data_6BDK
#
_model_server_result.job_id            LB-Pi_JCvArTGIFX83yxTA 
_model_server_result.datetime_utc      '2024-11-29 01:52:13' 
_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          6bdk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":602}' 
#
_entry.id    6BDK 
#
_exptl.entry_id    6BDK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              551.743 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'tert-butyl [(2S)-1-{[(2R)-2-(cyclopentylamino)-3-oxo-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}-3-(1H-indol-3-yl)propan-2-yl]carbamate' 
_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            6BDK 
_cell.length_a            77.479 
_cell.length_b            102.39 
_cell.length_c            127.76 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6BDK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -102.39 0 
3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
4 'crystal symmetry operation' 4_545 x,-y-1,-z 1 0 0 0 -1 0 0 0 -1 0 -102.39 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
metalc ? metalc1 A SG CYS 422 A CYS 442 1_555 B FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc2 B FE HEM . A HEM 601 1_555 C N28 DJ1 . A DJ1 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? 
#
_chem_comp.formula           'C30 H41 N5 O3 S' 
_chem_comp.formula_weight    551.743 
_chem_comp.id                DJ1 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'tert-butyl [(2S)-1-{[(2R)-2-(cyclopentylamino)-3-oxo-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}-3-(1H-indol-3-yl)propan-2-yl]carbamate' 
_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
N33 C34 DJ1 sing 83 n y 
N33 C32 DJ1 sing 84 n y 
C39 C34 DJ1 doub 85 n y 
C39 C38 DJ1 sing 86 n y 
C04 C02 DJ1 sing 87 n n 
C34 C35 DJ1 sing 88 n y 
C01 C02 DJ1 sing 89 n n 
C32 C31 DJ1 doub 90 n y 
C38 C37 DJ1 doub 91 n y 
C02 C03 DJ1 sing 92 n n 
C02 O05 DJ1 sing 93 n n 
C35 C31 DJ1 sing 94 n y 
C35 C36 DJ1 doub 95 n y 
C31 C30 DJ1 sing 96 n n 
N08 C06 DJ1 sing 97 n n 
N08 C09 DJ1 sing 98 n n 
O05 C06 DJ1 sing 99 n n 
C37 C36 DJ1 sing 100 n y 
C06 O07 DJ1 doub 101 n n 
C09 C30 DJ1 sing 102 n n 
C09 C10 DJ1 sing 103 n n 
C26 C27 DJ1 doub 104 n y 
C26 C25 DJ1 sing 105 n y 
C27 N28 DJ1 sing 106 n y 
C10 S11 DJ1 sing 107 n n 
N28 C29 DJ1 doub 108 n y 
C25 C24 DJ1 doub 109 n y 
S11 C12 DJ1 sing 110 n n 
C29 C24 DJ1 sing 111 n y 
C18 C19 DJ1 sing 112 n n 
C18 C17 DJ1 sing 113 n n 
C24 C23 DJ1 sing 114 n n 
C19 C15 DJ1 sing 115 n n 
