data_1F5K
#
_model_server_result.job_id            6Xx2_SZdeArm54noWcwRbA 
_model_server_result.datetime_utc      '2024-11-14 21:01:24' 
_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          1f5k 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":300}' 
#
_entry.id    1F5K 
#
_exptl.entry_id    1F5K 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              120.152 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            BENZAMIDINE 
_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            1F5K 
_cell.length_a            52.8 
_cell.length_b            54.6 
_cell.length_c            82.9 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1F5K 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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                      3 
_struct_asym.id                             D 
_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 31 U CYS 42 1_555 A SG CYS 47 U CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 A SG CYS 39 U CYS 50 1_555 A SG CYS 110 U CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
disulf ? disulf3 A SG CYS 135 U CYS 136 1_555 A SG CYS 204 U CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf4 A SG CYS 167 U CYS 168 1_555 A SG CYS 183 U CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.863 ? 
disulf ? disulf5 A SG CYS 194 U CYS 191 1_555 A SG CYS 222 U CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
#
_chem_comp.formula           'C7 H8 N2' 
_chem_comp.formula_weight    120.152 
_chem_comp.id                BEN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              BENZAMIDINE 
_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
C1 C2 BEN doub 70 n y 
C1 C6 BEN sing 71 n y 
C1 C BEN sing 72 n n 
C2 C3 BEN sing 73 n y 
C2 H2 BEN sing 74 n n 
C3 C4 BEN doub 75 n y 
C3 H3 BEN sing 76 n n 
C4 C5 BEN sing 77 n y 
C4 H4 BEN sing 78 n n 
C5 C6 BEN doub 79 n y 
C5 H5 BEN sing 80 n n 
C6 H6 BEN sing 81 n n 
C N1 BEN doub 82 e n 
C N2 BEN sing 83 n n 
N1 HN1 BEN sing 84 n n 
N2 HN21 BEN sing 85 n n 
N2 HN22 BEN sing 86 n n 
#
_atom_sites.entry_id                     1F5K 
_atom_sites.fract_transf_matrix[1][1]    0.018939 
_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]    0.018315 
_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]    0.012063 
_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 SO4 U 1 402 402 SO4 SO4 . 
C 2 SO4 U 1 403 403 SO4 SO4 . 
D 3 BEN U 1 300 300 BEN BNZ . 
E 4 HOH U 1 404 1 HOH WAT . 
E 4 HOH U 2 405 2 HOH WAT . 
E 4 HOH U 3 406 3 HOH WAT . 
E 4 HOH U 4 407 4 HOH WAT . 
E 4 HOH U 5 408 5 HOH WAT . 
E 4 HOH U 6 409 6 HOH WAT . 
E 4 HOH U 7 410 7 HOH WAT . 
E 4 HOH U 8 411 8 HOH WAT . 
E 4 HOH U 9 412 9 HOH WAT . 
E 4 HOH U 10 413 10 HOH WAT . 
E 4 HOH U 11 414 11 HOH WAT . 
E 4 HOH U 12 415 12 HOH WAT . 
E 4 HOH U 13 416 13 HOH WAT . 
E 4 HOH U 14 417 14 HOH WAT . 
E 4 HOH U 15 418 15 HOH WAT . 
E 4 HOH U 16 419 16 HOH WAT . 
E 4 HOH U 17 420 17 HOH WAT . 
E 4 HOH U 18 421 18 HOH WAT . 
E 4 HOH U 19 422 19 HOH WAT . 
E 4 HOH U 20 423 20 HOH WAT . 
E 4 HOH U 21 424 21 HOH WAT . 
E 4 HOH U 22 425 22 HOH WAT . 
E 4 HOH U 23 426 23 HOH WAT . 
E 4 HOH U 24 427 24 HOH WAT . 
E 4 HOH U 25 428 25 HOH WAT . 
E 4 HOH U 26 429 26 HOH WAT . 
E 4 HOH U 27 430 27 HOH WAT . 
E 4 HOH U 28 431 28 HOH WAT . 
E 4 HOH U 29 432 29 HOH WAT . 
E 4 HOH U 30 433 30 HOH WAT . 
E 4 HOH U 31 434 31 HOH WAT . 
E 4 HOH U 32 435 32 HOH WAT . 
E 4 HOH U 33 436 33 HOH WAT . 
E 4 HOH U 34 437 34 HOH WAT . 
E 4 HOH U 35 438 35 HOH WAT . 
E 4 HOH U 36 439 36 HOH WAT . 
E 4 HOH U 37 440 37 HOH WAT . 
E 4 HOH U 38 441 38 HOH WAT . 
E 4 HOH U 39 442 39 HOH WAT . 
E 4 HOH U 40 443 40 HOH WAT . 
E 4 HOH U 41 444 41 HOH WAT . 
E 4 HOH U 42 445 42 HOH WAT . 
E 4 HOH U 43 446 43 HOH WAT . 
E 4 HOH U 44 447 44 HOH WAT . 
