170.324 5.27 1 95.51 ? C5A C2E 601 F 1 
HETATM 29 C C4A C2E . . . N 6 100.099 171.317 6.196 1 94.89 ? C4A C2E 601 F 1 
HETATM 30 O O4A C2E . . . N 6 98.955 171.918 5.55 1 91.95 ? O4A C2E 601 F 1 
HETATM 31 C C3A C2E . . . N 6 99.528 170.734 7.48 1 99.8 ? C3A C2E 601 F 1 
HETATM 32 O O3A C2E . . . N 6 100.523 170.646 8.522 1 103.85 ? O3A C2E 601 F 1 
HETATM 33 C C2A C2E . . . N 6 98.476 171.766 7.867 1 93.55 ? C2A C2E 601 F 1 
HETATM 34 O O2A C2E . . . N 6 99.071 172.907 8.473 1 92.41 ? O2A C2E 601 F 1 
HETATM 35 C C1A C2E . . . N 6 97.907 172.104 6.488 1 90.95 ? C1A C2E 601 F 1 
HETATM 36 N N91 C2E . . . N 6 96.789 171.23 6.107 1 88.32 ? N91 C2E 601 F 1 
HETATM 37 C C81 C2E . . . N 6 96.825 170.161 5.249 1 86.68 ? C81 C2E 601 F 1 
HETATM 38 N N71 C2E . . . N 6 95.655 169.59 5.082 1 86.93 ? N71 C2E 601 F 1 
HETATM 39 C C51 C2E . . . N 6 94.797 170.33 5.879 1 85.77 ? C51 C2E 601 F 1 
HETATM 40 C C61 C2E . . . N 6 93.388 170.222 6.095 1 85.25 ? C61 C2E 601 F 1 
HETATM 41 O O61 C2E . . . N 6 92.619 169.395 5.609 1 85.92 ? O61 C2E 601 F 1 
HETATM 42 N N11 C2E . . . N 6 92.919 171.193 6.957 1 83.76 ? N11 C2E 601 F 1 
HETATM 43 C C21 C2E . . . N 6 93.688 172.152 7.559 1 86.67 ? C21 C2E 601 F 1 
HETATM 44 N N21 C2E . . . N 6 93.062 173.01 8.365 1 93.4 ? N21 C2E 601 F 1 
HETATM 45 N N31 C2E . . . N 6 95.001 172.264 7.372 1 84.07 ? N31 C2E 601 F 1 
HETATM 46 C C41 C2E . . . N 6 95.484 171.337 6.523 1 86.57 ? C41 C2E 601 F 1 
#
_model_server_stats.io_time_ms              34 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           368 
_model_server_stats.encode_time_ms          26 
_model_server_stats.element_count           46 
#