data_6ZXM
#
_model_server_result.job_id            KHD26g4qfaTRLeDxxV--JA 
_model_server_result.datetime_utc      '2024-11-28 15:37:46' 
_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          6zxm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":301}' 
#
_entry.id    6ZXM 
#
_exptl.entry_id    6ZXM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              690.411 
_entity.id                          2 
_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    12 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          118.2 
_cell.angle_gamma         90 
_cell.entry_id            6ZXM 
_cell.length_a            122.603 
_cell.length_b            72.917 
_cell.length_c            125.729 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6ZXM 
_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
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_defined_assembly 2 
? dimeric 2 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,B,G,H,I,J,K,L 1 1 
C,D,M,N,O,P,Q,R 2 1 
E,F,S,T,U,V,W,X 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 H N N 
? 2 J N N 
? 2 K N N 
? 2 M N N 
? 2 N N N 
? 2 P N N 
? 2 Q N N 
? 2 S N N 
? 2 T N N 
? 2 V N N 
? 2 W 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 OE2 GLU 32 A GLU 12 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc2 A OD1 ASP 33 A ASP 13 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc3 A OD2 ASP 76 A ASP 56 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc4 B OE2 GLU 32 B GLU 12 1_555 L MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc5 B OD1 ASP 33 B ASP 13 1_555 L MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc6 B OD2 ASP 76 B ASP 56 1_555 L MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc7 L MG MG . B MG 303 1_555 F O GLY 107 F GLY 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? 
metalc ? metalc8 C OE2 GLU 32 C GLU 12 1_555 O MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc9 C OD1 ASP 33 C ASP 13 1_555 O MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
metalc ? metalc10 C OD2 ASP 76 C ASP 56 1_555 O MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc11 D OE2 GLU 32 D GLU 12 1_555 R MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc12 D OD1 ASP 33 D ASP 13 1_555 R MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc13 D OD2 ASP 76 D ASP 56 1_555 R MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc14 E OE2 GLU 32 E GLU 12 1_555 U MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc15 E OD1 ASP 33 E ASP 13 1_555 U MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
metalc ? metalc16 E OD2 ASP 76 E ASP 56 1_555 U MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc17 F OE2 GLU 32 F GLU 12 1_555 X MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
metalc ? metalc18 F OD1 ASP 33 F ASP 13 1_555 X MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc19 F OD2 ASP 76 F ASP 56 1_555 X MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? 
#
_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                     6ZXM 
_atom_sites.fract_transf_matrix[1][1]    0.008156 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004374 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013714 
_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]    0.009025 
_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 C2E A 1 301 301 C2E C2E . 
H 2 C2E A 1 302 302 C2E C2E . 
I 3 MG A 1 303 303 MG MG . 
J 2 C2E B 1 301 301 C2E C2E . 
K 2 C2E B 1 302 302 C2E C2E . 
L 3 MG B 1 303 303 MG MG . 
M 2 C2E C 1 301 301 C2E C2E . 
N 2 C2E C 1 302 302 C2E C2E . 
O 3 MG C 1 303 303 MG MG . 
P 2 C2E D 1 301 301 C2E C2E . 
Q 2 C2E D 1 302 302 C2E C2E . 
R 3 MG D 1 303 303 MG MG . 
S 2 C2E E 1 301 301 C2E C2E . 
T 2 C2E E 1 302 302 C2E C2E . 
U 3 MG E 1 303 303 MG MG . 
V 2 C2E F 1 301 301 C2E C2E . 
