data_4EF4 # _model_server_result.job_id SiryGjg1I4Bp8OdtSLfUwA _model_server_result.datetime_utc '2024-10-19 03:37:01' _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 4ef4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4EF4 # _exptl.entry_id 4EF4 _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.03 _cell.angle_gamma 90 _cell.entry_id 4EF4 _cell.length_a 61.375 _cell.length_b 72.84 _cell.length_c 62.44 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4EF4 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OD2 ASP 91 A ASP 205 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.851 ? metalc ? metalc2 A OE1 GLU 202 A GLU 316 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc3 A OE2 GLU 202 A GLU 316 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? metalc ? metalc4 D CA CA . A CA 402 1_555 F O HOH . A HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc5 D CA CA . A CA 402 1_555 F O HOH . A HOH 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? metalc ? metalc6 D CA CA . A CA 402 1_555 F O HOH . A HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc7 B O VAL 227 B VAL 341 1_555 E CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc8 E CA CA . B CA 401 1_555 G O HOH . B HOH 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? # _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 4EF4 _atom_sites.fract_transf_matrix[1][1] 0.016293 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002009 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013729 _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] 0.016137 _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 C 2 C2E A 1 401 1 C2E C2E . D 3 CA A 1 402 2 CA CA . E 3 CA B 1 401 1 CA CA . F 4 HOH A 1 501 1 HOH HOH . F 4 HOH A 2 502 2 HOH HOH . F 4 HOH A 3 503 3 HOH HOH . F 4 HOH A 4 504 6 HOH HOH . F 4 HOH A 5 505 10 HOH HOH . F 4 HOH A 6 506 11 HOH HOH . F 4 HOH A 7 507 12 HOH HOH . F 4 HOH A 8 508 13 HOH HOH . F 4 HOH A 9 509 14 HOH HOH . F 4 HOH A 10 510 15 HOH HOH . F 4 HOH A 11 511 17 HOH HOH . F 4 HOH A 12 512 18 HOH HOH . F 4 HOH A 13 513 19 HOH HOH . F 4 HOH A 14 514 20 HOH HOH . F 4 HOH A 15 515 21 HOH HOH . F 4 HOH A 16 516 22 HOH HOH . F 4 HOH A 17 517 23 HOH HOH . F 4 HOH A 18 518 24 HOH HOH . F 4 HOH A 19 519 26 HOH HOH . F 4 HOH A 20 520 31 HOH HOH . F 4 HOH A 21 521 34 HOH HOH . F 4 HOH A 22 522 36 HOH HOH . F 4 HOH A 23 523 37 HOH HOH . F 4 HOH A 24 524 39 HOH HOH . F 4 HOH A 25 525 40 HOH HOH . F 4 HOH A 26 526 41 HOH HOH . F 4 HOH A 27 527 42 HOH HOH . F 4 HOH A 28 528 43 HOH HOH . F 4 HOH A 29 529 44 HOH HOH . F 4 HOH A 30 530 45 HOH HOH . F 4 HOH A 31 531 50 HOH HOH . F 4 HOH A 32 532 53 HOH HOH . F 4 HOH A 33 533 54 HOH HOH . F 4 HOH A 34 534 56 HOH HOH . F 4 HOH A 35 535 57 HOH HOH . F 4 HOH A 36 536 58 HOH HOH . F 