data_5BQX # _model_server_result.job_id 2NJsqcbuFp3vSa2BvRxtiw _model_server_result.datetime_utc '2024-11-24 10:26:12' _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 5bqx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5BQX # _exptl.entry_id 5BQX _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 "3'2'-cGAMP" _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 90 _cell.angle_gamma 90 _cell.entry_id 5BQX _cell.length_a 111.061 _cell.length_b 111.061 _cell.length_c 35.889 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5BQX _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -17.9445 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H24 N10 O13 P2' _chem_comp.formula_weight 674.411 _chem_comp.id 4UR _chem_comp.mon_nstd_flag . _chem_comp.name "3'2'-cGAMP" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 2-amino-9-[(2S,5R,7R,8R,10R,12aR,14R,15R,15aS,16R)-7-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxidooctahydro-12H-5,8-methanofuro[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-14-yl]-1,9-dihydro-6H-purin-6-one # 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 O25 P24 4UR doub 1 n n C22 O23 4UR sing 2 n n C22 C21 4UR sing 3 n n O26 P24 4UR sing 4 n n P24 O23 4UR sing 5 n n P24 O27 4UR sing 6 n n O31 C21 4UR sing 7 n n O31 C32 4UR sing 8 n n C21 C19 4UR sing 9 n n N35 C34 4UR doub 10 n y N35 C36 4UR sing 11 n y C34 N33 4UR sing 12 n y N38 C37 4UR sing 13 n n C36 C37 4UR doub 14 n y C36 C42 4UR sing 15 n y N33 C32 4UR sing 16 n n N33 C42 4UR sing 17 n y C32 C18 4UR sing 18 n n C37 N39 4UR sing 19 n y O27 C28 4UR sing 20 n n C42 N41 4UR doub 21 n y C19 O20 4UR sing 22 n n C19 C18 4UR sing 23 n n N39 C40 4UR doub 24 n y N41 C40 4UR sing 25 n y O30 C29 4UR sing 26 n n C18 O17 4UR sing 27 n n C28 C29 4UR sing 28 n n C28 C11 4UR sing 29 n n C29 C09 4UR sing 30 n n N01 C02 4UR sing 31 n n C02 N45 4UR sing 32 n n C02 N03 4UR doub 33 n n N45 C43 4UR sing 34 n n N03 C04 4UR sing 35 n n C43 O44 4UR doub 36 n n C43 C05 4UR sing 37 n n O17 P14 4UR sing 38 n n C04 C05 4UR doub 39 n y C04 N08 4UR sing 40 n y C05 N06 4UR sing 41 n y C11 C12 4UR sing 42 n n C11 O10 4UR sing 43 n n N08 C09 4UR sing 44 n n N08 C07 4UR sing 45 n y C09 O10 4UR sing 46 n n N06 C07 4UR doub 47 n y C12 O13 4UR sing 48 n n O13 P14 4UR sing 49 n n O15 P14 4UR doub 50 n n P14 O16 4UR sing 51 n n C21 H211 4UR sing 52 n n C22 H221 4UR sing 53 n n C22 H222 4UR sing 54 n n C28 H281 4UR sing 55 n n N01 H012 4UR sing 56 n n N01 H011 4UR sing 57 n n C07 H071 4UR sing 58 n n C09 H091 4UR sing 59 n n C11 H111 4UR sing 60 n n C12 H121 4UR sing 61 n n C12 H122 4UR sing 62 n n O16 H1 4UR sing 63 n n C18 H181 4UR sing 64 n n C19 H191 4UR sing 65 n n O20 H201 4UR sing 66 n n O26 H2 4UR sing 67 n n C29 H291 4UR sing 68 n n O30 H301 4UR sing 69 n n C32 H321 4UR sing 70 n n C34 H341 4UR sing 71 n n N38 H381 4UR sing 