data_1YEE
#
_model_server_result.job_id            azXPykBDcteuyY0CwwvWbQ 
_model_server_result.datetime_utc      '2024-12-29 01:33:17' 
_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          1yee 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":551}' 
#
_entry.id    1YEE 
#
_exptl.entry_id    1YEE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              360.256 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE 
_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          94.68 
_cell.angle_gamma         90 
_cell.entry_id            1YEE 
_cell.length_a            67.93 
_cell.length_b            76.98 
_cell.length_c            45.8 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1YEE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_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                      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 23 L CYS 23 1_555 A SG CYS 93 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? 
disulf ? disulf2 A SG CYS 139 L CYS 134 1_555 A SG CYS 199 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf3 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf4 B SG CYS 150 H CYS 140 1_555 B SG CYS 205 H CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
#
_chem_comp.formula           'C13 H17 N2 O8 P' 
_chem_comp.formula_weight    360.256 
_chem_comp.id                PNB 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE 
_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
N1 O4 PNB doub 260 n n 
N1 O5 PNB sing 261 n n 
N1 C4 PNB sing 262 n n 
C1 C2 PNB doub 263 n y 
C1 C6 PNB sing 264 n y 
C1 C7 PNB sing 265 n n 
C2 C3 PNB sing 266 n y 
C2 H2 PNB sing 267 n n 
C3 C4 PNB doub 268 n y 
C3 H3 PNB sing 269 n n 
C4 C5 PNB sing 270 n y 
C5 C6 PNB doub 271 n y 
C5 H5 PNB sing 272 n n 
C6 H6 PNB sing 273 n n 
C7 O1 PNB sing 274 n n 
C7 H71 PNB sing 275 n n 
C7 H72 PNB sing 276 n n 
O1 P1 PNB sing 277 n n 
P1 O2 PNB doub 278 n n 
P1 O3 PNB sing 279 n n 
P1 C8 PNB sing 280 n n 
O3 HO3 PNB sing 281 n n 
C8 C9 PNB sing 282 n n 
C8 H81 PNB sing 283 n n 
C8 H82 PNB sing 284 n n 
C9 C10 PNB sing 285 n n 
C9 H91 PNB sing 286 n n 
C9 H92 PNB sing 287 n n 
C10 C11 PNB sing 288 n n 
C10 H101 PNB sing 289 n n 
C10 H102 PNB sing 290 n n 
C11 O6 PNB doub 291 n n 
C11 N2 PNB sing 292 n n 
N2 C12 PNB sing 293 n n 
N2 HN2 PNB sing 294 n n 
C12 C13 PNB sing 295 n n 
C12 H121 PNB sing 296 n n 
C12 H122 PNB sing 297 n n 
C13 O7 PNB doub 298 n n 
C13 O8 PNB sing 299 n n 
O8 HO8 PNB sing 300 n n 
#
_atom_sites.entry_id                     1YEE 
_atom_sites.fract_transf_matrix[1][1]    0.014721 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001205 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01299 
_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]    0.021907 
_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 3 PNB H 1 551 551 PNB PNB . 
D 4 HOH L 1 215 6 HOH HOH . 
D 4 HOH L 2 216 7 HOH HOH . 
D 4 HOH L 3 217 8 HOH HOH . 
D 4 HOH L 4 218 10 HOH HOH . 
D 4 HOH L 5 219 11 HOH HOH . 
D 4 HOH L 6 220 13 HOH HOH . 
D 4 HOH L 7 221 14 HOH HOH . 
D 4 HOH L 8 222 15 HOH HOH . 
D 4 HOH L 9 223 17 HOH HOH . 
D 4 HOH L 10 224 18 HOH HOH . 
D 4 HOH L 11 225 19 HOH HOH . 
D 4 HOH L 12 226 20 HOH HOH . 
D 4 HOH L 13 227 23 HOH HOH . 
D 4 HOH L 14 228 24 HOH HOH . 
D 4 HOH L 15 229 25 HOH HOH . 
D 4 HOH L 16 230 26 HOH HOH . 
