data_1DWD
#
_model_server_result.job_id            qGr2WbrU7xiGW5ADBiFFPA 
_model_server_result.datetime_utc      '2024-10-12 16:37:46' 
_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          1dwd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1}' 
#
_entry.id    1DWD 
#
_exptl.entry_id    1DWD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              521.631 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine 
_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            1DWD 
_cell.length_a            90.8 
_cell.length_b            90.8 
_cell.length_c            132.5 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1DWD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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                      4 
_struct_asym.id                             D 
_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 9 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? 
#
_chem_comp.formula           'C27 H31 N5 O4 S' 
_chem_comp.formula_weight    521.631 
_chem_comp.id                MID 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine 
_chem_comp.type              peptide-like 
_chem_comp.pdbx_synonyms     NAPAP 
#
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
S O1S MID doub 237 n n 
S O2S MID doub 238 n n 
S C2 MID sing 239 n n 
C1 C2 MID doub 240 n y 
C1 C9 MID sing 241 n y 
C1 H1 MID sing 242 n n 
C2 C3 MID sing 243 n y 
C3 C4 MID doub 244 n y 
C3 H3 MID sing 245 n n 
C4 C10 MID sing 246 n y 
C4 H4 MID sing 247 n n 
C5 C6 MID doub 248 n y 
C5 C10 MID sing 249 n y 
C5 H5 MID sing 250 n n 
C6 C7 MID sing 251 n y 
C6 H6 MID sing 252 n n 
C7 C8 MID doub 253 n y 
C7 H7 MID sing 254 n n 
C8 C9 MID sing 255 n y 
C8 H8 MID sing 256 n n 
C9 C10 MID doub 257 n y 
N CA MID sing 258 n n 
N H MID sing 259 n n 
CA C MID sing 260 n n 
CA HA2 MID sing 261 n n 
CA HA3 MID sing 262 n n 
C O MID doub 263 n n 
N1 CA1 MID sing 264 n n 
N1 H2 MID sing 265 n n 
CA1 CB MID sing 266 n n 
CA1 CB1 MID sing 267 n n 
CA1 HA MID sing 268 n n 
CB O1 MID doub 269 n n 
CB1 CG MID sing 270 n n 
CB1 HB2 MID sing 271 n n 
CB1 HB3 MID sing 272 n n 
CG CD1 MID doub 273 n y 
CG CD2 MID sing 274 n y 
CD1 CE1 MID sing 275 n y 
CD1 HD1 MID sing 276 n n 
CD2 CE2 MID doub 277 n y 
CD2 HD2 MID sing 278 n n 
CE1 CZ MID doub 279 n y 
CE1 HE1 MID sing 280 n n 
CE2 CZ MID sing 281 n y 
CE2 HE2 MID sing 282 n n 
CZ CF MID sing 283 n n 
CF NG1 MID doub 284 n n 
CF NG2 MID sing 285 n n 
NG1 HG1 MID sing 286 n n 
NG2 HG21 MID sing 287 n n 
NG2 HG22 MID sing 288 n n 
N11 C21 MID sing 289 n n 
N11 C61 MID sing 290 n n 
C21 C31 MID sing 291 n n 
C21 H21 MID sing 292 n n 
C21 H22 MID sing 293 n n 
C31 C41 MID sing 294 n n 
C31 H31 MID sing 295 n n 
C31 H32 MID sing 296 n n 
C41 C51 MID sing 297 n n 
C41 H41 MID sing 298 n n 
C41 H42 MID sing 299 n n 
C51 C61 MID sing 300 n n 
C51 H51 MID sing 301 n n 
C51 H52 MID sing 302 n n 
C61 H61 MID sing 303 n n 
C61 H62 MID sing 304 n n 
S N MID sing 305 n n 
C N1 MID sing 306 n n 
CB N11 MID sing 307 n n 
#
_atom_sites.entry_id                     1DWD 
_atom_sites.fract_transf_matrix[1][1]    0.011013 
_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]    0.011013 
_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]    0.007547 
_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
D 4 MID H 1 1 1 MID MID . 
