data_1KDS
#
_model_server_result.job_id            dE6PrgizdDIgMMN40R3A_Q 
_model_server_result.datetime_utc      '2024-11-23 05:14:10' 
_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              67 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           12 
#