data_5JDQ
#
_model_server_result.job_id            ZdzX0ly6Qe_uTFyKP3JBXQ 
_model_server_result.datetime_utc      '2024-11-23 03:02:55' 
_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          5jdq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":411}' 
#
_entry.id    5JDQ 
#
_exptl.entry_id    5JDQ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              212.415 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            PENTADECANE 
_entity.pdbx_number_of_molecules    5 
_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            5JDQ 
_cell.length_a            49.876 
_cell.length_b            72.425 
_cell.length_c            95.913 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5JDQ 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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,H,I,J,K,L,M,N,O,P 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 6 J N N 
? 6 K N N 
? 6 L N N 
? 6 M N N 
? 6 N N 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 O ALA 47 A ALA 47 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? 
metalc ? metalc2 A OG1 THR 50 A THR 50 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? 
metalc ? metalc3 A O THR 50 A THR 50 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? 
metalc ? metalc4 A OG SER 51 A SER 51 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? 
metalc ? metalc5 A OE1 GLU 54 A GLU 54 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc6 A OE2 GLU 54 A GLU 54 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? 
metalc ? metalc7 A OE2 GLU 54 A GLU 54 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc8 A OG SER 77 A SER 77 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc9 A O ILE 118 A ILE 118 1_555 E SR SR . A SR 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc10 A OD1 ASP 121 A ASP 121 1_555 E SR SR . A SR 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? 
metalc ? metalc11 A O GLY 122 A GLY 122 1_555 E SR SR . A SR 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? 
metalc ? metalc12 A OD2 ASP 127 A ASP 127 1_555 E SR SR . A SR 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? 
metalc ? metalc13 A O ALA 206 A ALA 206 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? 
metalc ? metalc14 A O THR 209 A THR 209 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc15 A OG1 THR 209 A THR 209 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
metalc ? metalc16 A OG SER 210 A SER 210 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? 
metalc ? metalc17 A OE2 GLU 213 A GLU 213 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc18 A OE1 GLU 213 A GLU 213 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? 
metalc ? metalc19 A OE2 GLU 213 A GLU 213 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? 
metalc ? metalc20 A OG SER 236 A SER 236 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc21 E SR SR . A SR 404 1_555 P O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? 
#
_chem_comp.formula           'C15 H32' 
_chem_comp.formula_weight    212.415 
_chem_comp.id                MYS 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              PENTADECANE 
_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
C1 C2 MYS sing 274 n n 
C1 H11 MYS sing 275 n n 
C1 H12 MYS sing 276 n n 
C1 H13 MYS sing 277 n n 
C2 C3 MYS sing 278 n n 
C2 H21 MYS sing 279 n n 
C2 H22 MYS sing 280 n n 
C3 C4 MYS sing 281 n n 
C3 H31 MYS sing 282 n n 
C3 H32 MYS sing 283 n n 
C4 C5 MYS sing 284 n n 
C4 H41 MYS sing 285 n n 
C4 H42 MYS sing 286 n n 
C5 C6 MYS sing 287 n n 
C5 H51 MYS sing 288 n n 
C5 H52 MYS sing 289 n n 
C6 C7 MYS sing 290 n n 
C6 H61 MYS sing 291 n n 
C6 H62 MYS sing 292 n n 
C7 C8 MYS sing 293 n n 
C7 H71 MYS sing 294 n n 
C7 H72 MYS sing 295 n n 
C8 C9 MYS sing 296 n n 
C8 H81 MYS sing 297 n n 
C8 H82 MYS sing 298 n n 
C9 C10 MYS sing 299 n n 
C9 H91 MYS sing 300 n n 
C9 H92 MYS sing 301 n n 
C10 C11 MYS sing 302 n n 
C10 H101 MYS sing 303 n n 
C10 H102 MYS sing 304 n n 
C11 C12 MYS sing 305 n n 
C11 H111 MYS sing 306 n n 
C11 H112 MYS sing 307 n n 
C12 C13 MYS sing 308 n n 
C12 H121 MYS sing 309 n n 
C12 H122 MYS sing 310 n n 
C13 C14 MYS sing 311 n n 
C13 H131 MYS sing 312 n n 
C13 H132 MYS sing 313 n n 
C14 C15 MYS sing 314 n n 
C14 H141 MYS sing 315 n n 
C14 H142 MYS sing 316 n n 
C15 H151 MYS sing 317 n n 
C15 H152 MYS sing 318 n n 
C15 H153 MYS sing 319 n n 
#
_atom_sites.entry_id                     5JDQ 
_atom_sites.fract_transf_matrix[1][1]    0.02005 
_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]    0.013807 
_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]    0.010426 
_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 NA A 1 401 1 NA NA . 