E 4 HOH U 45 448 45 HOH WAT . 
E 4 HOH U 46 449 46 HOH WAT . 
E 4 HOH U 47 450 47 HOH WAT . 
E 4 HOH U 48 451 48 HOH WAT . 
E 4 HOH U 49 452 49 HOH WAT . 
E 4 HOH U 50 453 50 HOH WAT . 
E 4 HOH U 51 454 51 HOH WAT . 
E 4 HOH U 52 455 52 HOH WAT . 
E 4 HOH U 53 456 53 HOH WAT . 
E 4 HOH U 54 457 54 HOH WAT . 
E 4 HOH U 55 458 55 HOH WAT . 
E 4 HOH U 56 459 56 HOH WAT . 
E 4 HOH U 57 460 57 HOH WAT . 
E 4 HOH U 58 461 58 HOH WAT . 
E 4 HOH U 59 462 59 HOH WAT . 
E 4 HOH U 60 463 60 HOH WAT . 
E 4 HOH U 61 464 61 HOH WAT . 
E 4 HOH U 62 465 62 HOH WAT . 
E 4 HOH U 63 466 63 HOH WAT . 
E 4 HOH U 64 467 64 HOH WAT . 
E 4 HOH U 65 468 65 HOH WAT . 
E 4 HOH U 66 469 66 HOH WAT . 
E 4 HOH U 67 470 67 HOH WAT . 
E 4 HOH U 68 471 68 HOH WAT . 
E 4 HOH U 69 472 69 HOH WAT . 
E 4 HOH U 70 473 70 HOH WAT . 
E 4 HOH U 71 474 71 HOH WAT . 
E 4 HOH U 72 475 72 HOH WAT . 
E 4 HOH U 73 476 73 HOH WAT . 
E 4 HOH U 74 477 74 HOH WAT . 
E 4 HOH U 75 478 75 HOH WAT . 
E 4 HOH U 76 479 76 HOH WAT . 
E 4 HOH U 77 480 77 HOH WAT . 
E 4 HOH U 78 481 78 HOH WAT . 
E 4 HOH U 79 482 79 HOH WAT . 
E 4 HOH U 80 483 80 HOH WAT . 
E 4 HOH U 81 484 81 HOH WAT . 
E 4 HOH U 82 485 82 HOH WAT . 
E 4 HOH U 83 486 83 HOH WAT . 
E 4 HOH U 84 487 84 HOH WAT . 
E 4 HOH U 85 488 85 HOH WAT . 
E 4 HOH U 86 489 86 HOH WAT . 
E 4 HOH U 87 490 87 HOH WAT . 
E 4 HOH U 88 491 88 HOH WAT . 
E 4 HOH U 89 492 89 HOH WAT . 
E 4 HOH U 90 493 90 HOH WAT . 
E 4 HOH U 91 494 91 HOH WAT . 
E 4 HOH U 92 495 92 HOH WAT . 
E 4 HOH U 93 496 93 HOH WAT . 
E 4 HOH U 94 497 94 HOH WAT . 
E 4 HOH U 95 498 95 HOH WAT . 
E 4 HOH U 96 499 96 HOH WAT . 
E 4 HOH U 97 500 97 HOH WAT . 
E 4 HOH U 98 501 98 HOH WAT . 
E 4 HOH U 99 502 99 HOH WAT . 
E 4 HOH U 100 503 100 HOH WAT . 
E 4 HOH U 101 504 101 HOH WAT . 
E 4 HOH U 102 505 102 HOH WAT . 
E 4 HOH U 103 506 103 HOH WAT . 
E 4 HOH U 104 507 104 HOH WAT . 
E 4 HOH U 105 508 105 HOH WAT . 
E 4 HOH U 106 509 106 HOH WAT . 
E 4 HOH U 107 510 107 HOH WAT . 
E 4 HOH U 108 511 108 HOH WAT . 
E 4 HOH U 109 512 109 HOH WAT . 
E 4 HOH U 110 513 110 HOH WAT . 
E 4 HOH U 111 514 111 HOH WAT . 
E 4 HOH U 112 515 112 HOH WAT . 
E 4 HOH U 113 516 113 HOH WAT . 
E 4 HOH U 114 517 114 HOH WAT . 
E 4 HOH U 115 518 115 HOH WAT . 
E 4 HOH U 116 519 116 HOH WAT . 
E 4 HOH U 117 520 117 HOH WAT . 
E 4 HOH U 118 521 118 HOH WAT . 
E 4 HOH U 119 522 119 HOH WAT . 
E 4 HOH U 120 523 120 HOH WAT . 
E 4 HOH U 121 524 121 HOH WAT . 
E 4 HOH U 122 525 122 HOH WAT . 
E 4 HOH U 123 526 123 HOH WAT . 
E 4 HOH U 124 527 124 HOH WAT . 
E 4 HOH U 125 528 125 HOH WAT . 
E 4 HOH U 126 529 126 HOH WAT . 
E 4 HOH U 127 530 127 HOH WAT . 
E 4 HOH U 128 531 128 HOH WAT . 
E 4 HOH U 129 532 129 HOH WAT . 
E 4 HOH U 130 533 130 HOH WAT . 
E 4 HOH U 131 534 131 HOH WAT . 
E 4 HOH U 132 535 132 HOH WAT . 
E 4 HOH U 133 536 133 HOH WAT . 
E 4 HOH U 134 537 134 HOH WAT . 
E 4 HOH U 135 538 135 HOH WAT . 
E 4 HOH U 136 539 136 HOH WAT . 
E 4 HOH U 137 540 137 HOH WAT . 
E 4 HOH U 138 541 138 HOH WAT . 
E 4 HOH U 139 542 139 HOH WAT . 
E 4 HOH U 140 543 140 HOH WAT . 
E 4 HOH U 141 544 141 HOH WAT . 
E 4 HOH U 142 545 142 HOH WAT . 
E 4 HOH U 143 546 143 HOH WAT . 
E 4 HOH U 144 547 144 HOH WAT . 
E 4 HOH U 145 548 145 HOH WAT . 
E 4 HOH U 146 549 146 HOH WAT . 
E 4 HOH U 147 550 147 HOH WAT . 
E 4 HOH U 148 551 148 HOH WAT . 
E 4 HOH U 149 552 149 HOH WAT . 
E 4 HOH U 150 553 150 HOH WAT . 
E 4 HOH U 151 554 151 HOH WAT . 
E 4 HOH U 152 555 152 HOH WAT . 
E 4 HOH U 153 556 153 HOH WAT . 
E 4 HOH U 154 557 154 HOH WAT . 
E 4 HOH U 155 558 155 HOH WAT . 
E 4 HOH U 156 559 156 HOH WAT . 
E 4 HOH U 157 560 157 HOH WAT . 
E 4 HOH U 158 561 158 HOH WAT . 
E 4 HOH U 159 562 159 HOH WAT . 
E 4 HOH U 160 563 160 HOH WAT . 
E 4 HOH U 161 564 161 HOH WAT . 
E 4 HOH U 162 565 162 HOH WAT . 
E 4 HOH U 163 566 163 HOH WAT . 
E 4 HOH U 164 567 164 HOH WAT . 
E 4 HOH U 165 568 165 HOH WAT . 
E 4 HOH U 166 569 166 HOH WAT . 
E 4 HOH U 167 570 167 HOH WAT . 
E 4 HOH U 168 571 168 HOH WAT . 
E 4 HOH U 169 572 169 HOH WAT . 
E 4 HOH U 170 573 170 HOH WAT . 
E 4 HOH U 171 574 171 HOH WAT . 
E 4 HOH U 172 575 172 HOH WAT . 
E 4 HOH U 173 576 173 HOH WAT . 
E 4 HOH U 174 577 174 HOH WAT . 
E 4 HOH U 175 578 175 HOH WAT . 
E 4 HOH U 176 579 176 HOH WAT . 
E 4 HOH U 177 580 177 HOH WAT . 
E 4 HOH U 178 581 178 HOH WAT . 
E 4 HOH U 179 582 179 HOH WAT . 
E 4 HOH U 180 583 180 HOH WAT . 
E 4 HOH U 181 584 181 HOH WAT . 
E 4 HOH U 182 585 182 HOH WAT . 
E 4 HOH U 183 586 183 HOH WAT . 
E 4 HOH U 184 587 184 HOH WAT . 
E 4 HOH U 185 588 185 HOH WAT . 
E 4 HOH U 186 589 186 HOH WAT . 
E 4 HOH U 187 590 187 HOH WAT . 
E 4 HOH U 188 591 188 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 C C1 BEN . . . D 3 31.641 5.193 28.171 1 29.31 ? C1 BEN 300 U 1 
HETATM 2 C C2 BEN . . . D 3 30.516 4.739 28.917 1 26.29 ? C2 BEN 300 U 1 
HETATM 3 C C3 BEN . . . D 3 29.431 5.586 29.206 1 27.53 ? C3 BEN 300 U 1 
HETATM 4 C C4 BEN . . . D 3 29.431 6.922 28.757 1 28.02 ? C4 BEN 300 U 1 
HETATM 5 C C5 BEN . . . D 3 30.53 7.398 28.018 1 33.99 ? C5 BEN 300 U 1 
HETATM 6 C C6 BEN . . . D 3 31.615 6.547 27.731 1 27.76 ? C6 BEN 300 U 1 
HETATM 7 C C BEN . . . D 3 32.741 4.333 27.877 1 28.65 ? C BEN 300 U 1 
HETATM 8 N N1 BEN . . . D 3 33.796 4.745 27.187 1 25.62 ? N1 BEN 300 U 1 
HETATM 9 N N2 BEN . . . D 3 32.778 3.068 28.273 1 32.61 ? N2 BEN 300 U 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           48 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           1116 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           9 
#