data_3U4I # _model_server_result.job_id R9eCdUgY0lNLHbdXV1COvA _model_server_result.datetime_utc '2024-12-26 20:24:43' _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 3u4i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 3U4I # _exptl.entry_id 3U4I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.328 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "Cyclic adenosine 5'-diphosphocarbocyclic ribose" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 105.2 _cell.angle_beta 91.08 _cell.angle_gamma 94.68 _cell.entry_id 3U4I _cell.length_a 42.223 _cell.length_b 53.998 _cell.length_c 66.547 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3U4I _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D 1 1 B,E 2 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 disulf ? disulf1 A SG CYS 29 A CYS 67 1_555 A SG CYS 44 A CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf2 A SG CYS 61 A CYS 99 1_555 A SG CYS 142 A CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf3 A SG CYS 81 A CYS 119 1_555 A SG CYS 163 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf4 A SG CYS 122 A CYS 160 1_555 A SG CYS 135 A CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf5 A SG CYS 216 A CYS 254 1_555 A SG CYS 237 A CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf6 A SG CYS 249 A CYS 287 1_555 A SG CYS 258 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 B SG CYS 29 B CYS 67 1_555 B SG CYS 44 B CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf8 B SG CYS 61 B CYS 99 1_555 B SG CYS 142 B CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf9 B SG CYS 81 B CYS 119 1_555 B SG CYS 163 B CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf10 B SG CYS 122 B CYS 160 1_555 B SG CYS 135 B CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? disulf ? disulf11 B SG CYS 216 B CYS 254 1_555 B SG CYS 237 B CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? # _chem_comp.formula 'C16 H23 N5 O12 P2' _chem_comp.formula_weight 539.328 _chem_comp.id CVR _chem_comp.mon_nstd_flag . _chem_comp.name "Cyclic adenosine 5'-diphosphocarbocyclic ribose" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 N1 C2 CVR sing 70 n n N1 C6 CVR sing 71 n n N1 C1D CVR sing 72 n n C2 N3 CVR doub 73 n n N3 C4 CVR sing 74 n n C4 C5 CVR doub 75 n y C4 N9 CVR sing 76 n y C5 C6 CVR sing 77 n n C5 N7 CVR sing 78 n y C6 N6 CVR doub 79 n n N7 C8 CVR doub 80 n y C8 N9 CVR sing 81 n y N9 C1' CVR sing 82 n n PA O1A CVR sing 83 n n PA O2A CVR doub 84 n n PA O3A CVR sing 85 n n PA O5' CVR sing 86 n n PB O1B CVR doub 87 n n PB O2B CVR sing 88 n n PB O3A CVR sing 89 n n PB O5D CVR sing 90 n n C1' C2' CVR sing 91 n n C1' O4' CVR sing 92 n n C1D C2D CVR sing 93 n n C1D C4X CVR sing 94 n n C2' O2' CVR sing 95 n n C2' C3' CVR sing 96 n n C2D O2D CVR sing 97 n