data_5YB1
#
_model_server_result.job_id            bhG6twY4ewFs1CJaym2T-w 
_model_server_result.datetime_utc      '2024-10-19 16:49:25' 
_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          5yb1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":604}' 
#
_entry.id    5YB1 
#
_exptl.entry_id    5YB1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              256.424 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PALMITIC ACID' 
_entity.pdbx_number_of_molecules    14 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         104.67 
_cell.angle_beta          101.43 
_cell.angle_gamma         89.97 
_cell.entry_id            5YB1 
_cell.length_a            38.492 
_cell.length_b            95.653 
_cell.length_c            96.642 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YB1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,I,J,S 1 1 
B,K,L,M,N,O,P,Q,R,T 2 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
? 2 C N N 
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
? 2 Q 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
disulf ? disulf1 A SG CYS 51 A CYS 53 1_555 A SG CYS 60 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf2 A SG CYS 73 A CYS 75 1_555 A SG CYS 89 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
disulf ? disulf3 A SG CYS 88 A CYS 90 1_555 A SG CYS 99 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
disulf ? disulf4 A SG CYS 122 A CYS 124 1_555 A SG CYS 167 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf5 A SG CYS 166 A CYS 168 1_555 A SG CYS 175 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf6 A SG CYS 198 A CYS 200 1_555 A SG CYS 244 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf7 A SG CYS 243 A CYS 245 1_555 A SG CYS 251 A CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf8 A SG CYS 263 A CYS 265 1_555 A SG CYS 277 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf9 A SG CYS 276 A CYS 278 1_555 A SG CYS 287 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf10 A SG CYS 314 A CYS 316 1_555 A SG CYS 359 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf11 A SG CYS 358 A CYS 360 1_555 A SG CYS 367 A CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf12 A SG CYS 390 A CYS 392 1_555 A SG CYS 436 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf13 A SG CYS 435 A CYS 437 1_555 A SG CYS 446 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf14 A SG CYS 459 A CYS 461 1_555 A SG CYS 475 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf15 A SG CYS 474 A CYS 476 1_555 A SG CYS 485 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf16 A SG CYS 512 A CYS 514 1_555 A SG CYS 557 A CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf17 A SG CYS 556 A CYS 558 1_555 A SG CYS 565 A CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf18 B SG CYS 51 B CYS 53 1_555 B SG CYS 60 B CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf19 B SG CYS 73 B CYS 75 1_555 B SG CYS 89 B CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf20 B SG CYS 88 B CYS 90 1_555 B SG CYS 99 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
disulf ? disulf21 B SG CYS 122 B CYS 124 1_555 B SG CYS 167 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf22 B SG CYS 166 B CYS 168 1_555 B SG CYS 175 B CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf23 B SG CYS 198 B CYS 200 1_555 B SG CYS 244 B CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf24 B SG CYS 243 B CYS 245 1_555 B SG CYS 251 B CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf25 B SG CYS 263 B CYS 265 1_555 B SG CYS 277 B CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf26 B SG CYS 276 B CYS 278 1_555 B SG CYS 287 B CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf27 B SG CYS 314 B CYS 316 1_555 B SG CYS 359 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf28 B SG CYS 358 B CYS 360 1_555 B SG CYS 367 B CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf29 B SG CYS 390 B CYS 392 1_555 B SG CYS 436 B CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf30 B SG CYS 435 B CYS 437 1_555 B SG CYS 446 B CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf31 B SG CYS 459 B CYS 461 1_555 B SG CYS 475 B CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf32 B SG CYS 474 B CYS 476 1_555 B SG CYS 485 B CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf33 B SG CYS 512 B CYS 514 1_555 B SG CYS 557 B CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf34 B SG CYS 556 B CYS 558 1_555 B SG CYS 565 B CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
metalc ? metalc1 A NE2 HIS 144 A HIS 146 1_555 J CU1 8ZR . A 8ZR 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? 
metalc ? metalc2 B NE2 HIS 144 B HIS 146 1_555 R CU1 8ZR . B 8ZR 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? 
#
_chem_comp.formula           'C16 H32 O2' 
_chem_comp.formula_weight    256.424 
_chem_comp.id                PLM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PALMITIC ACID' 
_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 O1 PLM sing 292 n n 
C1 O2 PLM doub 293 n n 
C1 C2 PLM sing 294 n n 
O1 H PLM sing 295 n n 
C2 C3 PLM sing 296 n n 
C2 H21 PLM sing 297 n n 
C2 H22 PLM sing 298 n n 
C3 C4 PLM sing 299 n n 
C3 H31 PLM sing 300 n n 
C3 H32 PLM sing 301 n n 
C4 C5 PLM sing 302 n n 
C4 H41 PLM sing 303 n n 
C4 H42 PLM sing 304 n n 
C5 C6 PLM sing 305 n n 
C5 H51 PLM sing 306 n n 
C5 H52 PLM sing 307 n n 
C6 C7 PLM sing 308 n n 
C6 H61 PLM sing 309 n n 
C6 H62 PLM sing 310 n n 
C7 C8 PLM sing 311 n n 
C7 H71 PLM sing 312 n n 
C7 H72 PLM sing 313 n n 
C8 C9 PLM sing 314 n n 
C8 H81 PLM sing 315 n n 
C8 H82 PLM sing 316 n n 
C9 CA PLM sing 317 n n 
C9 H91 PLM sing 318 n n 
C9 H92 PLM sing 319 n n 
CA CB PLM sing 320 n n 
CA HA1 PLM sing 321 n n 
CA HA2 PLM sing 322 n n 
CB CC PLM sing 323 n n 
CB HB1 PLM sing 324 n n 
CB HB2 PLM sing 325 n n 
CC CD PLM sing 326 n n 
CC HC1 PLM sing 327 n n 
CC HC2 PLM sing 328 n n 
CD CE PLM sing 329 n n 
CD HD1 PLM sing 330 n n 
CD HD2 PLM sing 331 n n 
CE CF PLM sing 332 n n 
CE HE1 PLM sing 333 n n 
CE HE2 PLM sing 334 n n 
CF CG PLM sing 335 n n 
CF HF1 PLM sing 336 n n 
CF HF2 PLM sing 337 n n 
CG HG1 PLM sing 338 n n 
CG HG2 PLM sing 339 n n 
CG HG3 PLM sing 340 n n 
#
_atom_sites.entry_id                     5YB1 
_atom_sites.fract_transf_matrix[1][1]    0.025979 
_atom_sites.fract_transf_matrix[1][2]    -0.000015 
_atom_sites.fract_transf_matrix[1][3]    0.005433 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010454 
_atom_sites.fract_transf_matrix[2][3]    0.002796 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.010928 
_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 PLM A 1 601 1 PLM PLM . 
D 2 PLM A 1 602 2 PLM PLM . 
E 2 PLM A 1 603 3 PLM PLM . 
F 2 PLM A 1 604 4 PLM PLM . 
G 2 PLM A 1 605 5 PLM PLM . 
H 2 PLM A 1 606 6 PLM PLM . 
I 2 PLM A 1 607 13 PLM PLM . 
J 3 8ZR A 1 608 2 8ZR CUL . 
K 2 PLM B 1 601 7 PLM PLM . 
L 2 PLM B 1 602 8 PLM PLM . 
M 2 PLM B 1 603 9 PLM PLM . 
N 2 PLM B 1 604 10 PLM PLM . 
O 2 PLM B 1 605 11 PLM PLM . 
P 2 PLM B 1 606 12 PLM PLM . 
Q 2 PLM B 1 607 14 PLM PLM . 
R 3 8ZR B 1 608 1 8ZR CUL . 
S 4 HOH A 1 701 32 HOH HOH . 
S 4 HOH A 2 702 13 HOH HOH . 
S 4 HOH A 3 703 11 HOH HOH . 
S 4 HOH A 4 704 34 HOH HOH . 
S 4 HOH A 5 705 1 HOH HOH . 
S 4 HOH A 6 706 6 HOH HOH . 
S 4 HOH A 7 707 19 HOH HOH . 
S 4 HOH A 8 708 2 HOH HOH . 
S 4 HOH A 9 709 14 HOH HOH . 