E 5 HOH L 1 30 31 HOH HOH . 
E 5 HOH L 2 45 49 HOH HOH . 
E 5 HOH L 3 48 53 HOH HOH . 
E 5 HOH L 4 63 63 HOH HOH . 
F 5 HOH H 1 248 18 HOH HOH . 
F 5 HOH H 2 249 20 HOH HOH . 
F 5 HOH H 3 250 21 HOH HOH . 
F 5 HOH H 4 251 23 HOH HOH . 
F 5 HOH H 5 252 24 HOH HOH . 
F 5 HOH H 6 253 25 HOH HOH . 
F 5 HOH H 7 254 26 HOH HOH . 
F 5 HOH H 8 255 27 HOH HOH . 
F 5 HOH H 9 256 28 HOH HOH . 
F 5 HOH H 10 257 30 HOH HOH . 
F 5 HOH H 11 258 32 HOH HOH . 
F 5 HOH H 12 259 33 HOH HOH . 
F 5 HOH H 13 260 34 HOH HOH . 
F 5 HOH H 14 261 35 HOH HOH . 
F 5 HOH H 15 262 36 HOH HOH . 
F 5 HOH H 16 263 37 HOH HOH . 
F 5 HOH H 17 264 39 HOH HOH . 
F 5 HOH H 18 265 41 HOH HOH . 
F 5 HOH H 19 266 42 HOH HOH . 
F 5 HOH H 20 267 43 HOH HOH . 
F 5 HOH H 21 268 44 HOH HOH . 
F 5 HOH H 22 269 46 HOH HOH . 
F 5 HOH H 23 270 47 HOH HOH . 
F 5 HOH H 24 271 48 HOH HOH . 
F 5 HOH H 25 272 50 HOH HOH . 
F 5 HOH H 26 273 52 HOH HOH . 
F 5 HOH H 27 274 54 HOH HOH . 
F 5 HOH H 28 275 55 HOH HOH . 
F 5 HOH H 29 276 56 HOH HOH . 
F 5 HOH H 30 277 57 HOH HOH . 
F 5 HOH H 31 278 60 HOH HOH . 
F 5 HOH H 32 279 48 HOH HOH . 
F 5 HOH H 33 280 49 HOH HOH . 
F 5 HOH H 34 281 50 HOH HOH . 
F 5 HOH H 35 282 51 HOH HOH . 
F 5 HOH H 36 283 53 HOH HOH . 
F 5 HOH H 37 284 54 HOH HOH . 
F 5 HOH H 38 285 55 HOH HOH . 
F 5 HOH H 39 286 61 HOH HOH . 
F 5 HOH H 40 287 62 HOH HOH . 
F 5 HOH H 41 288 64 HOH HOH . 
F 5 HOH H 42 289 65 HOH HOH . 
G 5 HOH I 1 16 16 HOH HOH . 
G 5 HOH I 2 17 17 HOH HOH . 
G 5 HOH I 3 19 19 HOH HOH . 
G 5 HOH I 4 22 22 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 S S MID . . . D 4 29.341 12.438 27.058 1 24.09 ? S MID 1 H 1 
HETATM 2 O O1S MID . . . D 4 28.363 11.839 26.182 1 25.99 ? O1S MID 1 H 1 
HETATM 3 O O2S MID . . . D 4 29.062 12.809 28.435 1 29.33 ? O2S MID 1 H 1 
HETATM 4 C C1 MID . . . D 4 31.727 11.439 27.937 1 15.97 ? C1 MID 1 H 1 
HETATM 5 C C2 MID . . . D 4 30.64 11.263 27.135 1 19.26 ? C2 MID 1 H 1 
HETATM 6 C C3 MID . . . D 4 30.507 10.148 26.315 1 19.5 ? C3 MID 1 H 1 
HETATM 7 C C4 MID . . . D 4 31.464 9.171 26.3 1 19.62 ? C4 MID 1 H 1 
HETATM 8 C C5 MID . . . D 4 33.568 8.267 27.118 1 19.55 ? C5 MID 1 H 1 
HETATM 9 C C6 MID . . . D 4 34.69 8.415 27.878 1 20.84 ? C6 MID 1 H 1 
HETATM 10 C C7 MID . . . D 4 34.852 9.585 28.681 1 22.06 ? C7 MID 1 H 1 
HETATM 11 C C8 MID . . . D 4 33.893 10.593 28.702 1 19.05 ? C8 MID 1 H 1 
HETATM 12 C C9 MID . . . D 4 32.741 10.453 27.92 1 17.09 ? C9 MID 1 H 1 
HETATM 13 C C10 MID . . . D 4 32.582 9.285 27.133 1 18.24 ? C10 MID 1 H 1 
HETATM 14 N N MID . . . D 4 29.985 13.739 26.306 1 23.25 ? N MID 1 H 1 
HETATM 15 C CA MID . . . D 4 30.046 13.74 24.883 1 20.01 ? CA MID 1 H 1 
HETATM 16 C C MID . . . D 4 31.408 14.033 24.473 1 19.97 ? C MID 1 H 1 
HETATM 17 O O MID . . . D 4 32.378 14.117 25.235 1 22.6 ? O MID 1 H 1 
HETATM 18 N N1 MID . . . D 4 31.506 14.248 23.138 1 17.28 ? N1 MID 1 H 1 
HETATM 19 C CA1 MID . . . D 4 32.793 14.539 22.486 1 12.67 ? CA1 MID 1 H 1 
HETATM 20 C CB MID . . . D 4 32.978 13.472 21.462 1 16.44 ? CB MID 1 H 1 
HETATM 21 O O1 MID . . . D 4 32.744 13.595 20.255 1 20.52 ? O1 MID 1 H 1 
HETATM 22 C CB1 MID . . . D 4 32.722 15.891 21.79 1 6.47 ? CB1 MID 1 H 1 
HETATM 23 C CG MID . . . D 4 32.676 16.947 22.807 1 6 ? CG MID 1 H 1 
HETATM 24 C CD1 MID . . . D 4 33.838 17.468 23.309 1 7.87 ? CD1 MID 1 H 1 
HETATM 25 C CD2 MID . . . D 4 31.463 17.355 23.295 1 7.63 ? CD2 MID 1 H 1 
HETATM 26 C CE1 MID . . . D 4 33.78 18.485 24.28 1 9.1 ? CE1 MID 1 H 1 
HETATM 27 C CE2 MID . . . D 4 31.382 18.362 24.26 1 9.72 ? CE2 MID 1 H 1 
HETATM 28 C CZ MID . . . D 4 32.545 18.928 24.748 1 8.97 ? CZ MID 1 H 1 
HETATM 29 C CF MID . . . D 4 32.475 19.965 25.786 1 8.79 ? CF MID 1 H 1 
HETATM 30 N NG1 MID . . . D 4 31.296 20.429 26.237 1 6.31 ? NG1 MID 1 H 1 
HETATM 31 N NG2 MID . . . D 4 33.531 20.749 26.044 1 11.59 ? NG2 MID 1 H 1 
HETATM 32 N N11 MID . . . D 4 33.473 12.286 22.011 1 14.67 ? N11 MID 1 H 1 
HETATM 33 C C21 MID . . . D 4 33.756 12.198 23.456 1 15.23 ? C21 MID 1 H 1 
HETATM 34 C C31 MID . . . D 4 33.051 10.991 24.086 1 14.07 ? C31 MID 1 H 1 
HETATM 35 C C41 MID . . . D 4 33.331 9.715 23.265 1 13.89 ? C41 MID 1 H 1 
HETATM 36 C C51 MID . . . D 4 32.94 9.92 21.771 1 12.4 ? C51 MID 1 H 1 
HETATM 37 C C61 MID . . . D 4 33.69 11.116 21.167 1 12.35 ? C61 MID 1 H 1 
#
_model_server_stats.io_time_ms              71 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           37 
#