data_5VCK
#
_model_server_result.job_id            tCycLBflCyoARp9DXqYkVQ 
_model_server_result.datetime_utc      '2024-11-17 05:57:25' 
_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          5vck 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":100}' 
#
_entry.id    5VCK 
#
_exptl.entry_id    5VCK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              909.077 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-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         120 
_cell.entry_id            5VCK 
_cell.length_a            62.953 
_cell.length_b            62.953 
_cell.length_c            82.306 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VCK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G 
_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                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C50 H64 N6 O10' 
_chem_comp.formula_weight    909.077 
_chem_comp.id                3TL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate' 
_chem_comp.type              peptide-like 
_chem_comp.pdbx_synonyms     'TL-3, C2 symmetric inhibitor' 
#
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
C31 O8 3TL doub 1 n n 
C31 O9 3TL sing 2 n n 
C31 N4 3TL sing 3 n n 
O9 CA 3TL sing 4 n n 
CA C 3TL sing 5 n n 
CA HA1 3TL sing 6 n n 
CA HA2 3TL sing 7 n n 
C C13 3TL doub 8 n y 
C C17 3TL sing 9 n y 
C13 C14 3TL sing 10 n y 
C13 H13 3TL sing 11 n n 
C14 C15 3TL doub 12 n y 
C14 H14 3TL sing 13 n n 
C15 C16 3TL sing 14 n y 
C15 H15 3TL sing 15 n n 
C16 C17 3TL doub 16 n y 
C16 H16 3TL sing 17 n n 
C17 H17 3TL sing 18 n n 
N4 C18 3TL sing 19 n n 
N4 HN4 3TL sing 20 n n 
C18 C19 3TL sing 21 n n 
C18 C20 3TL sing 22 n n 
C18 H18 3TL sing 23 n n 
C19 O4 3TL doub 24 n n 
C19 N2 3TL sing 25 n n 
C20 H201 3TL sing 26 n n 
C20 H202 3TL sing 27 n n 
C20 H203 3TL sing 28 n n 
N2 C10 3TL sing 29 n n 
N2 HN2 3TL sing 30 n n 
C10 C11 3TL sing 31 n n 
C10 C12 3TL sing 32 n n 
C10 H10 3TL sing 33 n n 
C11 O2 3TL doub 34 n n 
C11 N1 3TL sing 35 n n 
C12 CG2 3TL sing 36 n n 
C12 CG1 3TL sing 37 n n 
C12 H12 3TL sing 38 n n 
CG2 HG21 3TL sing 39 n n 
CG2 HG22 3TL sing 40 n n 
CG2 HG23 3TL sing 41 n n 
CG1 HG11 3TL sing 42 n n 
CG1 HG12 3TL sing 43 n n 
CG1 HG13 3TL sing 44 n n 
C2 O1 3TL sing 45 n n 
C2 C1 3TL sing 46 n n 
C2 H2 3TL sing 47 n n 
C2 C52 3TL sing 48 n n 
O1 HO1 3TL sing 49 n n 
C1 N1 3TL sing 50 n n 
C1 C3 3TL sing 51 n n 
C1 H1 3TL sing 52 n n 
N1 HN1 3TL sing 53 n n 
C3 C4 3TL sing 54 n n 
C3 H31 3TL sing 55 n n 
C3 H32 3TL sing 56 n n 
C4 C5 3TL doub 57 n y 
C4 C9 3TL sing 58 n y 
C5 C6 3TL sing 59 n y 
C5 H5 3TL sing 60 n n 
C9 C8 3TL doub 61 n y 
C9 H9 3TL sing 62 n n 
C6 C7 3TL doub 63 n y 
C6 H6 3TL sing 64 n n 
C8 C7 3TL sing 65 n y 
C8 H8 3TL sing 66 n n 
C7 H7 3TL sing 67 n n 
N51 C51 3TL sing 68 n n 
N51 HN51 3TL sing 69 n n 
N51 C61 3TL sing 70 n n 
C51 C52 3TL sing 71 n n 
C51 C53 3TL sing 72 n n 
C51 H51 3TL sing 73 n n 
C52 O51 3TL sing 74 n n 
C52 H52 3TL sing 75 n n 
O51 HO51 3TL sing 76 n n 
C53 C54 3TL sing 77 n n 
C53 H531 3TL sing 78 n n 
C53 H532 3TL sing 79 n n 
C54 C55 3TL doub 80 n y 
C54 C59 3TL sing 81 n y 
C55 C56 3TL sing 82 n y 
C55 H55 3TL sing 83 n n 
C59 C58 3TL doub 84 n y 
C59 H59 3TL sing 85 n n 
C56 C57 3TL doub 86 n y 
C56 H56 3TL sing 87 n n 
C58 C57 3TL sing 88 n y 
C58 H58 3TL sing 89 n n 
C57 H57 3TL sing 90 n n 
N52 C60 3TL sing 91 n n 
N52 HN52 3TL sing 92 n n 
N52 C69 3TL sing 93 n n 
C60 C61 3TL sing 94 n n 
C60 C62 3TL sing 95 n n 
C60 H60 3TL sing 96 n n 
C61 O52 3TL doub 97 n n 
C62 CG6 3TL sing 98 n n 
C62 CG5 3TL sing 99 n n 
C62 H62 3TL sing 100 n n 
CG6 HG61 3TL sing 101 n n 
CG6 HG62 3TL sing 102 n n 
CG6 HG63 3TL sing 103 n n 
CG5 HG51 3TL sing 104 n n 
CG5 HG52 3TL sing 105 n n 
CG5 HG53 3TL sing 106 n n 
N54 C68 3TL sing 107 n n 
N54 HN54 3TL sing 108 n n 
N54 C81 3TL sing 109 n n 
C68 C69 3TL sing 110 n n 
C68 C70 3TL sing 111 n n 
C68 H68 3TL sing 112 n n 
C69 O54 3TL doub 113 n n 
C70 H701 3TL sing 114 n n 
C70 H702 3TL sing 115 n n 
C70 H703 3TL sing 116 n n 
C81 O58 3TL doub 117 n n 
C81 O59 3TL sing 118 n n 
O59 CA5 3TL sing 119 n n 
CA5 C50 3TL sing 120 n n 
CA5 HA51 3TL sing 121 n n 
CA5 HA52 3TL sing 122 n n 
C50 C63 3TL doub 123 n y 
C50 C67 3TL sing 124 n y 
C63 C64 3TL sing 125 n y 
C63 H63 3TL sing 126 n n 
C64 C65 3TL doub 127 n y 
C64 H64 3TL sing 128 n n 
C65 C66 3TL sing 129 n y 
C65 H65 3TL sing 130 n n 
C66 C67 3TL doub 131 n y 
C66 H66 3TL sing 132 n n 
C67 H67 3TL sing 133 n n 
#
_atom_sites.entry_id                     5VCK 
_atom_sites.fract_transf_matrix[1][1]    0.015885 
_atom_sites.fract_transf_matrix[1][2]    0.009171 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018342 
_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]    0.01215 
_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 3TL A 1 100 100 3TL TL3 . 
D 3 7GC A 1 101 101 7GC 288 . 
E 3 7GC B 1 101 102 7GC 288 . 
F 4 HOH A 1 201 1 HOH HOH . 
F 4 HOH A 2 202 38 HOH HOH . 
F 4 HOH A 3 203 30 HOH HOH . 
F 4 HOH A 4 204 6 HOH HOH . 
F 4 HOH A 5 205 67 HOH HOH . 
F 4 HOH A 6 206 48 HOH HOH . 
F 4 HOH A 7 207 5 HOH HOH . 
F 4 HOH A 8 208 53 HOH HOH . 
F 4 HOH A 9 209 16 HOH HOH . 
F 4 HOH A 10 210 64 HOH HOH . 
F 4 HOH A 11 211 33 HOH HOH . 
F 4 HOH A 12 212 44 HOH HOH . 
F 4 HOH A 13 213 26 HOH HOH . 
F 4 HOH A 14 214 4 HOH HOH . 
F 4 HOH A 15 215 13 HOH HOH . 
F 4 HOH A 16 216 75 HOH HOH . 
F 4 HOH A 17 217 32 HOH HOH . 
F 4 HOH A 18 218 24 HOH HOH . 
F 4 HOH A 19 219 15 HOH HOH . 
F 4 HOH A 20 220 19 HOH HOH . 
F 4 HOH A 21 221 51 HOH HOH . 
F 4 HOH A 22 222 34 HOH HOH . 
G 4 HOH B 1 201 43 HOH HOH . 
G 4 HOH B 2 202 2 HOH HOH . 
G 4 HOH B 3 203 47 HOH HOH . 
G 4 HOH B 4 204 9 HOH HOH . 
G 4 HOH B 5 205 29 HOH HOH . 
G 4 HOH B 6 206 35 HOH HOH . 
G 4 HOH B 7 207 76 HOH HOH . 
G 4 HOH B 8 208 23 HOH HOH . 
G 4 HOH B 9 209 12 HOH HOH . 
G 4 HOH B 10 210 14 HOH HOH . 
G 4 HOH B 11 211 45 HOH HOH . 
G 4 HOH B 12 212 83 HOH HOH . 
G 4 HOH B 13 213 39 HOH HOH . 
G 4 HOH B 14 214 11 HOH HOH . 
G 4 HOH B 15 215 77 HOH HOH . 
G 4 HOH B 16 216 71 HOH HOH . 
G 4 HOH B 17 217 3 HOH HOH . 
G 4 HOH B 18 218 66 HOH HOH . 
G 4 HOH B 19 219 20 HOH HOH . 
G 4 HOH B 20 220 84 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 C31 3TL . . . C 2 15.458 4.122 26.084 1 36.31 ? C31 3TL 100 A 1 
HETATM 2 O O8 3TL . . . C 2 14.194 3.766 25.806 1 35.64 ? O8 3TL 100 A 1 
HETATM 3 O O9 3TL . . . C 2 15.72 4.483 27.34 1 33.61 ? O9 3TL 100 A 1 
HETATM 4 C CA 3TL . . . C 2 14.798 4.885 28.388 1 36.64 ? CA 3TL 100 A 1 
HETATM 5 C C 3TL . . . C 2 14.031 6.153 28.133 1 39.19 ? C 3TL 100 A 1 
HETATM 6 C C13 3TL . . . C 2 12.698 6.184 28.56 1 42.14 ? C13 3TL 100 A 1 
HETATM 7 C C14 3TL . . . C 2 11.903 7.315 28.365 1 40.71 ? C14 3TL 100 A 1 
HETATM 8 C C15 3TL . . . C 2 12.424 8.447 27.729 1 44.84 ? C15 3TL 100 A 1 
HETATM 9 C C16 3TL . . . C 2 13.758 8.433 27.292 1 40.59 ? C16 3TL 100 A 1 
HETATM 10 C C17 3TL . . . C 2 14.529 7.292 27.501 1 40.24 ? C17 3TL 100 A 1 
HETATM 11 N N4 3TL . . . C 2 16.495 4.136 25.299 1 37.58 ? N4 3TL 100 A 1 
HETATM 12 C C18 3TL . . . C 2 16.7 4.203 23.85 1 34.63 ? C18 3TL 100 A 1 
HETATM 13 C C19 3TL . . . C 2 17.406 2.948 23.324 1 29.48 ? C19 3TL 100 A 1 
HETATM 14 O O4 3TL . . . C 2 18.705 2.701 23.506 1 26.95 ? O4 3TL 100 A 1 
HETATM 15 C C20 3TL . . . C 2 17.441 5.492 23.439 1 35.44 ? C20 3TL 100 A 1 
HETATM 16 N N2 3TL . . . C 2 16.757 2.078 22.65 1 28.71 ? N2 3TL 100 A 1 
HETATM 17 C C10 3TL . . . C 2 17.491 0.895 22.157 1 31.37 ? C10 3TL 100 A 1 
HETATM 18 C C11 3TL . . . C 2 17.317 0.81 20.649 1 32.51 ? C11 3TL 100 A 1 
HETATM 19 O O2 3TL . . . C 2 16.141 0.441 20.144 1 38.29 ? O2 3TL 100 A 1 
HETATM 20 C C12 3TL . . . C 2 17.222 -0.392 22.951 1 30.64 ? C12 3TL 100 A 1 
HETATM 21 C CG2 3TL . . . C 2 18.013 -1.552 22.354 1 27.35 ? CG2 3TL 100 A 1 
HETATM 22 C CG1 3TL . . . C 2 17.741 -0.266 24.392 1 32.16 ? CG1 3TL 100 A 1 
HETATM 23 C C2 3TL . . . C 2 19.518 0.204 17.962 1 36.15 ? C2 3TL 100 A 1 
HETATM 24 O O1 3TL . . . C 2 20.871 0.347 18.415 1 31.4 ? O1 3TL 100 A 1 
HETATM 25 C C1 3TL . . . C 2 18.583 1.265 18.553 1 37.46 ? C1 3TL 100 A 1 
HETATM 26 N N1 3TL . . . C 2 18.37 1.11 19.986 1 38.11 ? N1 3TL 100 A 1 
HETATM 27 C C3 3TL . . . C 2 18.77 2.724 18.124 1 43.64 ? C3 3TL 100 A 1 
HETATM 28 C C4 3TL . . . C 2 17.539 3.588 18.321 1 42.45 ? C4 3TL 100 A 1 
HETATM 29 C C5 3TL . . . C 2 17.205 4.11 19.574 1 44.75 ? C5 3TL 100 A 1 
HETATM 30 C C9 3TL . . . C 2 16.707 3.885 17.239 1 46.44 ? C9 3TL 100 A 1 
HETATM 31 C C6 3TL . . . C 2 16.073 4.907 19.744 1 49.33 ? C6 3TL 100 A 1 
HETATM 32 C C8 3TL . . . C 2 15.568 4.685 17.398 1 41.19 ? C8 3TL 100 A 1 
HETATM 33 C C7 3TL . . . C 2 15.247 5.196 18.653 1 45.01 ? C7 3TL 100 A 1 
HETATM 34 N N51 3TL . . . C 2 18.165 -1.898 16.128 1 36.39 ? N51 3TL 100 A 1 
HETATM 35 C C51 3TL . . . C 2 17.995 -1.908 17.584 1 36.21 ? C51 3TL 100 A 1 
HETATM 36 C C52 3TL . . . C 2 19.098 -1.22 18.357 1 36.03 ? C52 3TL 100 A 1 
HETATM 37 O O51 3TL . . . C 2 20.216 -2.097 18.312 1 33.07 ? O51 3TL 100 A 1 
HETATM 38 C C53 3TL . . . C 2 17.973 -3.3 18.201 1 37.79 ? C53 3TL 100 A 1 
HETATM 39 C C54 3TL . . . C 2 16.81 -4.147 17.863 1 37.18 ? C54 3TL 100 A 1 
HETATM 40 C C55 3TL . . . C 2 16.956 -5.122 16.884 1 36.22 ? C55 3TL 100 A 1 
HETATM 41 C C59 3TL . . . C 2 15.606 -3.954 18.548 1 40.52 ? C59 3TL 100 A 1 
HETATM 42 C C56 3TL . . . C 2 15.858 -5.913 16.568 1 39.55 ? C56 3TL 100 A 1 
HETATM 43 C C58 3TL . . . C 2 14.513 -4.756 18.245 1 39.52 ? C58 3TL 100 A 1 
HETATM 44 C C57 3TL . . . C 2 14.649 -5.7 17.234 1 42.27 ? C57 3TL 100 A 1 
HETATM 45 N N52 3TL . . . C 2 16.936 -2.146 13.126 1 35.75 ? N52 3TL 100 A 1 
HETATM 46 C C60 3TL . . . C 2 17.653 -1.111 13.843 1 33.95 ? C60 3TL 100 A 1 
HETATM 47 C C61 3TL . . . C 2 17.32 -1.26 15.306 1 31.13 ? C61 3TL 100 A 1 
HETATM 48 O O52 3TL . . . C 2 16.293 -0.809 15.778 1 31.28 ? O52 3TL 100 A 1 
HETATM 49 C C62 3TL . . . C 2 17.321 0.284 13.288 1 38.09 ? C62 3TL 100 A 1 
HETATM 50 C CG6 3TL . . . C 2 18.113 1.369 14.024 1 38.86 ? CG6 3TL 100 A 1 
HETATM 51 C CG5 3TL . . . C 2 17.58 0.431 11.781 1 43.23 ? CG5 3TL 100 A 1 
HETATM 52 N N54 3TL . . . C 2 16.748 -4.588 10.7 1 36.68 ? N54 3TL 100 A 1 
HETATM 53 C C68 3TL . . . C 2 16.506 -4.208 12.085 1 33.56 ? C68 3TL 100 A 1 
HETATM 54 C C69 3TL . . . C 2 17.441 -3.085 12.415 1 36.02 ? C69 3TL 100 A 1 
HETATM 55 O O54 3TL . . . C 2 18.697 -3.075 11.964 1 35.08 ? O54 3TL 100 A 1 
HETATM 56 C C70 3TL . . . C 2 16.709 -5.382 13.051 1 32.78 ? C70 3TL 100 A 1 
HETATM 57 C C81 3TL . . . C 2 15.79 -4.375 9.876 1 35.93 ? C81 3TL 100 A 1 
HETATM 58 O O58 3TL . . . C 2 14.66 -3.838 10.304 1 35.4 ? O58 3TL 100 A 1 
HETATM 59 O O59 3TL . . . C 2 15.895 -4.742 8.604 1 36.7 ? O59 3TL 100 A 1 
HETATM 60 C CA5 3TL . . . C 2 14.724 -4.99 7.762 1 36.13 ? CA5 3TL 100 A 1 
HETATM 61 C C50 3TL . . . C 2 13.815 -6.108 8.261 1 36.59 ? C50 3TL 100 A 1 
HETATM 62 C C63 3TL . . . C 2 12.744 -6.502 7.445 1 35.49 ? C63 3TL 100 A 1 
HETATM 63 C C64 3TL . . . C 2 11.885 -7.526 7.867 1 36.62 ? C64 3TL 100 A 1 
HETATM 64 C C65 3TL . . . C 2 12.075 -8.166 9.104 1 36.94 ? C65 3TL 100 A 1 
HETATM 65 C C66 3TL . . . C 2 13.136 -7.788 9.935 1 35.47 ? C66 3TL 100 A 1 
HETATM 66 C C67 3TL . . . C 2 13.997 -6.762 9.499 1 35.42 ? C67 3TL 100 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           216 
_model_server_stats.create_model_time_ms    47 
_model_server_stats.query_time_ms           432 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           66 
#