data_1KDS # _model_server_result.job_id whXh-NHfozVoKJ8QrRkmWw _model_server_result.datetime_utc '2024-11-05 21:02:24' _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 1kds # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":364}' # _entry.id 1KDS # _exptl.entry_id 1KDS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 166.927 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-NITROPHENYLBORONIC ACID' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 115.86 _cell.angle_gamma 90 _cell.entry_id 1KDS _cell.length_a 119.108 _cell.length_b 77.73 _cell.length_c 99.01 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KDS _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,E 1 1 B,D,F 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D 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 covale ? covale1 A OG SER 61 A SER 64 1_555 C B NPB . A NPB 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.675 ? covale ? covale2 B OG SER 61 B SER 64 1_555 D B NPB . B NPB 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.675 ? # _chem_comp.formula 'C6 H6 B N O4' _chem_comp.formula_weight 166.927 _chem_comp.id NPB _chem_comp.mon_nstd_flag . _chem_comp.name '3-NITROPHENYLBORONIC ACID' _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 B OB1 NPB sing 224 n n B OB2 NPB sing 225 n n B CP1 NPB sing 226 n n OB1 HO11 NPB sing 227 n n OB2 HO21 NPB sing 228 n n CP1 CP2 NPB doub 229 n y CP1 CP6 NPB sing 230 n y CP2 CP3 NPB sing 231 n y CP2 HC21 NPB sing 232 n n CP3 NT NPB sing 233 n n CP3 CP4 NPB doub 234 n y NT O1 NPB doub 235 n n NT O2 NPB sing 236 n n CP4 CP5 NPB sing 237 n y CP4 HC41 NPB sing 238 n n CP5 CP6 NPB doub 239 n y CP5 HC51 NPB sing 240 n n CP6 HC61 NPB sing 241 n n # _atom_sites.entry_id 1KDS _atom_sites.fract_transf_matrix[1][1] 0.008396 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004069 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012865 _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] 0.011224 _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 NPB A 1 364 364 NPB NPB . D 2 NPB B 1 364 364 NPB NPB . E 3 HOH A 1 400 400 HOH WAT . E 3 HOH A 2 401 401 HOH WAT . E 3 HOH A 3 406 406 HOH WAT . E 3 HOH A 4 407 407 HOH WAT . E 3 HOH A 5 408 408 HOH WAT . E 3 HOH A 6 409 409 HOH WAT . E 3 HOH A 7 410 410 HOH WAT . E 3 HOH A 8 411 411 HOH WAT . E 3 HOH A 9 412 412 HOH WAT . E 3 HOH A 10 413 413 HOH WAT . E 3 HOH A 11 414 414 HOH WAT . E 3 HOH A 12 415 415 HOH WAT . E 3 HOH A 13 416 416 HOH WAT . E 3 HOH A 14 417 417 HOH WAT . E 3 HOH A 15 418 418 HOH WAT . E 3 HOH A 16 419 419 HOH WAT . E 3 HOH A 17 420 420 HOH WAT . E 3 HOH A 18 421 421 HOH WAT . E 3 HOH A 19 422 422 HOH WAT . E 3 HOH A 20 423 423 HOH WAT . E 3 HOH A 21 424 424 HOH WAT . E 3 HOH A 22 425 425 HOH WAT . E 3 HOH A 23 426 426 HOH WAT . E 3 HOH A 24 427 427 HOH WAT . E 3 HOH A 25 428 428 HOH WAT . E 3 HOH A 26 429 429 HOH WAT . E 3 HOH A 27 430 430 HOH WAT . E 3 HOH A 28 431 431 HOH WAT . E 3 HOH A 29 432 432 HOH WAT . E 3 HOH A 30 433 433 HOH WAT . E 3 HOH A 31 434 434 HOH WAT . E 3 HOH A 32 435 435 HOH WAT . E 3 HOH A 33 436 436 HOH WAT . E 3 HOH A 34 437 437 HOH WAT . E 3 HOH A 35 438 438 HOH WAT . E 3 HOH A 36 439 439 HOH WAT . E 3 HOH A 37 440 440 HOH WAT . E 3 HOH A 38 441 441 HOH WAT . E 3 HOH A 39 442 442 HOH WAT . E 3 HOH A 40 443 443 HOH WAT . E 3 HOH A 41 462 462 HOH WAT . E 3 HOH A 42 472 472 HOH WAT . E 3 HOH A 43 480 480 HOH WAT . E 3 HOH A 44 506 506 HOH WAT . E 3 HOH A 45 508 508 HOH WAT . E 3 HOH A 46 509 509 HOH WAT . E 3 HOH A 47 510 510 HOH WAT . E 3 HOH A 48 511 511 HOH WAT . E 3 HOH A 49 513 513 HOH WAT . E 3 HOH A 50 514 514 HOH WAT . E 3 HOH A 51 515 515 HOH WAT . E 3 HOH A 52 516 516 HOH WAT . E 3 