72 n n N38 H382 4UR sing 73 n n C40 H401 4UR sing 74 n n N45 H451 4UR sing 75 n n # _atom_sites.entry_id 5BQX _atom_sites.fract_transf_matrix[1][1] 0.009004 _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] 0.009004 _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] 0.027864 _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 4UR A 1 401 1 4UR LIG . C 3 HOH A 1 501 72 HOH HOH . C 3 HOH A 2 502 48 HOH HOH . C 3 HOH A 3 503 76 HOH HOH . C 3 HOH A 4 504 23 HOH HOH . C 3 HOH A 5 505 55 HOH HOH . C 3 HOH A 6 506 10 HOH HOH . C 3 HOH A 7 507 50 HOH HOH . C 3 HOH A 8 508 6 HOH HOH . C 3 HOH A 9 509 20 HOH HOH . C 3 HOH A 10 510 13 HOH HOH . C 3 HOH A 11 511 5 HOH HOH . C 3 HOH A 12 512 19 HOH HOH . C 3 HOH A 13 513 73 HOH HOH . C 3 HOH A 14 514 43 HOH HOH . C 3 HOH A 15 515 12 HOH HOH . C 3 HOH A 16 516 14 HOH HOH . C 3 HOH A 17 517 3 HOH HOH . C 3 HOH A 18 518 22 HOH HOH . C 3 HOH A 19 519 77 HOH HOH . C 3 HOH A 20 520 28 HOH HOH . C 3 HOH A 21 521 81 HOH HOH . C 3 HOH A 22 522 11 HOH HOH . C 3 HOH A 23 523 31 HOH HOH . C 3 HOH A 24 524 78 HOH HOH . C 3 HOH A 25 525 36 HOH HOH . C 3 HOH A 26 526 52 HOH HOH . C 3 HOH A 27 527 34 HOH HOH . C 3 HOH A 28 528 16 HOH HOH . C 3 HOH A 29 529 39 HOH HOH . C 3 HOH A 30 530 38 HOH HOH . C 3 HOH A 31 531 9 HOH HOH . C 3 HOH A 32 532 58 HOH HOH . C 3 HOH A 33 533 21 HOH HOH . C 3 HOH A 34 534 74 HOH HOH . C 3 HOH A 35 535 35 HOH HOH . C 3 HOH A 36 536 80 HOH HOH . C 3 HOH A 37 537 18 HOH HOH . C 3 HOH A 38 538 1 HOH HOH . C 3 HOH A 39 539 2 HOH HOH . C 3 HOH A 40 540 8 HOH HOH . C 3 HOH A 41 541 27 HOH HOH . C 3 HOH A 42 542 26 HOH HOH . C 3 HOH A 43 543 25 HOH HOH . C 3 HOH A 44 544 7 HOH HOH . C 3 HOH A 45 545 17 HOH HOH . C 3 HOH A 46 546 32 HOH HOH . C 3 HOH A 47 547 54 HOH HOH . C 3 HOH A 48 548 33 HOH HOH . C 3 HOH A 49 549 46 HOH HOH . C 3 HOH A 50 550 67 HOH HOH . C 3 HOH A 51 551 4 HOH HOH . C 3 HOH A 52 552 47 HOH HOH . C 3 HOH A 53 553 85 HOH HOH . C 3 HOH A 54 554 66 HOH HOH . C 3 HOH A 55 555 84 HOH HOH . C 3 HOH A 56 556 62 HOH HOH . C 3 HOH A 57 557 51 HOH HOH . C 3 HOH A 58 558 49 HOH HOH . C 3 HOH A 59 559 40 HOH HOH . C 3 HOH A 60 560 15 HOH HOH . C 3 HOH A 61 561 61 HOH HOH . C 3 HOH A 62 562 30 HOH HOH . C 3 HOH A 63 563 86 HOH HOH . C 3 HOH A 64 564 53 HOH HOH . C 3 HOH A 65 565 24 HOH HOH . C 3 HOH A 66 566 65 HOH HOH . C 3 HOH A 67 567 87 HOH HOH . C 3 HOH A 68 568 64 HOH HOH . C 3 HOH A 69 569 88 HOH HOH . C 3 HOH A 70 570 90 HOH HOH . C 3 HOH A 71 571 68 HOH HOH . C 3 HOH A 72 572 41 HOH HOH . C 3 HOH A 73 573 89 HOH HOH . C 3 HOH A 74 574 29 HOH HOH . C 3 HOH A 75 575 44 HOH HOH . C 3 HOH A 76 576 75 HOH HOH . C 3 HOH A 77 577 37 HOH HOH . C 3 HOH A 78 578 70 HOH HOH . C 3 HOH A 79 579 60 HOH HOH . C 3 HOH A 80 580 45 HOH HOH . C 3 HOH A 81 581 71 HOH HOH . C 3 HOH A 82 582 69 HOH HOH . C 3 HOH A 83 583 82 HOH HOH . C 3 HOH A 84 584 42 HOH HOH . C 3 HOH A 85 585 56 HOH HOH . C 3 HOH A 86 586 59 HOH HOH . C 3 HOH A 87 587 63 HOH HOH . C 3 HOH A 88 588 79 HOH HOH . C 3 HOH A 89 589 57 HOH HOH . C 3 HOH A 90 590 83 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 C21 4UR . . . B 2 -23.322 20.818 -11.107 0.5 22.93 ? C21 4UR 401 A 1 HETATM 2 C C22 4UR . . . B 2 -22.269 21.7 -11.802 0.5 24.62 ? C22 4UR 401 A 1 HETATM 3 C C28 4UR . . . B 2 -19.191 22.699 -8.729 0.5 28.95 ? C28 4UR 401 A 1 HETATM 4 N N01 4UR . . . B 2 -11.891 21.849 -8.226 0.5 39.07 ? N01 4UR 401 A 1 HETATM 5 C C02 4UR . . . B 2 -13.079 21.126 -7.992 0.5 40.24 ? C02 4UR 401 A 1 HETATM 6 N N03 4UR . . . B 2 -14.251 21.811 -7.819 0.5 31.55 ? N03 4UR 401 A 1 HETATM 7 C C04 4UR . . . B 2 -15.383 21.001 -7.58 0.5 36.26 ? C04 4UR 401 A 1 HETATM 8 C C05 4UR . . . B 2 -15.375 19.588 -7.511 0.5 33.1 ? C05 4UR 401 A 1 HETATM 9 N N06 4UR . . . B 2 -16.668 19.096 -7.253 0.5 37.99 ? N06 4UR 401 A 1 HETATM 10 C C07 4UR . . . B 2 -17.447 20.192 -7.162 0.5 34.54 ? C07 4UR 401 A 1 HETATM 11 N N08 4UR . . . B 2 -16.7 21.381 -7.342 0.5 35.36 ? N08 4UR 401 A 1 HETATM 12 C C09 4UR . . . B 2 -17.288 22.738 -7.317 0.5 32.43 ? C09 4UR 401 A 1 HETATM 13 O O10 4UR . . . B 2 -18.462 22.834 -6.517 0.5 26.94 ? O10 4UR 401 A 1 HETATM 14 C C11 4UR . . . B 2 -19.613 23.151 -7.349 0.5 25.54 ? C11 4UR 401 A 1 HETATM 15 C C12 4UR . . . B 2 -20.876 22.433 -6.841 0.5 26.94 ? C12 4UR 401 A 1 HETATM 16 O O13 4UR . . . B 2 -20.724 21.046 -6.789 0.5 29.46 ? O13 4UR 401 A 1 HETATM 17 P P14 4UR . . . B 2 -21.834 19.9 -6.436 0.5 22.86 ? P14 4UR 401 A 1 HETATM 18 O O15 4UR . . . B 2 -21.112 18.542 -6.506 0.5 18.44 ? O15 4UR 401 A 1 HETATM 19 O O16 4UR . . . B 2 -22.458 20.286 -5.141 0.5 27.12 ? O16 4UR 401 A 1 HETATM 20 O O17 4UR . . . B 2 -22.942 19.765 -7.677 0.5 26.8 ? O17 4UR 401 A 1 HETATM 21 C C18 4UR . . . B 2 -22.522 20.058 -8.956 0.5 31.7 ? C18 4UR 401 A 1 HETATM 22 C C19 4UR . . . B 2 -23.41 21.127 -9.618 0.5 28.83 ? C19 4UR 401 A 1 HETATM 23 O O20 4UR . . . B 2 -24.757 21.04 -9.19 0.5 28.24 ? O20 4UR 401 A 1 HETATM 24 O O23 4UR . . . B 2 -21.002 21.405 -11.283 0.5 28.79 ? O23 4UR 401 A 1 HETATM 25 P P24 4UR . . . B 2 -19.779 22.578 -11.317 0.5 27.36 ? P24 4UR 401 A 1 HETATM 26 O O25 4UR . . . B 2 -20.304 23.647 -12.268 0.5 34.14 ? O25 4UR 401 A 1 HETATM 27 O O26 4UR . . . B 2 -18.429 22.016 -11.616 0.5 27.83 ? O26 4UR 401 A 1 HETATM 28 O O27 4UR . . . B 2 -19.877 23.232 -9.797 0.5 30.37 ? O27 4UR 401 A 1 HETATM 29 C C29 4UR . . . B 2 -17.739 23.136 -8.715 0.5 33.58 ? C29 4UR 401 A 1 HETATM 30 O O30 4UR . . . B 2 -17.666 24.52 -8.993 0.5 28.93 ? O30 4UR 401 A 1 HETATM 31 O O31 4UR . . . B 2 -22.98 19.414 -11.206 0.5 26.2 ? O31 4UR 401 A 1 HETATM 32 C C32 4UR . . . B 2 -22.76 18.872 -9.913 0.5 25.35 ? C32 4UR 401 A 1 HETATM 33 N N33 4UR . . . B 2 -21.557 17.917 -10.021 0.5 33.82 ? N33 4UR 401 A 1 HETATM 34 C C34 4UR . . . B 2 -20.305 18.327 -10.486 0.5 33.66 ? C34 4UR 401 A 1 HETATM 35 N N35 4UR . . . B 2 -19.386 17.321 -10.523 0.5 37.2 ? N35 4UR 401 A 1 HETATM 36 C C36 4UR . . . B 2 -20.051 16.17 -10.066 0.5 34.36 ? C36 4UR 401 A 1 HETATM 37 C C37 4UR . . . B 2 -19.612 14.808 -9.864 0.5 35.64 ? C37 4UR 401 A 1 HETATM 38 N N38 4UR . . . B 2 -18.303 14.353 -10.147 0.5 44.58 ? N38 4UR 401 A 1 HETATM 39 N N39 4UR . . . B 2 -20.522 13.886 -9.388 0.5 39.42 ? N39 4UR 401 A 1 HETATM 40 C C40 4UR . . . B 2 -21.813 14.332 -9.124 0.5 30.32 ? C40 4UR 401 A 1 HETATM 41 N N41 4UR . . . B 2 -22.317 15.585 -9.268 0.5 37.99 ? N41 4UR 401 A 1 HETATM 42 C C42 4UR . . . B 2 -21.411 16.524 -9.745 0.5 33.25 ? C42 4UR 401 A 1 HETATM 43 C C43 4UR . . . B 2 -14.14 18.859 -7.696 0.5 42.29 ? C43 4UR 401 A 1 HETATM 44 O O44 4UR . . . B 2 -13.911 17.661 -7.68 0.5 46.46 ? O44 4UR 401 A 1 HETATM 45 N N45 4UR . . . B 2 -12.979 19.713 -7.944 0.5 41.28 ? N45 4UR 401 A 1 HETATM 46 H H211 4UR . . . B 2 -24.297 21.012 -11.591 0.5 27.51 ? H211 4UR 401 A 1 HETATM 47 H H221 4UR . . . B 2 -22.303 21.498 -12.886 0.5 29.55 ? H221 4UR 401 A 1 HETATM 48 H H222 4UR . . . B 2 -22.482 22.763 -11.667 0.5 29.55 ? H222 4UR 401 A 1 HETATM 49 H H281 4UR . . . B 2 -19.229 21.606 -8.71 0.5 34.75 ? H281 4UR 401 A 1 HETATM 50 H H012 4UR . . . B 2 -11.325 21.804 -9.059 0.5 46.88 ? H012 4UR 401 A 1 HETATM 51 H H011 4UR . . . B 2 -11.513 22.48 -7.559 0.5 46.88 ? H011 4UR 401 A 1 HETATM 52 H H071 4UR . . . B 2 -18.531 20.195 -6.972 0.5 41.45 ? H071 4UR 401 A 1 HETATM 53 H H091 4UR . . . B 2 -16.463 23.377 -6.959 0.5 38.92 ? H091 4UR 401 A 1 HETATM 54 H H111 4UR . . . B 2 -19.763 24.262 -7.323 0.5 30.65 ? H111 4UR 401 A 1 HETATM 55 H H121 4UR . . . B 2 -21.716 22.706 -7.493 0.5 32.33 ? H121 4UR 401 A 1 HETATM 56 H H122 4UR . . . B 2 -21.142 22.759 -5.836 0.5 32.33 ? H122 4UR 401 A 1 HETATM 57 H H181 4UR . . . B 2 -21.492 20.379 -9.015 0.5 38.04 ? H181 4UR 401 A 1 HETATM 58 H H191 4UR . . . B 2 -22.997 22.133 -9.45 0.5 34.59 ? H191 4UR 401 A 1 HETATM 59 H H201 4UR . . . B 2 -25.223 21.825 -9.457 0.5 33.89 ? H201 4UR 401 A 1 HETATM 60 H H291 4UR . . . B 2 -17.225 22.58 -9.51 0.5 40.29 ? H291 4UR 401 A 1 HETATM 61 H H301 4UR . . . B 2 -17.019 24.694 -9.656 0.5 34.72 ? H301 4UR 401 A 1 HETATM 62 H H321 4UR . . . B 2 -23.529 18.198 -9.566 0.5 30.42 ? H321 4UR 401 A 1 HETATM 63 H H341 4UR . . . B 2 -20.152 19.379 -10.778 0.5 40.4 ? H341 4UR 401 A 1 HETATM 64 H H381 4UR . . . B 2 -18.123 13.435 -10.482 0.5 53.49 ? H381 4UR 401 A 1 HETATM 65 H H382 4UR . . . B 2 -17.458 14.885 -10.044 0.5 53.49 ? H382 4UR 401 A 1 HETATM 66 H H401 4UR . . . B 2 -22.53 13.569 -8.735 0.5 36.39 ? H401 4UR 401 A 1 HETATM 67 H H451 4UR . . . B 2 -12.08 19.261 -8.082 0.5 49.54 ? H451 4UR 401 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 388 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 67 #