4 HOH A 37 537 59 HOH HOH . F 4 HOH A 38 538 66 HOH HOH . F 4 HOH A 39 539 67 HOH HOH . F 4 HOH A 40 540 71 HOH HOH . F 4 HOH A 41 541 72 HOH HOH . F 4 HOH A 42 542 78 HOH HOH . F 4 HOH A 43 543 79 HOH HOH . F 4 HOH A 44 544 81 HOH HOH . F 4 HOH A 45 545 83 HOH HOH . F 4 HOH A 46 546 87 HOH HOH . F 4 HOH A 47 547 91 HOH HOH . F 4 HOH A 48 548 94 HOH HOH . F 4 HOH A 49 549 97 HOH HOH . F 4 HOH A 50 550 99 HOH HOH . G 4 HOH B 1 501 4 HOH HOH . G 4 HOH B 2 502 5 HOH HOH . G 4 HOH B 3 503 7 HOH HOH . G 4 HOH B 4 504 8 HOH HOH . G 4 HOH B 5 505 9 HOH HOH . G 4 HOH B 6 506 16 HOH HOH . G 4 HOH B 7 507 25 HOH HOH . G 4 HOH B 8 508 27 HOH HOH . G 4 HOH B 9 509 28 HOH HOH . G 4 HOH B 10 510 29 HOH HOH . G 4 HOH B 11 511 30 HOH HOH . G 4 HOH B 12 512 32 HOH HOH . G 4 HOH B 13 513 33 HOH HOH . G 4 HOH B 14 514 35 HOH HOH . G 4 HOH B 15 515 38 HOH HOH . G 4 HOH B 16 516 46 HOH HOH . G 4 HOH B 17 517 47 HOH HOH . G 4 HOH B 18 518 48 HOH HOH . G 4 HOH B 19 519 49 HOH HOH . G 4 HOH B 20 520 51 HOH HOH . G 4 HOH B 21 521 52 HOH HOH . G 4 HOH B 22 522 55 HOH HOH . G 4 HOH B 23 523 60 HOH HOH . G 4 HOH B 24 524 61 HOH HOH . G 4 HOH B 25 525 62 HOH HOH . G 4 HOH B 26 526 63 HOH HOH . G 4 HOH B 27 527 64 HOH HOH . G 4 HOH B 28 528 65 HOH HOH . G 4 HOH B 29 529 68 HOH HOH . G 4 HOH B 30 530 69 HOH HOH . G 4 HOH B 31 531 70 HOH HOH . G 4 HOH B 32 532 73 HOH HOH . G 4 HOH B 33 533 74 HOH HOH . G 4 HOH B 34 534 75 HOH HOH . G 4 HOH B 35 535 76 HOH HOH . G 4 HOH B 36 536 77 HOH HOH . G 4 HOH B 37 537 80 HOH HOH . G 4 HOH B 38 538 82 HOH HOH . G 4 HOH B 39 539 84 HOH HOH . G 4 HOH B 40 540 85 HOH HOH . G 4 HOH B 41 541 86 HOH HOH . G 4 HOH B 42 542 88 HOH HOH . G 4 HOH B 43 543 89 HOH HOH . G 4 HOH B 44 544 90 HOH HOH . G 4 HOH B 45 545 92 HOH HOH . G 4 HOH B 46 546 93 HOH HOH . G 4 HOH B 47 547 95 HOH HOH . G 4 HOH B 48 548 96 HOH HOH . G 4 HOH B 49 549 98 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 . . . C 2 -10.806 18.934 -15.156 1 46.54 ? P1 C2E 401 A 1 HETATM 2 O O2P C2E . . . C 2 -10.924 20.018 -14.164 1 45.3 ? O2P C2E 401 A 1 HETATM 3 O O1P C2E . . . C 2 -9.376 18.951 -15.681 1 37.15 ? O1P C2E 401 A 1 HETATM 4 O O5' C2E . . . C 2 -11.67 19.151 -16.465 1 42.09 ? O5' C2E 401 A 1 HETATM 5 C C5' C2E . . . C 2 -13.136 19.085 -16.375 1 37.35 ? C5' C2E 401 A 1 HETATM 6 C C4' C2E . . . C 2 -13.834 19.084 -17.668 1 41.61 ? C4' C2E 401 A 1 HETATM 7 O O4' C2E . . . C 2 -13.506 20.25 -18.344 1 39.94 ? O4' C2E 401 A 1 HETATM 8 C C3' C2E . . . C 2 -13.346 18.017 -18.527 1 43.58 ? C3' C2E 401 A 1 HETATM 9 O O3' C2E . . . C 2 -14.003 16.781 -18.187 1 41.72 ? O3' C2E 401 A 1 HETATM 10 C C2' C2E . . . C 2 -13.77 18.457 -19.769 1 45.24 ? C2' C2E 401 A 1 HETATM 11 O O2' C2E . . . C 2 -15.122 18.213 -19.948 1 39.78 ? O2' C2E 401 A 1 HETATM 12 C C1' C2E . . . C 2 -13.459 19.925 -19.705 1 41.46 ? C1' C2E 401 A 1 HETATM 13 N N9 C2E . . . C 2 -12.111 20.131 -20.253 1 42.64 ? N9 C2E 401 A 1 HETATM 14 C C8 C2E . . . C 2 -10.915 20.019 -19.649 1 44.21 ? C8 C2E 401 A 1 HETATM 15 N N7 C2E . . . C 2 -9.965 20.26 -20.569 1 44.66 ? N7 C2E 401 A 1 HETATM 16 C C5 C2E . . . C 2 -10.565 20.514 -21.759 1 46.08 ? C5 C2E 401 A 1 HETATM 17 C C6 C2E . . . C 2 -10.095 20.832 -23.044 1 55.14 ? C6 C2E 401 A 1 HETATM 18 O O6 C2E . . . C 2 -8.705 20.928 -23.281 1 68.06 ? O6 C2E 401 A 1 HETATM 19 N N1 C2E . . . C 2 -10.973 21.047 -24.033 1 54.98 ? N1 C2E 401 A 1 HETATM 20 C C2 C2E . . . C 2 -12.286 20.959 -23.789 1 54.73 ? C2 C2E 401 A 1 HETATM 21 N N2 C2E . . . C 2 -13.213 21.188 -24.883 1 52.87 ? N2 C2E 401 A 1 HETATM 22 N N3 C2E . . . C 2 -12.783 20.654 -22.57 1 50.03 ? N3 C2E 401 A 1 HETATM 23 C C4 C2E . . . C 2 -11.939 20.428 -21.55 1 45.09 ? C4 C2E 401 A 1 HETATM 24 P P11 C2E . . . C 2 -13.304 15.353 -18.233 1 47.46 ? P11 C2E 401 A 1 HETATM 25 O O21 C2E . . . C 2 -14.277 14.246 -18.218 1 41.42 ? O21 C2E 401 A 1 HETATM 26 O O11 C2E . . . C 2 -12.559 15.261 -19.51 1 37.47 ? O11 C2E 401 A 1 HETATM 27 O O5A C2E . . . C 2 -12.168 15.167 -17.072 1 44.1 ? O5A C2E 401 A 1 HETATM 28 C C5A C2E . . . C 2 -12.515 14.939 -15.691 1 45.11 ? C5A C2E 401 A 1 HETATM 29 C C4A C2E . . . C 2 -11.483 15.087 -14.784 1 43.18 ? C4A C2E 401 A 1 HETATM 30 O O4A C2E . . . C 2 -10.591 13.893 -14.876 1 44.58 ? O4A C2E 401 A 1 HETATM 31 C C3A C2E . . . C 2 -10.588 16.22 -15.091 1 39.55 ? C3A C2E 401 A 1 HETATM 32 O O3A C2E . . . C 2 -11.02 17.431 -14.527 1 47.49 ? O3A C2E 401 A 1 HETATM 33 C C2A C2E . . . C 2 -9.334 15.797 -14.453 1 50.61 ? C2A C2E 401 A 1 HETATM 34 O O2A C2E . . . C 2 -9.321 16.087 -13.12 1 40.96 ? O2A C2E 401 A 1 HETATM 35 C C1A C2E . . . C 2 -9.29 14.337 -14.68 1 41.58 ? C1A C2E 401 A 1 HETATM 36 N N91 C2E . . . C 2 -8.442 13.986 -15.869 1 44.56 ? N91 C2E 401 A 1 HETATM 37 C C81 C2E . . . C 2 -8.806 14.014 -17.168 1 41.3 ? C81 C2E 401 A 1 HETATM 38 N N71 C2E . . . C 2 -7.751 13.637 -17.912 1 45.29 ? N71 C2E 401 A 1 HETATM 39 C C51 C2E . . . C 2 -6.704 13.361 -17.095 1 49.37 ? C51 C2E 401 A 1 HETATM 40 C C61 C2E . . . C 2 -5.382 12.937 -17.262 1 50.66 ? C61 C2E 401 A 1 HETATM 41 O O61 C2E . . . C 2 -4.854 12.686 -18.526 1 55.2 ? O61 C2E 401 A 1 HETATM 42 N N11 C2E . . . C 2 -4.611 12.766 -16.167 1 50.6 ? N11 C2E 401 A 1 HETATM 43 C C21 C2E . . . C 2 -5.102 13.001 -14.937 1 51.98 ? C21 C2E 401 A 1 HETATM 44 N N21 C2E . . . C 2 -4.27 12.816 -13.807 1 49.32 ? N21 C2E 401 A 1 HETATM 45 N N31 C2E . . . C 2 -6.361 13.413 -14.74 1 46.72 ? N31 C2E 401 A 1 HETATM 46 C C41 C2E . . . C 2 -7.164 13.595 -15.796 1 43.92 ? C41 C2E 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 374 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #