data_7V9B # _model_server_result.job_id rMS-aSlAkA4JgB8NVcNXUA _model_server_result.datetime_utc '2024-11-25 07:52:51' _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 7v9b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":301}' # _entry.id 7V9B # _exptl.entry_id 7V9B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 414.453 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate _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 7V9B _cell.length_a 77.88 _cell.length_b 81.04 _cell.length_c 83.28 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7V9B _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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' 3_955 -x+4,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 311.52 0 41.64 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _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 covale ? covale1 B N ARG 1 B ARG 248 1_555 G C25 323 . B 323 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale2 B C VAL 5 B VAL 252 1_555 B N SEP 6 B SEP 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 B C SEP 6 B SEP 253 1_555 B N MET 7 B MET 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? # _chem_comp.formula 'C25 H22 N2 O4' _chem_comp.formula_weight 414.453 _chem_comp.id 323 _chem_comp.mon_nstd_flag . _chem_comp.name 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "5-Carboxy-N,N'-tetramethyl rhodamine" # 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 O4 C25 323 doub 1 n n C25 C21 323 sing 2 n n C21 C22 323 doub 3 n y C21 C20 323 sing 4 n y C22 C23 323 sing 5 n y C20 C19 323 doub 6 n y O3 C24 323 doub 7 n n C23 C24 323 sing 8 n n C23 C18 323 doub 9 n y C19 C18 323 sing 10 n y C24 O2 323 sing 11 n n C18 C1 323 sing 12 n n C10 C11 323 doub 13 n y C10 C2 323 sing 14 n y C1 C2 323 doub 15 n n C1 C5 323 sing 16 n n C11 C12 323 sing 17 n y C2 C3 323 sing 18 n y C9 C5 323 doub 19 n y C9 C8 323 sing 20 n y C5 C4 323 sing 21 n y C17 N1 323 sing 22 n n C12 N1 323 doub 23 n n C12 C13 323 sing 24 n y C8 C7 323 doub 25 n y C3 C13 323 doub 26 n y C3 O1 323 sing 27 n n N1 C16 323 sing 28 n n C4 O1 323 sing 29 n n C4 C6 323 doub 30 n y C7 C6 323 sing 31 n y C7 N2 323 sing 32 n n C15 N2 323 sing 33 n n N2 C14 323 sing 34 n n C10 H10 323 sing 35 n n C11 H11 323 sing 36 n n C13 H13 323 sing 37 n n C14 H114 323 sing 38 n n C14 H214 323 sing 39 n n C14 H314 323 sing 40 n n C15 H115 323 sing 41 n n C15 H215 323 sing 42 n n C15 H315 323 sing 43 n n C16 H116 323 sing 44 n n C16 H216 323 sing 45 n n C16 H316 323 sing 46 n n C17 H117 323 sing 47 n n C17 H217 323 sing 48 n n C17 H317 323 sing 49 n n C19 H19 323 sing 50 n n C20 H20 323 sing 51 n n C22 H22 323 sing 52 n n C25 H25 323 sing 53 n n C6 H6 323 sing 54 n n C8 H8 323 sing 55 n n C9 H9 323 sing 56 n n # _atom_sites.entry_id 7V9B _atom_sites.fract_transf_matrix[1][1] 0.01284 _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] 0.01234 _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] 0.012008 _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 3 GOL A 1 301 1 GOL GOL . D 3 GOL A 1 302 2 GOL GOL . E 4 MPD A 1 303 1 MPD MPD . F 5 IMD A 1 304 3 IMD IMD . G 6 323 B 1 301 247 323 323 . H 7 HOH A 1 401 123 HOH HOH . H 7 HOH A 2 402 161 HOH HOH . H 7 HOH A 3 403 126 HOH HOH . H 7 HOH A 4 404 158 HOH HOH . H 7 HOH A 5 405 122 HOH HOH . H 7 HOH A 6 406 112 HOH HOH . H 7 HOH A 7 407 33 HOH HOH . H 7 HOH A 8 408 171 HOH HOH . H 7 HOH A 9 409 16 HOH HOH . H 7 HOH A 10 410 24 HOH HOH . H 7 HOH A 11 411 160 HOH HOH . H 7 HOH A 12 412 86 HOH HOH . H 7 HOH A 13 413 78 HOH HOH . H 7 HOH A 14 414 32 HOH HOH . H 7 HOH A 15 415 83 HOH HOH . H 7 HOH A 16 416 97 HOH HOH . H 7 HOH A 17 417 125 HOH HOH . H 7 HOH A 18 418 130 HOH HOH . H 7 HOH A 19 419 157 HOH HOH . H 7 HOH A 20 420 11 HOH HOH . H 7 HOH A 21 421 35 HOH HOH . H 7 HOH A 22 422 57 HOH HOH . H 7 HOH A 23 423 68 HOH HOH . H 7 HOH A 24 424 145 HOH HOH . H 7 HOH A 25 425 132 HOH HOH . H 7 HOH A 26 426 29 HOH HOH . H 7 HOH A 27 427 85 HOH HOH . H 7 HOH A 28 428 2 HOH HOH . H 7 HOH A 29 429 137 HOH HOH . H 7 HOH A 30 430 107 HOH HOH . H 7 HOH A 31 431 36 HOH HOH . H 7 HOH A 32 432 134 HOH HOH . H 7 HOH A 33 433 49 HOH HOH . H 7 HOH A 34 434 20 HOH HOH . H 7 HOH A 35 435 79 HOH HOH . H 7 HOH A 36 436 37 HOH HOH . H 7 HOH A 37 437 31 HOH HOH . H 7 HOH A 38 438 41 HOH HOH . H 7 HOH A 39 439 9 HOH HOH . H 7 HOH A 40 440 7 HOH HOH . H 7 HOH A 41 441 114 HOH HOH . H 7 HOH A 42 442 14 HOH HOH . H 7 HOH A 43 443 8 HOH HOH . H 7 HOH A 44 444 42 HOH HOH . H 7 HOH A 45 445 40 HOH HOH . H 7 HOH A 46 446 99 HOH HOH . H 7 HOH A 47 447 84 HOH HOH . H 7 HOH A 48 448 82 HOH HOH . H 7 HOH A 49 449 52 HOH HOH . H 7 HOH A 50 450 143 HOH HOH . H 7 HOH A 51 451 98 HOH HOH . H 7 HOH A 52 452 10 HOH HOH . H 7 HOH A 53 453 1 HOH HOH . H 7 HOH A 54 454 144 HOH HOH . H 7 HOH A 55 455 28 HOH HOH . H 7 HOH A 56 456 152 HOH HOH . H 7 HOH A 57 457 102 HOH HOH . H 7 HOH A 58 458 72 HOH HOH . H 7 HOH A 59 459 12 HOH HOH . H 7 HOH A 60 460 71 HOH HOH . H 7 HOH A 61 461 23 HOH HOH . H 7 HOH A 62 462 5 HOH HOH . H 7 HOH A 63 463 100 HOH HOH . H 7 HOH A 64 464 4 HOH HOH . H 7 HOH A 65 465 93 HOH HOH . H 7 HOH A 66 466 168 HOH HOH . H 7 HOH A 67 467 94 HOH HOH . H 7 HOH A 68 468 175 HOH HOH . H 7 HOH A 69 469 13 HOH HOH . H 7 HOH A 70 470 55 HOH HOH . H 7 HOH A 71 471 66 HOH HOH . H 7 HOH A 72 472 91 HOH HOH . H 7 HOH A 73 473 73 HOH HOH . H 7 HOH A 74 474 34 HOH HOH . H 7 HOH A 75 475 51 HOH HOH . H 7 HOH A 76 476 64 HOH HOH . H 7 HOH A 77 477 3 HOH HOH . H 7 HOH A 78 478 92 HOH HOH . H 7 HOH A 79 479 30 HOH HOH . H 7 HOH A 80 480 44 HOH HOH . H 7 HOH A 81 481 17 HOH HOH . H 7 HOH A 82 482 19 HOH HOH . H 7 HOH A 83 483 150 HOH HOH . H 7 HOH A 84 484 111 HOH HOH . H 7 HOH A 85 485 77 HOH HOH . H 7 HOH A 86 486 80 HOH HOH . H 7 HOH A 87 487 166 HOH HOH . H 7 HOH A 88 488 88 HOH HOH . H 7 HOH A 89 489 103 HOH HOH . H 7 HOH A 90 490 138 HOH HOH . H 7 HOH A 91 491 140 HOH HOH . H 7 HOH A 92 492 120 HOH HOH . H 7 HOH A 93 493 22 HOH HOH . H 7 HOH A 94 494 81 HOH HOH . H 7 HOH A 95 495 6 HOH HOH . H 7 HOH A 96 496 76 HOH HOH . H 7 HOH A 97 497 147 HOH HOH . H 7 HOH A 98 498 119 HOH HOH . H 7 HOH A 99 499 96 HOH HOH . H 7 HOH A 100 500 26 HOH HOH . H 7 HOH A 101 501 162 HOH HOH . H 7 HOH A 102 502 60 HOH HOH . H 7 HOH A 103 503 67 HOH HOH . H 7 HOH A 104 504 141 HOH HOH . H 7 HOH A 105 505 151 HOH HOH . H 7 HOH A 106 506 75 HOH HOH . H 7 HOH A 107 507 38 HOH HOH . H 7 HOH A 108 508 74 HOH HOH . H 7 HOH A 109 509 149 HOH HOH . H 7 HOH A 110 510 127 HOH HOH . H 7 HOH A 111 511 54 HOH HOH . H 7 HOH A 112 512 117 HOH HOH . H 7 HOH A 113 513 174 HOH HOH . H 7 HOH A 114 514 142 HOH HOH . H 7 HOH A 115 515 62 HOH HOH . H 7 HOH A 116 516 173 HOH HOH . H 7 HOH A 117 517 53 HOH HOH . H 7 HOH A 118 518 159 HOH HOH . H 7 HOH A 119 519 15 HOH HOH . H 7 HOH A 120 520 39 HOH HOH . H 7 HOH A 121 521 104 HOH HOH . H 7 HOH A 122 522 136 HOH HOH . H 7 HOH A 123 523 156 HOH HOH . H 7 HOH A 124 524 164 HOH HOH . H 7 HOH A 125 525 25 HOH HOH . H 7 HOH A 126 526 148 HOH HOH . H 7 HOH A 127 527 128 HOH HOH . H 7 HOH A 128 528 45 HOH HOH . H 7 HOH A 129 529 46 HOH HOH . H 7 HOH A 130 530 129 HOH HOH . H 7 HOH A 131 531 135 HOH HOH . H 7 HOH A 132 532 47 HOH HOH . H 7 HOH A 133 533 48 HOH HOH . H 7 HOH A 134 534 56 HOH HOH . H 7 HOH A 135 535 115 HOH HOH . H 7 HOH A 136 536 146 HOH HOH . H 7 HOH A 137 537 165 HOH HOH . H 7 HOH A 138 538 172 HOH HOH . H 7 HOH A 139 539 116 HOH HOH . H 7 HOH A 140 540 87 HOH HOH . H 7 HOH A 141 541 170 HOH HOH . H 7 HOH A 142 542 69 HOH HOH . H 7 HOH A 143 543 27 HOH HOH . H 7 HOH A 144 544 155 HOH HOH . H 7 HOH A 145 545 65 HOH HOH . H 7 HOH A 146 546 139 HOH HOH . H 7 HOH A 147 547 101 HOH HOH . H 7 HOH A 148 548 163 HOH HOH . H 7 HOH A 149 549 121 HOH HOH . I 7 HOH B 1 401 18 HOH HOH . I 7 HOH B 2 402 58 HOH HOH . I 7 HOH B 3 403 70 HOH HOH . I 7 HOH B 4 404 110 HOH HOH . I 7 HOH B 5 405 131 HOH HOH . I 7 HOH B 6 406 50 HOH HOH . I 7 HOH B 7 407 95 HOH HOH . I 7 HOH B 8 408 59 HOH HOH . I 7 HOH B 9 409 169 HOH HOH . I 7 HOH B 10 410 61 HOH HOH . I 7 HOH B 11 411 63 HOH HOH . I 7 HOH B 12 412 21 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 C1 323 . . . G 6 170.822 84.471 -0.157 1 26.27 ? C1 323 301 B 1 HETATM 2 O O1 323 . . . G 6 171.643 86.549 -1.884 1 25.37 ? O1 323 301 B 1 HETATM 3 N N1 323 . . . G 6 168.732 89.692 0.236 1 30.67 ? N1 323 301 B 1 HETATM 4 C C10 323 . . . G 6 169.368 86.125 0.991 1 24.57 ? C10 323 301 B 1 HETATM 5 C C11 323 . . . G 6 168.846 87.408 1.062 1 26.37 ? C11 323 301 B 1 HETATM 6 C C12 323 . . . G 6 169.237 88.408 0.149 1 26.91 ? C12 323 301 B 1 HETATM 7 C C13 323 . . . G 6 170.198 88.071 -0.815 1 24.08 ? C13 323 301 B 1 HETATM 8 C C14 323 . . . G 6 174.765 84.737 -5.259 1 33.75 ? C14 323 301 B 1 HETATM 9 C C15 323 . . . G 6 175.32 82.444 -4.504 1 38.79 ? C15 323 301 B 1 HETATM 10 C C16 323 . . . G 6 167.795 90.068 1.285 1 29.71 ? C16 323 301 B 1 HETATM 11 C C17 323 . . . G 6 168.9 90.658 -0.84 1 31.34 ? C17 323 301 B 1 HETATM 12 C C18 323 . . . G 6 170.592 83.405 0.817 1 26.1 ? C18 323 301 B 1 HETATM 13 C C19 323 . . . G 6 171.622 83.018 1.709 1 27.1 ? C19 323 301 B 1 HETATM 14 O O2 323 . . . G 6 168.429 83.478 -1.17 1 25.03 ? O2 323 301 B 1 HETATM 15 N N2 323 . . . G 6 174.556 83.671 -4.292 1 35.51 ? N2 323 301 B 1 HETATM 16 C C2 323 . . . G 6 170.279 85.771 -0.028 1 26.2 ? C2 323 301 B 1 HETATM 17 C C20 323 . . . G 6 171.358 82.107 2.709 1 28.31 ? C20 323 301 B 1 HETATM 18 C C21 323 . . . G 6 170.103 81.516 2.84 1 27.25 ? C21 323 301 B 1 HETATM 19 C C22 323 . . . G 6 169.096 81.87 1.943 1 28.4 ? C22 323 301 B 1 HETATM 20 C C23 323 . . . G 6 169.312 82.839 0.961 1 29.08 ? C23 323 301 B 1 HETATM 21 C C24 323 . . . G 6 168.169 83.134 0.022 1 26.97 ? C24 323 301 B 1 HETATM 22 C C25 323 . . . G 6 169.745 80.813 4.062 1 31.42 ? C25 323 301 B 1 HETATM 23 O O3 323 . . . G 6 167.023 83.325 0.549 1 29.63 ? O3 323 301 B 1 HETATM 24 C C3 323 . . . G 6 170.69 86.779 -0.901 1 25.71 ? C3 323 301 B 1 HETATM 25 O O4 323 . . . G 6 170.171 81.041 5.175 1 30.44 ? O4 323 301 B 1 HETATM 26 C C4 323 . . . G 6 172.141 85.256 -2.002 1 25.09 ? C4 323 301 B 1 HETATM 27 C C5 323 . . . G 6 171.755 84.229 -1.183 1 26.34 ? C5 323 301 B 1 HETATM 28 C C6 323 . . . G 6 173.081 85.086 -2.988 1 27.64 ? C6 323 301 B 1 HETATM 29 C C7 323 . . . G 6 173.669 83.839 -3.232 1 29.07 ? C7 323 301 B 1 HETATM 30 C C8 323 . . . G 6 173.277 82.766 -2.419 1 29.89 ? C8 323 301 B 1 HETATM 31 C C9 323 . . . G 6 172.338 82.947 -1.409 1 27.77 ? C9 323 301 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #