data_1IVP
#
_model_server_result.job_id            g5MeYhXQyKjJhrYqFN1iaw 
_model_server_result.datetime_utc      '2024-10-11 05:26:55' 
_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          1ivp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":100}' 
#
_entry.id    1IVP 
#
_exptl.entry_id    1IVP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              813.016 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '4-[(2R)-3-{[(1S,2S,3R,4S)-1-(cyclohexylmethyl)-2,3-dihydroxy-5-methyl-4-({(1S,2R)-2-methyl-1-[(pyridin-2-ylmethyl)carba moyl]butyl}carbamoyl)hexyl]amino}-2-{[(naphthalen-1-yloxy)acetyl]amino}-3-oxopropyl]-1H-imidazol-3-ium' 
_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            1IVP 
_cell.length_a            33.19 
_cell.length_b            44.95 
_cell.length_c            135.65 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1IVP 
_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        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 
_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           'C45 H62 N7 O7 1' 
_chem_comp.formula_weight    813.016 
_chem_comp.id                1ZK 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '4-[(2R)-3-{[(1S,2S,3R,4S)-1-(cyclohexylmethyl)-2,3-dihydroxy-5-methyl-4-({(1S,2R)-2-methyl-1-[(pyridin-2-ylmethyl)carba moyl]butyl}carbamoyl)hexyl]amino}-2-{[(naphthalen-1-yloxy)acetyl]amino}-3-oxopropyl]-1H-imidazol-3-ium' 
_chem_comp.type              peptide-like 
_chem_comp.pdbx_synonyms     U75875 
#
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
C CA 1ZK sing 1 n n 
C O 1ZK doub 2 n n 
CA O1 1ZK sing 3 n n 
CA HA1 1ZK sing 4 n n 
CA HA2 1ZK sing 5 n n 
C1 C2 1ZK doub 6 n y 
C1 C1A 1ZK sing 7 n y 
C1 O1 1ZK sing 8 n n 
C2 C3 1ZK sing 9 n y 
C2 H2 1ZK sing 10 n n 
C3 C4 1ZK doub 11 n y 
C3 H3 1ZK sing 12 n n 
C4 C4A 1ZK sing 13 n y 
C4 H4 1ZK sing 14 n n 
C4A C5 1ZK doub 15 n y 
C4A C1A 1ZK sing 16 n y 
C5 C6 1ZK sing 17 n y 
C5 H5 1ZK sing 18 n n 
C6 C7 1ZK doub 19 n y 
C6 H6 1ZK sing 20 n n 
C7 C8 1ZK sing 21 n y 
C7 H7 1ZK sing 22 n n 
C8 C1A 1ZK doub 23 n y 
C8 H8 1ZK sing 24 n n 
N CA1 1ZK sing 25 n n 
N H 1ZK sing 26 n n 
CA1 C9 1ZK sing 27 n n 
CA1 CB 1ZK sing 28 n n 
CA1 HA 1ZK sing 29 n n 
C9 O2 1ZK doub 30 n n 
CB CG 1ZK sing 31 n n 
CB HB2 1ZK sing 32 n n 
CB HB3 1ZK sing 33 n n 
CG ND1 1ZK sing 34 n y 
CG CD2 1ZK doub 35 n y 
ND1 CE1 1ZK doub 36 n y 
ND1 HD1 1ZK sing 37 n n 
CD2 NE2 1ZK sing 38 n y 
CD2 HD2 1ZK sing 39 n n 
CE1 NE2 1ZK sing 40 n y 
CE1 HE1 1ZK sing 41 n n 
NE2 HE2 1ZK sing 42 n n 
N1 CA2 1ZK sing 43 n n 
N1 H1 1ZK sing 44 n n 
CA2 CB1 1ZK sing 45 n n 
CA2 CH 1ZK sing 46 n n 
CA2 HA3 1ZK sing 47 n n 
CB1 CG1 1ZK sing 48 n n 
CB1 HB21 1ZK sing 49 n n 
CB1 HB31 1ZK sing 50 n n 
CG1 CD1 1ZK sing 51 n n 
CG1 CD21 1ZK sing 52 n n 
CG1 HG 1ZK sing 53 n n 
CD1 CE11 1ZK sing 54 n n 
CD1 HD12 1ZK sing 55 n n 
CD1 HD13 1ZK sing 56 n n 
CD21 CE2 1ZK sing 57 n n 
CD21 HD23 1ZK sing 58 n n 
CD21 HD22 1ZK sing 59 n n 
CE11 CZ 1ZK sing 60 n n 
CE11 HE12 1ZK sing 61 n n 
CE11 HE13 1ZK sing 62 n n 
CE2 CZ 1ZK sing 63 n n 
CE2 HE23 1ZK sing 64 n n 
CE2 HE22 1ZK sing 65 n n 
CZ HZ2 1ZK sing 66 n n 
CZ HZ3 1ZK sing 67 n n 
CH OH 1ZK sing 68 n n 
CH CB11 1ZK sing 69 n n 
CH HH 1ZK sing 70 n n 
OH HO 1ZK sing 71 n n 
CB11 CA' 1ZK sing 72 n n 
CB11 OB1 1ZK sing 73 n n 
CB11 HB1 1ZK sing 74 n n 
CA' CB' 1ZK sing 75 n n 
CA' CC 1ZK sing 76 n n 
CA' HA' 1ZK sing 77 n n 
CB' CG11 1ZK sing 78 n n 
CB' CG2 1ZK sing 79 n n 
CB' HB' 1ZK sing 80 n n 
CG11 HG11 1ZK sing 81 n n 
CG11 HG12 1ZK sing 82 n n 
CG11 HG13 1ZK sing 83 n n 
CG2 HG21 1ZK sing 84 n n 
CG2 HG22 1ZK sing 85 n n 
CG2 HG23 1ZK sing 86 n n 
OB1 HOB1 1ZK sing 87 n n 
CC O3 1ZK doub 88 n n 
N2 CA3 1ZK sing 89 n n 
N2 H9 1ZK sing 90 n n 
CA3 CD 1ZK sing 91 n n 
CA3 CB2 1ZK sing 92 n n 
CA3 HA4 1ZK sing 93 n n 
CD O4 1ZK doub 94 n n 
CB2 CG12 1ZK sing 95 n n 
CB2 CG21 1ZK sing 96 n n 
CB2 HB 1ZK sing 97 n n 
CG12 CD11 1ZK sing 98 n n 
CG12 HG14 1ZK sing 99 n n 
CG12 HG15 1ZK sing 100 n n 
CG21 HG24 1ZK sing 101 n n 
CG21 HG25 1ZK sing 102 n n 
CG21 HG26 1ZK sing 103 n n 
CD11 HD11 1ZK sing 104 n n 
CD11 HD14 1ZK sing 105 n n 
CD11 HD15 1ZK sing 106 n n 
N3 CM 1ZK sing 107 n n 
N3 HN1 1ZK sing 108 n n 
CM C21 1ZK sing 109 n n 
CM HM1 1ZK sing 110 n n 
CM HM2 1ZK sing 111 n n 
C21 C31 1ZK sing 112 n y 
C21 N11 1ZK doub 113 n y 
C31 C41 1ZK doub 114 n y 
C31 H31 1ZK sing 115 n n 
C41 C51 1ZK sing 116 n y 
C41 H41 1ZK sing 117 n n 
C51 C61 1ZK doub 118 n y 
C51 H51 1ZK sing 119 n n 
C61 N11 1ZK sing 120 n y 
C61 H61 1ZK sing 121 n n 
C N 1ZK sing 122 n n 
C9 N1 1ZK sing 123 n n 
CC N2 1ZK sing 124 n n 
CD N3 1ZK sing 125 n n 
#
_atom_sites.entry_id                     1IVP 
_atom_sites.fract_transf_matrix[1][1]    0.03013 
_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]    0.022247 
_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]    0.007372 
_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 1ZK B 1 100 1 1ZK NOA . 
D 3 HOH A 1 400 400 HOH HOH . 
D 3 HOH A 2 401 401 HOH HOH . 
D 3 HOH A 3 402 402 HOH HOH . 
D 3 HOH A 4 403 403 HOH HOH . 
D 3 HOH A 5 404 404 HOH HOH . 
D 3 HOH A 6 405 405 HOH HOH . 
D 3 HOH A 7 406 406 HOH HOH . 
D 3 HOH A 8 407 407 HOH HOH . 
D 3 HOH A 9 408 408 HOH HOH . 
D 3 HOH A 10 417 417 HOH HOH . 
D 3 HOH A 11 418 418 HOH HOH . 
D 3 HOH A 12 419 419 HOH HOH . 
D 3 HOH A 13 420 420 HOH HOH . 
D 3 HOH A 14 422 422 HOH HOH . 
D 3 HOH A 15 423 423 HOH HOH . 
D 3 HOH A 16 424 424 HOH HOH . 
D 3 HOH A 17 425 425 HOH HOH . 
D 3 HOH A 18 426 426 HOH HOH . 
D 3 HOH A 19 427 427 HOH HOH . 
D 3 HOH A 20 428 428 HOH HOH . 
D 3 HOH A 21 429 429 HOH HOH . 
D 3 HOH A 22 436 436 HOH HOH . 
D 3 HOH A 23 437 437 HOH HOH . 
D 3 HOH A 24 438 438 HOH HOH . 
E 3 HOH B 1 409 409 HOH HOH . 
E 3 HOH B 2 410 410 HOH HOH . 
E 3 HOH B 3 411 411 HOH HOH . 
E 3 HOH B 4 412 412 HOH HOH . 
E 3 HOH B 5 413 413 HOH HOH . 
E 3 HOH B 6 414 414 HOH HOH . 
E 3 HOH B 7 415 415 HOH HOH . 
E 3 HOH B 8 421 421 HOH HOH . 
E 3 HOH B 9 430 430 HOH HOH . 
E 3 HOH B 10 431 431 HOH HOH . 
E 3 HOH B 11 432 432 HOH HOH . 
E 3 HOH B 12 433 433 HOH HOH . 
E 3 HOH B 13 434 434 HOH HOH . 
E 3 HOH B 14 435 435 HOH HOH . 
E 3 HOH B 15 439 439 HOH HOH . 
E 3 HOH B 16 440 440 HOH HOH . 
E 3 HOH B 17 441 441 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 C 1ZK . . . C 2 4.312 13.086 17.86 0.5 18.24 ? C 1ZK 100 B 1 
HETATM 2 C CA 1ZK . . . C 2 4.533 11.657 18.372 0.5 18.78 ? CA 1ZK 100 B 1 
HETATM 3 C C1 1ZK . . . C 2 5.099 10.61 20.55 0.5 20.36 ? C1 1ZK 100 B 1 
HETATM 4 C C2 1ZK . . . C 2 6.413 10.411 21.013 0.5 20.84 ? C2 1ZK 100 B 1 
HETATM 5 C C3 1ZK . . . C 2 6.706 9.32 21.85 0.5 21.17 ? C3 1ZK 100 B 1 
HETATM 6 C C4 1ZK . . . C 2 5.694 8.437 22.228 0.5 20.95 ? C4 1ZK 100 B 1 
HETATM 7 C C4A 1ZK . . . C 2 4.385 8.645 21.778 0.5 21.01 ? C4A 1ZK 100 B 1 
HETATM 8 C C5 1ZK . . . C 2 3.379 7.74 22.165 0.5 21.13 ? C5 1ZK 100 B 1 
HETATM 9 C C6 1ZK . . . C 2 2.067 7.934 21.703 0.5 21.2 ? C6 1ZK 100 B 1 
HETATM 10 C C7 1ZK . . . C 2 1.771 9.028 20.869 0.5 21.1 ? C7 1ZK 100 B 1 
HETATM 11 C C8 1ZK . . . C 2 2.786 9.926 20.504 0.5 20.98 ? C8 1ZK 100 B 1 
HETATM 12 C C1A 1ZK . . . C 2 4.098 9.733 20.948 0.5 20.67 ? C1A 1ZK 100 B 1 
HETATM 13 O O 1ZK . . . C 2 5.155 13.679 17.16 0.5 17.86 ? O 1ZK 100 B 1 
HETATM 14 O O1 1ZK . . . C 2 4.871 11.678 19.753 0.5 19.9 ? O1 1ZK 100 B 1 
HETATM 15 N N 1ZK . . . C 2 3.157 13.62 18.206 0.5 17.21 ? N 1ZK 100 B 1 
HETATM 16 C CA1 1ZK . . . C 2 2.701 14.968 17.813 0.5 15.97 ? CA1 1ZK 100 B 1 
HETATM 17 C C9 1ZK . . . C 2 2.075 15.585 19.056 0.5 15.41 ? C9 1ZK 100 B 1 
HETATM 18 O O2 1ZK . . . C 2 0.902 15.291 19.364 0.5 14.98 ? O2 1ZK 100 B 1 
HETATM 19 C CB 1ZK . . . C 2 1.625 14.82 16.689 0.5 16.4 ? CB 1ZK 100 B 1 
HETATM 20 C CG 1ZK . . . C 2 2.192 13.971 15.585 0.5 16.52 ? CG 1ZK 100 B 1 
HETATM 21 N ND1 1ZK . . . C 2 2.32 12.615 15.639 0.5 16.82 ? ND1 1ZK 100 B 1 
HETATM 22 C CD2 1ZK . . . C 2 2.726 14.323 14.392 0.5 16.82 ? CD2 1ZK 100 B 1 
HETATM 23 C CE1 1ZK . . . C 2 2.906 12.162 14.543 0.5 16.83 ? CE1 1ZK 100 B 1 
HETATM 24 N NE2 1ZK . . . C 2 3.161 13.194 13.771 0.5 16.62 ? NE2 1ZK 100 B 1 
HETATM 25 N N1 1ZK . . . C 2 2.88 16.383 19.75 0.5 14.15 ? N1 1ZK 100 B 1 
HETATM 26 C CA2 1ZK . . . C 2 2.409 17.022 20.996 0.5 13.48 ? CA2 1ZK 100 B 1 
HETATM 27 C CB1 1ZK . . . C 2 2.964 16.55 22.196 0.5 13.46 ? CB1 1ZK 100 B 1 
HETATM 28 C CG1 1ZK . . . C 2 3.383 15.08 22.229 0.5 13.27 ? CG1 1ZK 100 B 1 
HETATM 29 C CD1 1ZK . . . C 2 2.794 14.39 23.479 0.5 13.1 ? CD1 1ZK 100 B 1 
HETATM 30 C CD21 1ZK . . . C 2 4.93 15.046 22.292 0.5 12.81 ? CD21 1ZK 100 B 1 
HETATM 31 C CE11 1ZK . . . C 2 3.254 12.911 23.455 0.5 12.81 ? CE11 1ZK 100 B 1 
HETATM 32 C CE2 1ZK . . . C 2 5.494 13.656 22.512 0.5 12.8 ? CE2 1ZK 100 B 1 
HETATM 33 C CZ 1ZK . . . C 2 4.79 12.901 23.631 0.5 13.36 ? CZ 1ZK 100 B 1 
HETATM 34 C CH 1ZK . . . C 2 2.381 18.544 20.85 0.5 13.45 ? CH 1ZK 100 B 1 
HETATM 35 O OH 1ZK . . . C 2 3.32 19.337 20.887 0.5 12.6 ? OH 1ZK 100 B 1 
HETATM 36 C CB11 1ZK . . . C 2 1.193 18.891 19.949 0.5 13.49 ? CB11 1ZK 100 B 1 
HETATM 37 C CA' 1ZK . . . C 2 0.492 20.118 20.532 0.5 13.67 ? CA' 1ZK 100 B 1 
HETATM 38 C CB' 1ZK . . . C 2 -0.593 20.446 19.564 0.5 13.55 ? CB' 1ZK 100 B 1 
HETATM 39 C CG11 1ZK . . . C 2 -1.527 19.31 19.094 0.5 13.82 ? CG11 1ZK 100 B 1 
HETATM 40 C CG2 1ZK . . . C 2 -1.44 21.637 19.986 0.5 13.58 ? CG2 1ZK 100 B 1 
HETATM 41 O OB1 1ZK . . . C 2 1.72 19.141 18.631 0.5 13.1 ? OB1 1ZK 100 B 1 
HETATM 42 C CC 1ZK . . . C 2 -0.123 19.8 21.913 0.5 14.17 ? CC 1ZK 100 B 1 
HETATM 43 O O3 1ZK . . . C 2 -0.307 18.668 22.401 0.5 14.52 ? O3 1ZK 100 B 1 
HETATM 44 N N2 1ZK . . . C 2 -0.446 20.905 22.547 0.5 13.87 ? N2 1ZK 100 B 1 
HETATM 45 C CA3 1ZK . . . C 2 -1.1 21.133 23.816 0.5 14.04 ? CA3 1ZK 100 B 1 
HETATM 46 C CD 1ZK . . . C 2 -1.679 22.555 23.702 0.5 14.49 ? CD 1ZK 100 B 1 
HETATM 47 O O4 1ZK . . . C 2 -1.129 23.587 24.101 0.5 14.2 ? O4 1ZK 100 B 1 
HETATM 48 C CB2 1ZK . . . C 2 -0.412 20.701 25.124 0.5 14.08 ? CB2 1ZK 100 B 1 
HETATM 49 C CG12 1ZK . . . C 2 -0.888 21.613 26.285 0.5 13.97 ? CG12 1ZK 100 B 1 
HETATM 50 C CG21 1ZK . . . C 2 1.11 20.503 25.122 0.5 13.77 ? CG21 1ZK 100 B 1 
HETATM 51 C CD11 1ZK . . . C 2 -2.43 21.741 26.382 0.5 14.44 ? CD11 1ZK 100 B 1 
HETATM 52 N N3 1ZK . . . C 2 -2.843 22.555 23.074 0.5 14.84 ? N3 1ZK 100 B 1 
HETATM 53 C CM 1ZK . . . C 2 -3.678 23.707 22.756 0.5 15.42 ? CM 1ZK 100 B 1 
HETATM 54 C C21 1ZK . . . C 2 -5.057 23.273 22.381 0.5 16.51 ? C21 1ZK 100 B 1 
HETATM 55 C C31 1ZK . . . C 2 -5.47 21.937 22.492 0.5 16.91 ? C31 1ZK 100 B 1 
HETATM 56 C C41 1ZK . . . C 2 -6.784 21.587 22.164 0.5 17.02 ? C41 1ZK 100 B 1 
HETATM 57 C C51 1ZK . . . C 2 -7.663 22.585 21.712 0.5 17.27 ? C51 1ZK 100 B 1 
HETATM 58 C C61 1ZK . . . C 2 -7.201 23.907 21.625 0.5 17 ? C61 1ZK 100 B 1 
HETATM 59 N N11 1ZK . . . C 2 -5.933 24.196 21.95 0.5 16.98 ? N11 1ZK 100 B 1 
#
_model_server_stats.io_time_ms              5 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           59 
#