C12 C13 DJ1 sing 116 n n 
N22 C23 DJ1 sing 117 n n 
N22 C20 DJ1 sing 118 n n 
C13 C20 DJ1 sing 119 n n 
C13 N14 DJ1 sing 120 n n 
C17 C16 DJ1 sing 121 n n 
C20 O21 DJ1 doub 122 n n 
C15 N14 DJ1 sing 123 n n 
C15 C16 DJ1 sing 124 n n 
C15 H1 DJ1 sing 125 n n 
C17 H2 DJ1 sing 126 n n 
C17 H3 DJ1 sing 127 n n 
C12 H4 DJ1 sing 128 n n 
N14 H5 DJ1 sing 129 n n 
C16 H7 DJ1 sing 130 n n 
C16 H8 DJ1 sing 131 n n 
C18 H9 DJ1 sing 132 n n 
C18 H10 DJ1 sing 133 n n 
C19 H11 DJ1 sing 134 n n 
C19 H12 DJ1 sing 135 n n 
C01 H13 DJ1 sing 136 n n 
C01 H14 DJ1 sing 137 n n 
C01 H15 DJ1 sing 138 n n 
C03 H16 DJ1 sing 139 n n 
C03 H17 DJ1 sing 140 n n 
C03 H18 DJ1 sing 141 n n 
C04 H19 DJ1 sing 142 n n 
C04 H20 DJ1 sing 143 n n 
C04 H21 DJ1 sing 144 n n 
C09 H22 DJ1 sing 145 n n 
C10 H23 DJ1 sing 146 n n 
C10 H24 DJ1 sing 147 n n 
C13 H25 DJ1 sing 148 n n 
C23 H26 DJ1 sing 149 n n 
C23 H27 DJ1 sing 150 n n 
C25 H28 DJ1 sing 151 n n 
C26 H29 DJ1 sing 152 n n 
C27 H30 DJ1 sing 153 n n 
C29 H31 DJ1 sing 154 n n 
C30 H32 DJ1 sing 155 n n 
C30 H33 DJ1 sing 156 n n 
C32 H34 DJ1 sing 157 n n 
C36 H35 DJ1 sing 158 n n 
C37 H36 DJ1 sing 159 n n 
C38 H37 DJ1 sing 160 n n 
C39 H38 DJ1 sing 161 n n 
N08 H39 DJ1 sing 162 n n 
N22 H40 DJ1 sing 163 n n 
N33 H41 DJ1 sing 164 n n 
C12 H42 DJ1 sing 165 n n 
#
_atom_sites.entry_id                     6BDK 
_atom_sites.fract_transf_matrix[1][1]    0.012907 
_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]    0.009767 
_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]    0.007827 
_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 HEM A 1 601 500 HEM HEM . 
C 3 DJ1 A 1 602 700 DJ1 68D . 
#
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 C15 DJ1 . . . C 3 -15.861 -35.541 -6.452 1 129.26 ? C15 DJ1 602 A 1 
HETATM 2 C C17 DJ1 . . . C 3 -14.465 -33.58 -7.069 1 134.96 ? C17 DJ1 602 A 1 
HETATM 3 C C20 DJ1 . . . C 3 -17.912 -32.943 -6.619 1 112.86 ? C20 DJ1 602 A 1 
HETATM 4 C C12 DJ1 . . . C 3 -19.271 -34.879 -7.545 1 110.73 ? C12 DJ1 602 A 1 
HETATM 5 N N14 DJ1 . . . C 3 -17.302 -35.398 -6.322 1 119.02 ? N14 DJ1 602 A 1 
HETATM 6 C C16 DJ1 . . . C 3 -15.091 -34.319 -5.854 1 129.87 ? C16 DJ1 602 A 1 
HETATM 7 C C18 DJ1 . . . C 3 -14.376 -34.528 -8.2 1 140.19 ? C18 DJ1 602 A 1 
HETATM 8 C C19 DJ1 . . . C 3 -15.49 -35.631 -7.929 1 139.44 ? C19 DJ1 602 A 1 
HETATM 9 C C01 DJ1 . . . C 3 -16.252 -30.816 -13.703 1 106.47 ? C01 DJ1 602 A 1 
HETATM 10 C C02 DJ1 . . . C 3 -17.075 -29.728 -13 1 114.36 ? C02 DJ1 602 A 1 