S 4 HOH A 10 710 7 HOH HOH . 
S 4 HOH A 11 711 10 HOH HOH . 
S 4 HOH A 12 712 25 HOH HOH . 
S 4 HOH A 13 713 30 HOH HOH . 
S 4 HOH A 14 714 8 HOH HOH . 
S 4 HOH A 15 715 33 HOH HOH . 
S 4 HOH A 16 716 21 HOH HOH . 
S 4 HOH A 17 717 28 HOH HOH . 
S 4 HOH A 18 718 29 HOH HOH . 
S 4 HOH A 19 719 26 HOH HOH . 
S 4 HOH A 20 720 24 HOH HOH . 
T 4 HOH B 1 701 16 HOH HOH . 
T 4 HOH B 2 702 12 HOH HOH . 
T 4 HOH B 3 703 31 HOH HOH . 
T 4 HOH B 4 704 35 HOH HOH . 
T 4 HOH B 5 705 15 HOH HOH . 
T 4 HOH B 6 706 5 HOH HOH . 
T 4 HOH B 7 707 17 HOH HOH . 
T 4 HOH B 8 708 36 HOH HOH . 
T 4 HOH B 9 709 4 HOH HOH . 
T 4 HOH B 10 710 22 HOH HOH . 
T 4 HOH B 11 711 3 HOH HOH . 
T 4 HOH B 12 712 9 HOH HOH . 
T 4 HOH B 13 713 23 HOH HOH . 
T 4 HOH B 14 714 18 HOH HOH . 
T 4 HOH B 15 715 20 HOH HOH . 
T 4 HOH B 16 716 27 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 C1 PLM . . . F 2 -2.292 2.929 -19.402 1 79.36 ? C1 PLM 604 A 1 
HETATM 2 O O1 PLM . . . F 2 -2.233 4.194 -19.392 1 79.03 ? O1 PLM 604 A 1 
HETATM 3 O O2 PLM . . . F 2 -2.925 2.323 -20.31 1 80.48 ? O2 PLM 604 A 1 
HETATM 4 C C2 PLM . . . F 2 -1.606 2.116 -18.305 1 77.21 ? C2 PLM 604 A 1 
HETATM 5 C C3 PLM . . . F 2 -2.466 2.038 -17.045 1 74.1 ? C3 PLM 604 A 1 
HETATM 6 C C4 PLM . . . F 2 -2.567 3.396 -16.354 1 70.27 ? C4 PLM 604 A 1 
HETATM 7 C C5 PLM . . . F 2 -3.762 3.486 -15.417 1 65.86 ? C5 PLM 604 A 1 
HETATM 8 C C6 PLM . . . F 2 -4.075 4.925 -15.031 1 63.44 ? C6 PLM 604 A 1 
HETATM 9 C C7 PLM . . . F 2 -5.469 5.33 -15.488 1 62.3 ? C7 PLM 604 A 1 
HETATM 10 C C8 PLM . . . F 2 -5.94 6.619 -14.831 1 61.5 ? C8 PLM 604 A 1 
HETATM 11 C C9 PLM . . . F 2 -7.43 6.837 -15.061 1 62.58 ? C9 PLM 604 A 1 
HETATM 12 C CA PLM . . . F 2 -7.788 8.314 -15.181 1 63.86 ? CA PLM 604 A 1 
HETATM 13 C CB PLM . . . F 2 -9.226 8.575 -14.748 1 65.78 ? CB PLM 604 A 1 
HETATM 14 C CC PLM . . . F 2 -9.333 8.698 -13.231 1 67.52 ? CC PLM 604 A 1 
HETATM 15 C CD PLM . . . F 2 -10.695 8.251 -12.704 1 69.42 ? CD PLM 604 A 1 
HETATM 16 C CE PLM . . . F 2 -10.844 8.485 -11.201 1 70.66 ? CE PLM 604 A 1 
HETATM 17 C CF PLM . . . F 2 -12.309 8.57 -10.769 1 71.07 ? CF PLM 604 A 1 
HETATM 18 C CG PLM . . . F 2 -12.467 8.708 -9.255 1 70.03 ? CG PLM 604 A 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    30 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           18 
#