D 4 HOH L 17 231 32 HOH HOH . 
D 4 HOH L 18 232 35 HOH HOH . 
D 4 HOH L 19 233 36 HOH HOH . 
D 4 HOH L 20 234 37 HOH HOH . 
D 4 HOH L 21 235 38 HOH HOH . 
D 4 HOH L 22 236 39 HOH HOH . 
D 4 HOH L 23 237 42 HOH HOH . 
D 4 HOH L 24 238 46 HOH HOH . 
D 4 HOH L 25 239 48 HOH HOH . 
D 4 HOH L 26 240 49 HOH HOH . 
D 4 HOH L 27 241 51 HOH HOH . 
D 4 HOH L 28 242 52 HOH HOH . 
D 4 HOH L 29 243 54 HOH HOH . 
D 4 HOH L 30 244 55 HOH HOH . 
D 4 HOH L 31 245 57 HOH HOH . 
D 4 HOH L 32 246 68 HOH HOH . 
D 4 HOH L 33 247 70 HOH HOH . 
D 4 HOH L 34 248 71 HOH HOH . 
D 4 HOH L 35 249 72 HOH HOH . 
D 4 HOH L 36 250 74 HOH HOH . 
D 4 HOH L 37 251 78 HOH HOH . 
D 4 HOH L 38 252 79 HOH HOH . 
D 4 HOH L 39 253 83 HOH HOH . 
D 4 HOH L 40 254 85 HOH HOH . 
D 4 HOH L 41 255 86 HOH HOH . 
D 4 HOH L 42 256 88 HOH HOH . 
D 4 HOH L 43 257 89 HOH HOH . 
D 4 HOH L 44 258 93 HOH HOH . 
E 4 HOH H 1 552 1 HOH HOH . 
E 4 HOH H 2 553 2 HOH HOH . 
E 4 HOH H 3 554 3 HOH HOH . 
E 4 HOH H 4 555 4 HOH HOH . 
E 4 HOH H 5 556 5 HOH HOH . 
E 4 HOH H 6 557 9 HOH HOH . 
E 4 HOH H 7 558 12 HOH HOH . 
E 4 HOH H 8 559 16 HOH HOH . 
E 4 HOH H 9 560 21 HOH HOH . 
E 4 HOH H 10 561 22 HOH HOH . 
E 4 HOH H 11 562 27 HOH HOH . 
E 4 HOH H 12 563 28 HOH HOH . 
E 4 HOH H 13 564 29 HOH HOH . 
E 4 HOH H 14 565 30 HOH HOH . 
E 4 HOH H 15 566 31 HOH HOH . 
E 4 HOH H 16 567 33 HOH HOH . 
E 4 HOH H 17 568 34 HOH HOH . 
E 4 HOH H 18 569 40 HOH HOH . 
E 4 HOH H 19 570 41 HOH HOH . 
E 4 HOH H 20 571 43 HOH HOH . 
E 4 HOH H 21 572 44 HOH HOH . 
E 4 HOH H 22 573 45 HOH HOH . 
E 4 HOH H 23 574 47 HOH HOH . 
E 4 HOH H 24 575 50 HOH HOH . 
E 4 HOH H 25 576 53 HOH HOH . 
E 4 HOH H 26 577 56 HOH HOH . 
E 4 HOH H 27 578 58 HOH HOH . 
E 4 HOH H 28 579 59 HOH HOH . 
E 4 HOH H 29 580 60 HOH HOH . 
E 4 HOH H 30 581 61 HOH HOH . 
E 4 HOH H 31 582 62 HOH HOH . 
E 4 HOH H 32 583 63 HOH HOH . 
E 4 HOH H 33 584 64 HOH HOH . 
E 4 HOH H 34 585 65 HOH HOH . 
E 4 HOH H 35 586 66 HOH HOH . 
E 4 HOH H 36 587 67 HOH HOH . 
E 4 HOH H 37 588 69 HOH HOH . 
E 4 HOH H 38 589 73 HOH HOH . 
E 4 HOH H 39 590 75 HOH HOH . 
E 4 HOH H 40 591 76 HOH HOH . 
E 4 HOH H 41 592 77 HOH HOH . 
E 4 HOH H 42 593 80 HOH HOH . 
E 4 HOH H 43 594 81 HOH HOH . 
E 4 HOH H 44 595 82 HOH HOH . 
E 4 HOH H 45 596 84 HOH HOH . 
E 4 HOH H 46 597 87 HOH HOH . 
E 4 HOH H 47 598 90 HOH HOH . 
E 4 HOH H 48 599 91 HOH HOH . 
E 4 HOH H 49 600 92 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 N N1 PNB . . . C 3 4.696 -2.252 7.542 1 15.96 ? N1 PNB 551 H 1 
HETATM 2 O O4 PNB . . . C 3 3.661 -1.609 7.763 1 15.45 ? O4 PNB 551 H 1 
HETATM 3 O O5 PNB . . . C 3 5.825 -1.694 7.429 1 16.66 ? O5 PNB 551 H 1 
HETATM 4 C C1 PNB . . . C 3 4.806 -6.367 6.784 1 16.04 ? C1 PNB 551 H 1 
HETATM 5 C C2 PNB . . . C 3 3.581 -5.778 7.208 1 15.15 ? C2 PNB 551 H 1 
HETATM 6 C C3 PNB . . . C 3 3.499 -4.426 7.503 1 13.93 ? C3 PNB 551 H 1 
HETATM 7 C C4 PNB . . . C 3 4.662 -3.678 7.363 1 15.36 ? C4 PNB 551 H 1 
HETATM 8 C C5 PNB . . . C 3 5.875 -4.261 6.953 1 15.13 ? C5 PNB 551 H 1 
HETATM 9 C C6 PNB . . . C 3 5.952 -5.612 6.661 1 15.49 ? C6 PNB 551 H 1 
HETATM 10 C C7 PNB . . . C 3 4.927 -7.788 6.431 1 16.8 ? C7 PNB 551 H 1 
HETATM 11 O O1 PNB . . . C 3 3.621 -8.31 6.113 1 18.91 ? O1 PNB 551 H 1 
HETATM 12 P P1 PNB . . . C 3 3.175 -8.584 4.609 1 20.83 ? P1 PNB 551 H 1 
HETATM 13 O O2 PNB . . . C 3 2.151 -7.67 4.338 1 22.61 ? O2 PNB 551 H 1 
HETATM 14 O O3 PNB . . . C 3 4.297 -8.545 3.786 1 22.17 ? O3 PNB 551 H 1 
HETATM 15 C C8 PNB . . . C 3 2.507 -10.174 4.572 1 20.93 ? C8 PNB 551 H 1 
HETATM 16 C C9 PNB . . . C 3 2.205 -10.895 5.878 1 22.33 ? C9 PNB 551 H 1 
HETATM 17 C C10 PNB . . . C 3 1.474 -12.151 5.428 1 24.3 ? C10 PNB 551 H 1 
HETATM 18 C C11 PNB . . . C 3 1.105 -13.242 6.397 1 26.09 ? C11 PNB 551 H 1 
HETATM 19 O O6 PNB . . . C 3 -0.046 -13.569 6.486 1 26.66 ? O6 PNB 551 H 1 
HETATM 20 N N2 PNB . . . C 3 2.046 -13.873 7.141 1 28.01 ? N2 PNB 551 H 1 
HETATM 21 C C12 PNB . . . C 3 1.703 -14.865 7.973 1 29.34 ? C12 PNB 551 H 1 
HETATM 22 C C13 PNB . . . C 3 1.448 -14.378 9.393 1 30.77 ? C13 PNB 551 H 1 
HETATM 23 O O7 PNB . . . C 3 1.878 -15.11 10.335 1 32.12 ? O7 PNB 551 H 1 
HETATM 24 O O8 PNB . . . C 3 0.76 -13.347 9.609 1 30.68 ? O8 PNB 551 H 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           24 
#