HETATM 11 C C03 DJ1 . . . C 3 -16.148 -28.694 -12.362 1 117.12 ? C03 DJ1 602 A 1 
HETATM 12 C C04 DJ1 . . . C 3 -17.94 -28.996 -14.039 1 113.32 ? C04 DJ1 602 A 1 
HETATM 13 C C06 DJ1 . . . C 3 -17.65 -31.644 -11.67 1 127.22 ? C06 DJ1 602 A 1 
HETATM 14 C C09 DJ1 . . . C 3 -19.162 -33.534 -11.168 1 112.1 ? C09 DJ1 602 A 1 
HETATM 15 C C10 DJ1 . . . C 3 -19.348 -32.893 -9.816 1 105.81 ? C10 DJ1 602 A 1 
HETATM 16 C C13 DJ1 . . . C 3 -17.851 -34.394 -7.262 1 111.9 ? C13 DJ1 602 A 1 
HETATM 17 C C23 DJ1 . . . C 3 -18.09 -30.429 -7.031 1 80.59 ? C23 DJ1 602 A 1 
HETATM 18 C C24 DJ1 . . . C 3 -18.715 -29.632 -8.135 1 60.91 ? C24 DJ1 602 A 1 
HETATM 19 C C25 DJ1 . . . C 3 -18.02 -29.081 -9.19 1 40.92 ? C25 DJ1 602 A 1 
HETATM 20 C C26 DJ1 . . . C 3 -18.64 -28.39 -10.205 1 47.42 ? C26 DJ1 602 A 1 
HETATM 21 C C27 DJ1 . . . C 3 -20.002 -28.259 -10.203 1 43.15 ? C27 DJ1 602 A 1 
HETATM 22 C C29 DJ1 . . . C 3 -20.065 -29.458 -8.226 1 69.05 ? C29 DJ1 602 A 1 
HETATM 23 C C30 DJ1 . . . C 3 -18.192 -34.811 -10.964 1 115.65 ? C30 DJ1 602 A 1 
HETATM 24 C C31 DJ1 . . . C 3 -17.651 -35.461 -12.251 1 123.17 ? C31 DJ1 602 A 1 
HETATM 25 C C32 DJ1 . . . C 3 -17.99 -35.106 -13.532 1 126.43 ? C32 DJ1 602 A 1 
HETATM 26 C C34 DJ1 . . . C 3 -16.51 -36.806 -13.799 1 135.97 ? C34 DJ1 602 A 1 
HETATM 27 C C35 DJ1 . . . C 3 -16.692 -36.567 -12.366 1 133.88 ? C35 DJ1 602 A 1 
HETATM 28 C C36 DJ1 . . . C 3 -15.939 -37.415 -11.503 1 146.28 ? C36 DJ1 602 A 1 
HETATM 29 C C37 DJ1 . . . C 3 -15.073 -38.418 -11.962 1 151.83 ? C37 DJ1 602 A 1 
HETATM 30 C C38 DJ1 . . . C 3 -14.92 -38.623 -13.364 1 152.43 ? C38 DJ1 602 A 1 
HETATM 31 C C39 DJ1 . . . C 3 -15.635 -37.822 -14.259 1 145.93 ? C39 DJ1 602 A 1 
HETATM 32 N N08 DJ1 . . . C 3 -18.622 -32.578 -12.089 1 114.36 ? N08 DJ1 602 A 1 
HETATM 33 N N22 DJ1 . . . C 3 -17.988 -31.801 -7.481 1 98.84 ? N22 DJ1 602 A 1 
HETATM 34 N N28 DJ1 . . . C 3 -20.666 -28.785 -9.206 1 62.42 ? N28 DJ1 602 A 1 
HETATM 35 N N33 DJ1 . . . C 3 -17.325 -35.877 -14.438 1 133.66 ? N33 DJ1 602 A 1 
HETATM 36 O O05 DJ1 . . . C 3 -17.948 -30.342 -12.084 1 122.94 ? O05 DJ1 602 A 1 
HETATM 37 O O07 DJ1 . . . C 3 -16.762 -31.864 -10.855 1 137.65 ? O07 DJ1 602 A 1 
HETATM 38 O O21 DJ1 . . . C 3 -17.873 -32.757 -5.458 1 119.8 ? O21 DJ1 602 A 1 
HETATM 39 S S11 DJ1 . . . C 3 -20.174 -34.153 -8.921 1 106.66 ? S11 DJ1 602 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           276 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           39 
#