data_7DZD
#
_model_server_result.job_id            NEsyVPlWfzl2eqSoSWJT3A 
_model_server_result.datetime_utc      '2024-11-06 18:29:04' 
_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          7dzd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    7DZD 
#
_exptl.entry_id    7DZD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              179.176 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '4-carbamimidamidobenzoic acid' 
_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         120 
_cell.entry_id            7DZD 
_cell.length_a            120.317 
_cell.length_b            120.317 
_cell.length_c            42.451 
_cell.Z_PDB               9 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7DZD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
_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                      2 
_struct_asym.id                             B 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf2 A SG CYS 39 U CYS 50 1_555 A SG CYS 110 U CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
disulf ? disulf3 A SG CYS 135 U CYS 136 1_555 A SG CYS 204 U CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf4 A SG CYS 167 U CYS 168 1_555 A SG CYS 183 U CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
disulf ? disulf5 A SG CYS 194 U CYS 191 1_555 A SG CYS 222 U CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
covale ? covale1 A OG SER 198 U SER 195 1_555 B C6 GBS . U GBS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? 
#
_chem_comp.formula           'C8 H9 N3 O2' 
_chem_comp.formula_weight    179.176 
_chem_comp.id                GBS 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '4-carbamimidamidobenzoic acid' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'Nafamostat, bound form' 
#
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
C6 O GBS doub 83 n n 
C6 C5 GBS sing 84 n n 
C5 C GBS doub 85 n y 
C5 C4 GBS sing 86 n y 
C C1 GBS sing 87 n y 
C4 C3 GBS doub 88 n y 
C1 C2 GBS doub 89 n y 
C3 C2 GBS sing 90 n y 
C2 N2 GBS sing 91 n n 
N2 C18 GBS sing 92 n n 
C18 N4 GBS doub 93 n n 
C18 N3 GBS sing 94 n n 
C6 O1 GBS sing 95 n n 
C3 H1 GBS sing 96 n n 
C4 H2 GBS sing 97 n n 
C1 H3 GBS sing 98 n n 
N4 H4 GBS sing 99 n n 
N2 H5 GBS sing 100 n n 
N3 H6 GBS sing 101 n n 
N3 H7 GBS sing 102 n n 
C H8 GBS sing 103 n n 
O1 H9 GBS sing 104 n n 
#
_atom_sites.entry_id                     7DZD 
_atom_sites.fract_transf_matrix[1][1]    0.008311 
_atom_sites.fract_transf_matrix[1][2]    0.004799 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009597 
_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]    0.023557 
_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 GBS U 1 301 301 GBS GBS . 
C 3 PGE U 1 302 302 PGE PGE . 
D 3 PGE U 1 303 303 PGE PGE . 
E 4 HOH U 1 401 401 HOH HOH . 
E 4 HOH U 2 402 402 HOH HOH . 
E 4 HOH U 3 403 403 HOH HOH . 
E 4 HOH U 4 404 404 HOH HOH . 
E 4 HOH U 5 405 405 HOH HOH . 
E 4 HOH U 6 406 406 HOH HOH . 
E 4 HOH U 7 407 407 HOH HOH . 
E 4 HOH U 8 408 408 HOH HOH . 
E 4 HOH U 9 409 409 HOH HOH . 
E 4 HOH U 10 410 410 HOH HOH . 
E 4 HOH U 11 411 411 HOH HOH . 
E 4 HOH U 12 412 412 HOH HOH . 
E 4 HOH U 13 413 413 HOH HOH . 
E 4 HOH U 14 414 414 HOH HOH . 
E 4 HOH U 15 415 415 HOH HOH . 
E 4 HOH U 16 416 416 HOH HOH . 
E 4 HOH U 17 417 417 HOH HOH . 
E 4 HOH U 18 418 418 HOH HOH . 
E 4 HOH U 19 419 419 HOH HOH . 
E 4 HOH U 20 420 420 HOH HOH . 
E 4 HOH U 21 421 421 HOH HOH . 
E 4 HOH U 22 422 422 HOH HOH . 
E 4 HOH U 23 423 423 HOH HOH . 
E 4 HOH U 24 424 424 HOH HOH . 
E 4 HOH U 25 425 425 HOH HOH . 
E 4 HOH U 26 426 426 HOH HOH . 
E 4 HOH U 27 427 427 HOH HOH . 
E 4 HOH U 28 428 428 HOH HOH . 
E 4 HOH U 29 429 429 HOH HOH . 
E 4 HOH U 30 430 430 HOH HOH . 
E 4 HOH U 31 431 431 HOH HOH . 
E 4 HOH U 32 432 432 HOH HOH . 
E 4 HOH U 33 433 433 HOH HOH . 
E 4 HOH U 34 434 434 HOH HOH . 
E 4 HOH U 35 435 435 HOH HOH . 
E 4 HOH U 36 436 436 HOH HOH . 
E 4 HOH U 37 437 437 HOH HOH . 
E 4 HOH U 38 438 438 HOH HOH . 
E 4 HOH U 39 439 439 HOH HOH . 
E 4 HOH U 40 440 440 HOH HOH . 
E 4 HOH U 41 441 441 HOH HOH . 
E 4 HOH U 42 442 442 HOH HOH . 
E 4 HOH U 43 443 443 HOH HOH . 
E 4 HOH U 44 444 444 HOH HOH . 
E 4 HOH U 45 445 445 HOH HOH . 
E 4 HOH U 46 446 446 HOH HOH . 
E 4 HOH U 47 447 447 HOH HOH . 
E 4 HOH U 48 448 448 HOH HOH . 
E 4 HOH U 49 449 449 HOH HOH . 
E 4 HOH U 50 450 450 HOH HOH . 
E 4 HOH U 51 451 451 HOH HOH . 
E 4 HOH U 52 452 452 HOH HOH . 
E 4 HOH U 53 453 453 HOH HOH . 
E 4 HOH U 54 454 454 HOH HOH . 
E 4 HOH U 55 455 455 HOH HOH . 
E 4 HOH U 56 456 456 HOH HOH . 
E 4 HOH U 57 457 457 HOH HOH . 
E 4 HOH U 58 458 458 HOH HOH . 
E 4 HOH U 59 459 459 HOH HOH . 
E 4 HOH U 60 460 460 HOH HOH . 
E 4 HOH U 61 461 461 HOH HOH . 
E 4 HOH U 62 462 462 HOH HOH . 
E 4 HOH U 63 463 463 HOH HOH . 
E 4 HOH U 64 464 464 HOH HOH . 
E 4 HOH U 65 465 465 HOH HOH . 
E 4 HOH U 66 466 466 HOH HOH . 
E 4 HOH U 67 467 467 HOH HOH . 
E 4 HOH U 68 468 468 HOH HOH . 
E 4 HOH U 69 469 469 HOH HOH . 
E 4 HOH U 70 470 470 HOH HOH . 
E 4 HOH U 71 471 471 HOH HOH . 
E 4 HOH U 72 472 472 HOH HOH . 
E 4 HOH U 73 473 473 HOH HOH . 
E 4 HOH U 74 474 475 HOH HOH . 
E 4 HOH U 75 475 476 HOH HOH . 
E 4 HOH U 76 476 477 HOH HOH . 
E 4 HOH U 77 477 478 HOH HOH . 
E 4 HOH U 78 478 479 HOH HOH . 
E 4 HOH U 79 479 480 HOH HOH . 
E 4 HOH U 80 480 481 HOH HOH . 
E 4 HOH U 81 481 482 HOH HOH . 
E 4 HOH U 82 482 474 HOH HOH . 
E 4 HOH U 83 483 483 HOH HOH . 
E 4 HOH U 84 484 484 HOH HOH . 
E 4 HOH U 85 485 485 HOH HOH . 
E 4 HOH U 86 486 486 HOH HOH . 
E 4 HOH U 87 487 487 HOH HOH . 
E 4 HOH U 88 488 488 HOH HOH . 
E 4 HOH U 89 489 489 HOH HOH . 
E 4 HOH U 90 490 490 HOH HOH . 
E 4 HOH U 91 491 491 HOH HOH . 
E 4 HOH U 92 492 492 HOH HOH . 
E 4 HOH U 93 493 493 HOH HOH . 
E 4 HOH U 94 494 494 HOH HOH . 
E 4 HOH U 95 495 495 HOH HOH . 
E 4 HOH U 96 496 496 HOH HOH . 
E 4 HOH U 97 497 497 HOH HOH . 
E 4 HOH U 98 498 498 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 C2 GBS . . . B 2 -30.47 -18.675 -3.426 1 10.57 ? C2 GBS 301 U 1 
HETATM 2 C C3 GBS . . . B 2 -30.896 -18.209 -4.666 1 10.36 ? C3 GBS 301 U 1 
HETATM 3 C C4 GBS . . . B 2 -29.988 -17.571 -5.505 1 10.5 ? C4 GBS 301 U 1 
HETATM 4 C C6 GBS . . . B 2 -27.76 -16.677 -5.941 1 10.72 ? C6 GBS 301 U 1 
HETATM 5 C C1 GBS . . . B 2 -29.154 -18.428 -3.002 1 10.78 ? C1 GBS 301 U 1 
HETATM 6 N N4 GBS . . . B 2 -32.415 -20.752 -4.06 1 10.8 ? N4 GBS 301 U 1 
HETATM 7 C C5 GBS . . . B 2 -28.673 -17.343 -5.108 1 10.52 ? C5 GBS 301 U 1 
HETATM 8 C C18 GBS . . . B 2 -32.212 -20.247 -2.83 1 10.87 ? C18 GBS 301 U 1 
HETATM 9 O O GBS . . . B 2 -26.492 -16.557 -5.775 1 10.97 ? O GBS 301 U 1 
HETATM 10 N N2 GBS . . . B 2 -31.289 -19.294 -2.578 1 10.48 ? N2 GBS 301 U 1 
HETATM 11 N N3 GBS . . . B 2 -32.969 -20.707 -1.81 1 10.86 ? N3 GBS 301 U 1 
HETATM 12 C C GBS . . . B 2 -28.263 -17.775 -3.845 1 10.79 ? C GBS 301 U 1 
#
_model_server_stats.io_time_ms              71 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           12 
#