HOH A 53 517 517 HOH WAT . E 3 HOH A 54 518 518 HOH WAT . E 3 HOH A 55 519 519 HOH WAT . E 3 HOH A 56 520 520 HOH WAT . E 3 HOH A 57 521 521 HOH WAT . E 3 HOH A 58 522 522 HOH WAT . E 3 HOH A 59 523 523 HOH WAT . E 3 HOH A 60 525 525 HOH WAT . E 3 HOH A 61 539 539 HOH WAT . F 3 HOH B 1 402 402 HOH WAT . F 3 HOH B 2 403 403 HOH WAT . F 3 HOH B 3 404 404 HOH WAT . F 3 HOH B 4 405 405 HOH WAT . F 3 HOH B 5 444 444 HOH WAT . F 3 HOH B 6 445 445 HOH WAT . F 3 HOH B 7 446 446 HOH WAT . F 3 HOH B 8 447 447 HOH WAT . F 3 HOH B 9 448 448 HOH WAT . F 3 HOH B 10 449 449 HOH WAT . F 3 HOH B 11 450 450 HOH WAT . F 3 HOH B 12 451 451 HOH WAT . F 3 HOH B 13 452 452 HOH WAT . F 3 HOH B 14 453 453 HOH WAT . F 3 HOH B 15 454 454 HOH WAT . F 3 HOH B 16 455 455 HOH WAT . F 3 HOH B 17 456 456 HOH WAT . F 3 HOH B 18 457 457 HOH WAT . F 3 HOH B 19 458 458 HOH WAT . F 3 HOH B 20 459 459 HOH WAT . F 3 HOH B 21 460 460 HOH WAT . F 3 HOH B 22 461 461 HOH WAT . F 3 HOH B 23 463 463 HOH WAT . F 3 HOH B 24 464 464 HOH WAT . F 3 HOH B 25 465 465 HOH WAT . F 3 HOH B 26 466 466 HOH WAT . F 3 HOH B 27 467 467 HOH WAT . F 3 HOH B 28 468 468 HOH WAT . F 3 HOH B 29 469 469 HOH WAT . F 3 HOH B 30 470 470 HOH WAT . F 3 HOH B 31 471 471 HOH WAT . F 3 HOH B 32 473 473 HOH WAT . F 3 HOH B 33 474 474 HOH WAT . F 3 HOH B 34 475 475 HOH WAT . F 3 HOH B 35 476 476 HOH WAT . F 3 HOH B 36 477 477 HOH WAT . F 3 HOH B 37 478 478 HOH WAT . F 3 HOH B 38 479 479 HOH WAT . F 3 HOH B 39 481 481 HOH WAT . F 3 HOH B 40 482 482 HOH WAT . F 3 HOH B 41 483 483 HOH WAT . F 3 HOH B 42 484 484 HOH WAT . F 3 HOH B 43 485 485 HOH WAT . F 3 HOH B 44 486 486 HOH WAT . F 3 HOH B 45 487 487 HOH WAT . F 3 HOH B 46 488 488 HOH WAT . F 3 HOH B 47 489 489 HOH WAT . F 3 HOH B 48 490 490 HOH WAT . F 3 HOH B 49 491 491 HOH WAT . F 3 HOH B 50 492 492 HOH WAT . F 3 HOH B 51 493 493 HOH WAT . F 3 HOH B 52 494 494 HOH WAT . F 3 HOH B 53 495 495 HOH WAT . F 3 HOH B 54 496 496 HOH WAT . F 3 HOH B 55 497 497 HOH WAT . F 3 HOH B 56 498 498 HOH WAT . F 3 HOH B 57 499 499 HOH WAT . F 3 HOH B 58 500 500 HOH WAT . F 3 HOH B 59 501 501 HOH WAT . F 3 HOH B 60 502 502 HOH WAT . F 3 HOH B 61 503 503 HOH WAT . F 3 HOH B 62 504 504 HOH WAT . F 3 HOH B 63 505 505 HOH WAT . F 3 HOH B 64 507 507 HOH WAT . F 3 HOH B 65 512 512 HOH WAT . F 3 HOH B 66 524 524 HOH WAT . F 3 HOH B 67 526 526 HOH WAT . F 3 HOH B 68 527 527 HOH WAT . F 3 HOH B 69 528 528 HOH WAT . F 3 HOH B 70 529 529 HOH WAT . F 3 HOH B 71 530 530 HOH WAT . F 3 HOH B 72 531 531 HOH WAT . F 3 HOH B 73 532 532 HOH WAT . F 3 HOH B 74 533 533 HOH WAT . F 3 HOH B 75 534 534 HOH WAT . F 3 HOH B 76 535 535 HOH WAT . F 3 HOH B 77 536 536 HOH WAT . F 3 HOH B 78 537 537 HOH WAT . F 3 HOH B 79 538 538 HOH WAT . # 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 B B NPB . . . C 2 26.492 5.297 16.869 1 17.33 ? B NPB 364 A 1 HETATM 2 O OB1 NPB . . . C 2 25.422 4.264 17.027 1 19.55 ? OB1 NPB 364 A 1 HETATM 3 O OB2 NPB . . . C 2 26.59 6.31 17.864 1 14.31 ? OB2 NPB 364 A 1 HETATM 4 C CP1 NPB . . . C 2 26.008 6.088 15.598 1 23.67 ? CP1 NPB 364 A 1 HETATM 5 C CP2 NPB . . . C 2 25.367 5.421 14.595 1 29.62 ? CP2 NPB 364 A 1 HETATM 6 C CP3 NPB . . . C 2 24.887 6.057 13.491 1 38.29 ? CP3 NPB 364 A 1 HETATM 7 N NT NPB . . . C 2 24.138 5.29 12.428 1 44.19 ? NT NPB 364 A 1 HETATM 8 O O1 NPB . . . C 2 23.571 5.857 11.565 1 46.87 ? O1 NPB 364 A 1 HETATM 9 O O2 NPB . . . C 2 24.003 4.105 12.511 1 48.13 ? O2 NPB 364 A 1 HETATM 10 C CP4 NPB . . . C 2 25.064 7.451 13.374 1 31.57 ? CP4 NPB 364 A 1 HETATM 11 C CP5 NPB . . . C 2 25.719 8.141 14.385 1 30 ? CP5 NPB 364 A 1 HETATM 12 C CP6 NPB . . . C 2 26.188 7.433 15.5 1 26.4 ? CP6 NPB 364 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 12 #