C 2 NA A 1 402 2 NA NA . 
D 2 NA A 1 403 4 NA NA . 
E 3 SR A 1 404 1 SR SR . 
F 4 CL A 1 405 1 CL CL . 
G 4 CL A 1 406 2 CL CL . 
H 5 OLC A 1 407 1 OLC MON . 
I 5 OLC A 1 408 2 OLC MON . 
J 6 MYS A 1 409 1 MYS FAT . 
K 6 MYS A 1 410 2 MYS FAT . 
L 6 MYS A 1 411 3 MYS FAT . 
M 6 MYS A 1 412 4 MYS FAT . 
N 6 MYS A 1 413 5 MYS FAT . 
O 7 1PE A 1 414 1 1PE PEG . 
P 8 HOH A 1 501 16 HOH HOH . 
P 8 HOH A 2 502 4 HOH HOH . 
P 8 HOH A 3 503 13 HOH HOH . 
P 8 HOH A 4 504 2 HOH HOH . 
P 8 HOH A 5 505 15 HOH HOH . 
P 8 HOH A 6 506 10 HOH HOH . 
P 8 HOH A 7 507 14 HOH HOH . 
P 8 HOH A 8 508 7 HOH HOH . 
P 8 HOH A 9 509 6 HOH HOH . 
P 8 HOH A 10 510 11 HOH HOH . 
P 8 HOH A 11 511 3 HOH HOH . 
P 8 HOH A 12 512 12 HOH HOH . 
P 8 HOH A 13 513 9 HOH HOH . 
P 8 HOH A 14 514 17 HOH HOH . 
P 8 HOH A 15 515 5 HOH HOH . 
P 8 HOH A 16 516 8 HOH HOH . 
P 8 HOH A 17 517 1 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 C2 MYS . . . L 6 -13.425 26.869 22.702 1 63.13 ? C2 MYS 411 A 1 
HETATM 2 C C3 MYS . . . L 6 -12.05 27.538 22.777 1 63.9 ? C3 MYS 411 A 1 
HETATM 3 C C4 MYS . . . L 6 -12.222 29.057 22.72 1 67.35 ? C4 MYS 411 A 1 
HETATM 4 C C5 MYS . . . L 6 -13.066 29.545 23.901 1 71.53 ? C5 MYS 411 A 1 
HETATM 5 C C6 MYS . . . L 6 -12.368 29.202 25.219 1 65.73 ? C6 MYS 411 A 1 
HETATM 6 C C7 MYS . . . L 6 -13.222 29.696 26.388 1 73.3 ? C7 MYS 411 A 1 
HETATM 7 C C8 MYS . . . L 6 -12.516 29.372 27.705 1 73.86 ? C8 MYS 411 A 1 
HETATM 8 C C9 MYS . . . L 6 -13.366 29.869 28.877 1 84.24 ? C9 MYS 411 A 1 
HETATM 9 C C10 MYS . . . L 6 -12.647 29.565 30.195 1 77.04 ? C10 MYS 411 A 1 
HETATM 10 C C11 MYS . . . L 6 -13.491 30.064 31.37 1 73.92 ? C11 MYS 411 A 1 
HETATM 11 C C12 MYS . . . L 6 -12.751 29.776 32.677 1 69.79 ? C12 MYS 411 A 1 
HETATM 12 C C13 MYS . . . L 6 -12.514 28.274 32.818 1 66.77 ? C13 MYS 411 A 1 
HETATM 13 C C14 MYS . . . L 6 -11.766 27.996 34.125 1 71.29 ? C14 MYS 411 A 1 
HETATM 14 C C15 MYS . . . L 6 -12.596 28.492 35.312 1 77.78 ? C15 MYS 411 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           333 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           14 
#