data_3PTB
#
_model_server_result.job_id            u5X7Mkeo9aa-8ReEG6UD3A 
_model_server_result.datetime_utc      '2024-11-22 06:02:49' 
_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          3ptb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1}' 
#
_entry.id    3PTB 
#
_exptl.entry_id    3PTB 
_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            3PTB 
_cell.length_a            54.89 
_cell.length_b            58.52 
_cell.length_c            67.63 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3PTB 
_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 
_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                             C 
_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 7 A CYS 22 1_555 A SG CYS 137 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 41 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf3 A SG CYS 109 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf4 A SG CYS 116 A CYS 136 1_555 A SG CYS 183 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
disulf ? disulf5 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf6 A SG CYS 173 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
metalc ? metalc1 A OE1 GLU 52 A GLU 70 1_555 B CA CA . A CA 480 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc2 A O ASN 54 A ASN 72 1_555 B CA CA . A CA 480 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc3 A O VAL 57 A VAL 75 1_555 B CA CA . A CA 480 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc4 A OE2 GLU 62 A GLU 80 1_555 B CA CA . A CA 480 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? 
metalc ? metalc5 B CA CA . A CA 480 1_555 D O HOH . A HOH 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? 
metalc ? metalc6 B CA CA . A CA 480 1_555 D O HOH . A HOH 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? 
#
_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                     3PTB 
_atom_sites.fract_transf_matrix[1][1]    0.018218 
_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]    0.017088 
_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]    0.014786 
_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 CA A 1 480 480 CA CA . 
C 3 BEN A 1 1 1 BEN BEN . 
D 4 HOH A 1 401 401 HOH HOH . 
D 4 HOH A 2 406 406 HOH HOH . 
D 4 HOH A 3 408 408 HOH HOH . 
D 4 HOH A 4 410 410 HOH HOH . 
D 4 HOH A 5 412 412 HOH HOH . 
D 4 HOH A 6 415 415 HOH HOH . 
D 4 HOH A 7 416 416 HOH HOH . 
D 4 HOH A 8 429 429 HOH HOH . 
D 4 HOH A 9 430 430 HOH HOH . 
D 4 HOH A 10 439 439 HOH HOH . 
D 4 HOH A 11 457 457 HOH HOH . 
D 4 HOH A 12 470 470 HOH HOH . 
D 4 HOH A 13 473 473 HOH HOH . 
D 4 HOH A 14 482 482 HOH HOH . 
D 4 HOH A 15 499 499 HOH HOH . 
D 4 HOH A 16 516 516 HOH HOH . 
D 4 HOH A 17 530 530 HOH HOH . 
D 4 HOH A 18 561 561 HOH HOH . 
D 4 HOH A 19 562 562 HOH HOH . 
D 4 HOH A 20 583 583 HOH HOH . 
D 4 HOH A 21 604 604 HOH HOH . 
D 4 HOH A 22 700 700 HOH HOH . 
D 4 HOH A 23 701 701 HOH HOH . 
D 4 HOH A 24 702 702 HOH HOH . 
D 4 HOH A 25 703 703 HOH HOH . 
D 4 HOH A 26 704 704 HOH HOH . 
D 4 HOH A 27 705 705 HOH HOH . 
D 4 HOH A 28 706 706 HOH HOH . 
D 4 HOH A 29 707 707 HOH HOH . 
D 4 HOH A 30 708 708 HOH HOH . 
D 4 HOH A 31 709 709 HOH HOH . 
D 4 HOH A 32 710 710 HOH HOH . 
D 4 HOH A 33 711 711 HOH HOH . 
D 4 HOH A 34 712 712 HOH HOH . 
D 4 HOH A 35 713 713 HOH HOH . 
D 4 HOH A 36 714 714 HOH HOH . 
D 4 HOH A 37 715 715 HOH HOH . 
D 4 HOH A 38 716 716 HOH HOH . 
D 4 HOH A 39 717 717 HOH HOH . 
D 4 HOH A 40 718 718 HOH HOH . 
D 4 HOH A 41 719 719 HOH HOH . 
D 4 HOH A 42 720 720 HOH HOH . 
D 4 HOH A 43 721 721 HOH HOH . 
D 4 HOH A 44 722 722 HOH HOH . 
D 4 HOH A 45 723 723 HOH HOH . 
D 4 HOH A 46 724 724 HOH HOH . 
D 4 HOH A 47 725 725 HOH HOH . 
D 4 HOH A 48 726 726 HOH HOH . 
D 4 HOH A 49 727 727 HOH HOH . 
D 4 HOH A 50 728 728 HOH HOH . 
D 4 HOH A 51 729 729 HOH HOH . 
D 4 HOH A 52 730 730 HOH HOH . 
D 4 HOH A 53 731 731 HOH HOH . 
D 4 HOH A 54 800 800 HOH HOH . 
D 4 HOH A 55 801 801 HOH HOH . 
D 4 HOH A 56 802 802 HOH HOH . 
D 4 HOH A 57 803 803 HOH HOH . 
D 4 HOH A 58 804 804 HOH HOH . 
D 4 HOH A 59 805 805 HOH HOH . 
D 4 HOH A 60 807 807 HOH HOH . 
D 4 HOH A 61 808 808 HOH HOH . 
D 4 HOH A 62 809 809 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 BEN . . . C 3 -1.853 14.311 16.658 1 19.86 ? C1 BEN 1 A 1 
HETATM 2 C C2 BEN . . . C 3 -2.107 15.653 16.758 1 19.86 ? C2 BEN 1 A 1 
HETATM 3 C C3 BEN . . . C 3 -1.774 16.341 17.932 1 19.86 ? C3 BEN 1 A 1 
HETATM 4 C C4 BEN . . . C 3 -1.175 15.662 19.005 1 19.86 ? C4 BEN 1 A 1 
HETATM 5 C C5 BEN . . . C 3 -0.914 14.295 18.885 1 19.86 ? C5 BEN 1 A 1 
HETATM 6 C C6 BEN . . . C 3 -1.257 13.634 17.708 1 19.86 ? C6 BEN 1 A 1 
HETATM 7 C C BEN . . . C 3 -2.193 13.627 15.496 1 19.86 ? C BEN 1 A 1 
HETATM 8 N N1 BEN . . . C 3 -2.797 14.235 14.491 1 19.86 ? N1 BEN 1 A 1 
HETATM 9 N N2 BEN . . . C 3 -1.762 12.391 15.309 1 19.86 ? N2 BEN 1 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           9 
#