n C2D C3D CVR sing 98 n n C3' O3' CVR sing 99 n n C3' C4' CVR sing 100 n n C3D O3D CVR sing 101 n n C3D C4D CVR sing 102 n n C4' O4' CVR sing 103 n n C4' C5' CVR sing 104 n n C4D C4X CVR sing 105 n n C4D C5D CVR sing 106 n n C5' O5' CVR sing 107 n n C5D O5D CVR sing 108 n n C2 H2 CVR sing 109 n n N6 HN6 CVR sing 110 n n C8 H8 CVR sing 111 n n C1' H1' CVR sing 112 n n O1A HO1A CVR sing 113 n n C1D H1D CVR sing 114 n n C2' H2' CVR sing 115 n n O2' HO2' CVR sing 116 n n O2B HO2B CVR sing 117 n n C2D H2D CVR sing 118 n n O2D HO2D CVR sing 119 n n C3' H3' CVR sing 120 n n O3' HO3' CVR sing 121 n n C3D H3D CVR sing 122 n n O3D HO3D CVR sing 123 n n C4' H4' CVR sing 124 n n C4D H4D CVR sing 125 n n C4X H4X CVR sing 126 n n C4X H4XA CVR sing 127 n n C5' H5' CVR sing 128 n n C5' "H5'A" CVR sing 129 n n C5D H5D CVR sing 130 n n C5D H5DA CVR sing 131 n n # _atom_sites.entry_id 3U4I _atom_sites.fract_transf_matrix[1][1] 0.023684 _atom_sites.fract_transf_matrix[1][2] 0.001939 _atom_sites.fract_transf_matrix[1][3] 0.000995 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018581 _atom_sites.fract_transf_matrix[2][3] 0.005099 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.015585 _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 CVR A 1 401 301 CVR CVR . D 3 HOH A 1 501 1 HOH HOH . D 3 HOH A 2 502 2 HOH HOH . D 3 HOH A 3 503 4 HOH HOH . D 3 HOH A 4 504 5 HOH HOH . D 3 HOH A 5 505 6 HOH HOH . D 3 HOH A 6 506 8 HOH HOH . D 3 HOH A 7 507 12 HOH HOH . D 3 HOH A 8 508 14 HOH HOH . D 3 HOH A 9 509 15 HOH HOH . D 3 HOH A 10 510 19 HOH HOH . D 3 HOH A 11 511 21 HOH HOH . D 3 HOH A 12 512 27 HOH HOH . D 3 HOH A 13 513 28 HOH HOH . D 3 HOH A 14 514 30 HOH HOH . D 3 HOH A 15 515 32 HOH HOH . D 3 HOH A 16 516 33 HOH HOH . D 3 HOH A 17 517 38 HOH HOH . D 3 HOH A 18 518 41 HOH HOH . D 3 HOH A 19 519 42 HOH HOH . D 3 HOH A 20 520 44 HOH HOH . D 3 HOH A 21 521 45 HOH HOH . D 3 HOH A 22 522 51 HOH HOH . D 3 HOH A 23 523 52 HOH HOH . D 3 HOH A 24 524 53 HOH HOH . D 3 HOH A 25 525 54 HOH HOH . D 3 HOH A 26 526 55 HOH HOH . D 3 HOH A 27 527 57 HOH HOH . D 3 HOH A 28 528 59 HOH HOH . D 3 HOH A 29 529 62 HOH HOH . D 3 HOH A 30 530 63 HOH HOH . D 3 HOH A 31 531 66 HOH HOH . D 3 HOH A 32 532 68 HOH HOH . D 3 HOH A 33 533 70 HOH HOH . D 3 HOH A 34 534 74 HOH HOH . D 3 HOH A 35 535 76 HOH HOH . D 3 HOH A 36 536 77 HOH HOH . D 3 HOH A 37 537 79 HOH HOH . D 3 HOH A 38 538 80 HOH HOH . D 3 HOH A 39 539 89 HOH HOH . D 3 HOH A 40 540 90 HOH HOH . D 3 HOH A 41 541 92 HOH HOH . D 3 HOH A 42 542 93 HOH HOH . D 3 HOH A 43 543 94 HOH HOH . D 3 HOH A 44 544 96 HOH HOH . D 3 HOH A 45 545 98 HOH HOH . D 3 HOH A 46 546 102 HOH HOH . D 3 HOH A 47 547 104 HOH HOH . D 3 HOH A 48 548 108 HOH HOH . D 3 HOH A 49 549 109 HOH HOH . D 3 HOH A 50 550 113 HOH HOH . D 3 HOH A 51 551 114 HOH HOH . D 3 HOH A 52 552 115 HOH HOH . D 3 HOH A 53 553 116 HOH HOH . D 3 HOH A 54 554 117 HOH HOH . D 3 HOH A 55 555 118 HOH HOH . D 3 HOH A 56 556 119 HOH HOH . D 3 HOH A 57 557 120 HOH HOH . D 3 HOH A 58 558 122 HOH HOH . D 3 HOH A 59 559 124 HOH HOH . D 3 HOH A 60 560 126 HOH HOH . D 3 HOH A 61 561 127 HOH HOH . D 3 HOH A 62 562 128 HOH HOH . D 3 HOH A 63 563 132 HOH HOH . D 3 HOH A 64 564 133 HOH HOH . D 3 HOH A 65 565 136 HOH HOH . D 3 HOH A 66 566 137 HOH HOH . D 3 HOH A 67 567 138 HOH HOH . D 3 HOH A 68 568 139 HOH HOH . D 3 HOH A 69 569 140 HOH HOH . D 3 HOH A 70 570 141 HOH HOH . D 3 HOH A 71 571 145 HOH HOH . D 3 HOH A 72 572 146 HOH HOH . D 3 HOH A 73 573 148 HOH HOH . D 3 HOH A 74 574 149 HOH HOH . E 3 HOH B 1 401 3 HOH HOH . E 3 HOH B 2 402 7 HOH HOH . E 3 HOH B 3 403 9 HOH HOH . E 3 HOH B 4 404 10 HOH HOH . E 3 HOH B 5 405 11 HOH HOH . E 3 HOH B 6 406 13 HOH HOH . E 3 HOH B 7 407 16 HOH HOH . E 3 HOH B 8 408 17 HOH HOH . E 3 HOH B 9 409 18 HOH HOH . E 3 HOH B 10 410 20 HOH HOH . E 3 HOH B 11 411 22 HOH HOH . E 3 HOH B 12 412 23 HOH HOH . E 3 HOH B 13 413 24 HOH HOH . E 3 HOH B 14 414 25 HOH HOH . E 3 HOH B 15 415 26 HOH HOH . E 3 HOH B 16 416 29 HOH HOH . E 3 HOH B 17 417 31 HOH HOH . E 3 HOH B 18 418 34 HOH HOH . E 3 HOH B 19 419 35 HOH HOH . E 3 HOH B 20 420 36 HOH HOH . E 3 HOH B 21 421 37 HOH HOH . E 3 HOH B 22 422 39 HOH HOH . E 3 HOH B 23 423 40 HOH HOH . E 3 HOH B 24 424 43 HOH HOH . E 3 HOH B 25 425 46 HOH HOH . E 3 HOH B 26 426 47 HOH HOH . E 3 HOH B 27 427 48 HOH HOH . E 3 HOH B 28 428 49 HOH HOH . E 3 HOH B 29 429 50 HOH HOH . E 3 HOH B 30 430 56 HOH HOH . E 3 HOH B 31 431 58 HOH HOH . E 3 HOH B 32 432 60 HOH HOH . E 3 HOH B 33 433 61 HOH HOH . E 3 HOH B 34 434 64 HOH HOH . E 3 HOH B 35 435 65 HOH HOH . E 3 HOH B 36 436 67 HOH HOH . E 3 HOH B 37 437 69 HOH HOH . E 3 HOH B 38 438 71 HOH HOH . E 3 HOH B 39 439 72 HOH HOH . E 3 HOH B 40 440 73 HOH HOH . E 3 HOH B 41 441 75 HOH HOH . E 3 HOH B 42 442 78 HOH HOH . E 3 HOH B 43 443 81 HOH HOH . E 3 HOH B 44 444 82 HOH HOH . E 3 HOH B 45 445 83 HOH HOH . E 3 HOH B 46 446 84 HOH HOH . E 3 HOH B 47 447 85 HOH HOH . E 3 HOH B 48 448 86 HOH HOH . E 3 HOH B 49 449 87 HOH HOH . E 3 HOH B 50 450 88 HOH HOH . E 3 HOH B 51 451 95 HOH HOH . E 3 HOH B 52 452 97 HOH HOH . E 3 HOH B 53 453 99 HOH HOH . E 3 HOH B 54 454 100 HOH HOH . E 3 HOH B 55 455 101 HOH HOH . E 3 HOH B 56 456 103 HOH HOH . E 3 HOH B 57 457 105 HOH HOH . E 3 HOH B 58 458 106 HOH HOH . E 3 HOH B 59 459 107 HOH HOH . E 3 HOH B 60 460 110 HOH HOH . E 3 HOH B 61 461 111 HOH HOH . E 3 HOH B 62 462 112 HOH HOH . E 3 HOH B 63 463 121 HOH HOH . E 3 HOH B 64 464 123 HOH HOH . E 3 HOH B 65 465 125 HOH HOH . E 3 HOH B 66 466 129 HOH HOH . E 3 HOH B 67 467 130 HOH HOH . E 3 HOH B 68 468 131 HOH HOH . E 3 HOH B 69 469 134 HOH HOH . E 3 HOH B 70 470 135 HOH HOH . E 3 HOH B 71 471 142 HOH HOH . E 3 HOH B 72 472 143 HOH HOH . E 3 HOH B 73 473 144 HOH HOH . E 3 HOH B 74 474 147 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 N N1 CVR . . . C 2 1.995 0.71 1.248 1 65.46 ? N1 CVR 401 A 1 HETATM 2 C C2 CVR . . . C 2 3.329 0.871 1.081 1 67.98 ? C2 CVR 401 A 1 HETATM 3 N N3 CVR . . . C 2 4.287 0.143 1.686 1 70.05 ? N3 CVR 401 A 1 HETATM 4 C C4 CVR . . . C 2 3.973 -0.852 2.555 1 74.52 ? C4 CVR 401 A 1 HETATM 5 C C5 CVR . . . C 2 2.544 -1.119 2.824 1 65.1 ? C5 CVR 401 A 1 HETATM 6 C C6 CVR . . . C 2 1.531 -0.293 2.13 1 63.39 ? C6 CVR 401 A 1 HETATM 7 N N6 CVR . . . C 2 0.218 -0.509 2.35 1 68.36 ? N6 CVR 401 A 1 HETATM 8 N N7 CVR . . . C 2 2.506 -2.131 3.703 1 62.81 ? N7 CVR 401 A 1 HETATM 9 C C8 CVR . . . C 2 3.787 -2.487 3.978 1 66.04 ? C8 CVR 401 A 1 HETATM 10 N N9 CVR . . . C 2 4.669 -1.726 3.3 1 74.42 ? N9 CVR 401 A 1 HETATM 11 P PA CVR . . . C 2 6.491 2.906 4.394 1 72.7 ? PA CVR 401 A 1 HETATM 12 P PB CVR . . . C 2 3.916 3.996 3.775 1 64.13 ? PB CVR 401 A 1 HETATM 13 C C1' CVR . . . C 2 6.152 -1.885 3.404 1 80.96 ? C1' CVR 401 A 1 HETATM 14 O O1A CVR . . . C 2 6.165 3.367 5.794 1 78.82 ? O1A CVR 401 A 1 HETATM 15 O O1B CVR . . . C 2 3.473 3.761 5.205 1 58.14 ? O1B CVR 401 A 1 HETATM 16 C C1D CVR . . . C 2 1.164 1.563 0.535 1 56.11 ? C1D CVR 401 A 1 HETATM 17 C C2' CVR . . . C 2 6.959 -1.149 2.384 1 82.1 ? C2' CVR 401 A 1 HETATM 18 O O2' CVR . . . C 2 7.176 -1.892 1.31 1 83 ? O2' CVR 401 A 1 HETATM 19 O O2A CVR . . . C 2 7.667 3.514 3.68 1 59.37 ? O2A CVR 401 A 1 HETATM 20 O O2B CVR . . . C 2 4.199 5.413 3.277 1 46.83 ? O2B CVR 401 A 1 HETATM 21 C C2D CVR . . . C 2 -0.18 2.044 1.037 1 61.12 ? C2D CVR 401 A 1 HETATM 22 O O2D CVR . . . C 2 -1.136 2.037 -0.029 1 58.75 ? O2D CVR 401 A 1 HETATM 23 C C3' CVR . . . C 2 8.093 -0.779 2.94 1 87.64 ? C3' CVR 401 A 1 HETATM 24 O O3' CVR . . . C 2 9.071 -1.62 2.614 1 88.94 ? O3' CVR 401 A 1 HETATM 25 O O3A CVR . . . C 2 5.17 3.029 3.46 1 45.22 ? O3A CVR 401 A 1 HETATM 26 C C3D CVR . . . C 2 0.041 3.512 1.388 1 57.84 ? C3D CVR 401 A 1 HETATM 27 O O3D CVR . . . C 2 -0.983 4.354 0.83 1 39.98 ? O3D CVR 401 A 1 HETATM 28 C C4' CVR . . . C 2 7.931 -0.741 4.423 1 86.24 ? C4' CVR 401 A 1 HETATM 29 O O4' CVR . . . C 2 6.66 -1.376 4.651 1 84.47 ? O4' CVR 401 A 1 HETATM 30 C C4D CVR . . . C 2 1.361 3.893 0.74 1 59.03 ? C4D CVR 401 A 1 HETATM 31 C C4X CVR . . . C 2 1.804 2.626 0.055 1 51.04 ? C4X CVR 401 A 1 HETATM 32 C C5' CVR . . . C 2 7.914 0.709 4.901 1 82.24 ? C5' CVR 401 A 1 HETATM 33 O O5' CVR . . . C 2 6.703 1.309 4.442 1 83.91 ? O5' CVR 401 A 1 HETATM 34 C C5D CVR . . . C 2 2.39 4.399 1.745 1 70.98 ? C5D CVR 401 A 1 HETATM 35 O O5D CVR . . . C 2 2.763 3.468 2.77 1 75.27 ? O5D CVR 401 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 35 #