W 2 C2E F 1 302 302 C2E C2E . 
X 3 MG F 1 303 303 MG MG . 
#
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 . . . M 2 -8.417 -2.579 -38.722 1 73.9 ? P1 C2E 301 C 1 
HETATM 2 O O2P C2E . . . M 2 -7.36 -2.599 -37.65 1 72.77 ? O2P C2E 301 C 1 
HETATM 3 O O1P C2E . . . M 2 -9.694 -3.349 -38.725 1 77.06 ? O1P C2E 301 C 1 
HETATM 4 O O5' C2E . . . M 2 -8.654 -1.039 -39.22 1 76.49 ? O5' C2E 301 C 1 
HETATM 5 C C5' C2E . . . M 2 -9.948 -0.83 -39.967 1 83 ? C5' C2E 301 C 1 
HETATM 6 C C4' C2E . . . M 2 -10.104 0.655 -40.184 1 86.91 ? C4' C2E 301 C 1 
HETATM 7 O O4' C2E . . . M 2 -9.778 1.304 -38.934 1 86.9 ? O4' C2E 301 C 1 
HETATM 8 C C3' C2E . . . M 2 -9.131 1.408 -41.094 1 87.68 ? C3' C2E 301 C 1 
HETATM 9 O O3' C2E . . . M 2 -9.14 1.133 -42.534 1 91.9 ? O3' C2E 301 C 1 
HETATM 10 C C2' C2E . . . M 2 -9.563 2.835 -40.694 1 88.67 ? C2' C2E 301 C 1 
HETATM 11 O O2' C2E . . . M 2 -10.833 3.244 -41.161 1 91.55 ? O2' C2E 301 C 1 
HETATM 12 C C1' C2E . . . M 2 -9.62 2.687 -39.171 1 88.06 ? C1' C2E 301 C 1 
HETATM 13 N N9 C2E . . . M 2 -8.451 3.177 -38.429 1 86.02 ? N9 C2E 301 C 1 
HETATM 14 C C8 C2E . . . M 2 -7.689 2.51 -37.49 1 82.52 ? C8 C2E 301 C 1 
HETATM 15 N N7 C2E . . . M 2 -6.718 3.24 -36.983 1 81.01 ? N7 C2E 301 C 1 
HETATM 16 C C5 C2E . . . M 2 -6.86 4.473 -37.624 1 85.31 ? C5 C2E 301 C 1 
HETATM 17 C C6 C2E . . . M 2 -6.11 5.678 -37.501 1 86.53 ? C6 C2E 301 C 1 
HETATM 18 O O6 C2E . . . M 2 -5.136 5.915 -36.768 1 85.49 ? O6 C2E 301 C 1 
HETATM 19 N N1 C2E . . . M 2 -6.62 6.693 -38.326 1 88.46 ? N1 C2E 301 C 1 
HETATM 20 C C2 C2E . . . M 2 -7.679 6.566 -39.187 1 89.12 ? C2 C2E 301 C 1 
HETATM 21 N N2 C2E . . . M 2 -8.002 7.65 -39.903 1 91.59 ? N2 C2E 301 C 1 
HETATM 22 N N3 C2E . . . M 2 -8.375 5.442 -39.319 1 89.14 ? N3 C2E 301 C 1 
HETATM 23 C C4 C2E . . . M 2 -7.925 4.448 -38.508 1 86.95 ? C4 C2E 301 C 1 
HETATM 24 P P11 C2E . . . M 2 -7.824 0.579 -43.325 1 89.38 ? P11 C2E 301 C 1 
HETATM 25 O O21 C2E . . . M 2 -6.605 1.476 -43.324 1 85.28 ? O21 C2E 301 C 1 
HETATM 26 O O11 C2E . . . M 2 -8.425 0.078 -44.624 1 91.53 ? O11 C2E 301 C 1 
HETATM 27 O O5A C2E . . . M 2 -7.26 -0.62 -42.422 1 80.7 ? O5A C2E 301 C 1 
HETATM 28 C C5A C2E . . . M 2 -7.784 -1.937 -42.641 1 80.05 ? C5A C2E 301 C 1 
HETATM 29 C C4A C2E . . . M 2 -6.768 -2.869 -42.057 1 76 ? C4A C2E 301 C 1 
HETATM 30 O O4A C2E . . . M 2 -5.495 -2.44 -42.567 1 73.22 ? O4A C2E 301 C 1 
HETATM 31 C C3A C2E . . . M 2 -6.557 -2.797 -40.549 1 74.5 ? C3A C2E 301 C 1 
HETATM 32 O O3A C2E . . . M 2 -7.691 -3.423 -39.883 1 75.95 ? O3A C2E 301 C 1 
HETATM 33 C C2A C2E . . . M 2 -5.127 -3.4 -40.456 1 70.19 ? C2A C2E 301 C 1 
HETATM 34 O O2A C2E . . . M 2 -4.79 -4.715 -40.883 1 68.66 ? O2A C2E 301 C 1 
HETATM 35 C C1A C2E . . . M 2 -4.491 -2.636 -41.601 1 69.12 ? C1A C2E 301 C 1 
HETATM 36 N N91 C2E . . . M 2 -3.867 -1.351 -41.318 1 67.67 ? N91 C2E 301 C 1 
HETATM 37 C C81 C2E . . . M 2 -4.088 -0.118 -41.885 1 69.57 ? C81 C2E 301 C 1 
HETATM 38 N N71 C2E . . . M 2 -3.176 0.768 -41.546 1 67.69 ? N71 C2E 301 C 1 
HETATM 39 C C51 C2E . . . M 2 -2.286 0.051 -40.749 1 64.79 ? C51 C2E 301 C 1 
HETATM 40 C C61 C2E . . . M 2 -1.086 0.457 -40.112 1 63.73 ? C61 C2E 301 C 1 
HETATM 41 O O61 C2E . . . M 2 -0.5 1.557 -40.206 1 62.41 ? O61 C2E 301 C 1 
HETATM 42 N N11 C2E . . . M 2 -0.506 -0.635 -39.462 1 62.31 ? N11 C2E 301 C 1 
HETATM 43 C C21 C2E . . . M 2 -1.024 -1.913 -39.371 1 61.14 ? C21 C2E 301 C 1 
HETATM 44 N N21 C2E . . . M 2 -0.344 -2.84 -38.728 1 58.27 ? N21 C2E 301 C 1 
HETATM 45 N N31 C2E . . . M 2 -2.131 -2.285 -39.961 1 63.17 ? N31 C2E 301 C 1 
HETATM 46 C C41 C2E . . . M 2 -2.695 -1.254 -40.627 1 64.65 ? C41 C2E 301 C 1 
#
_model_server_stats.io_time_ms              30 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    47 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           46 
#