data_5VK6
#
_model_server_result.job_id            EsiA1aPU_nm95USdIZMsNQ 
_model_server_result.datetime_utc      '2024-11-27 19:18:10' 
_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          5vk6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":2001}' 
#
_entry.id    5VK6 
#
_exptl.entry_id    5VK6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              144.254 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            NONAN-1-OL 
_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            5VK6 
_cell.length_a            156.544 
_cell.length_b            156.544 
_cell.length_c            74.618 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VK6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        79 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 
4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 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 22 A CYS 22 1_555 A SG CYS 96 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
disulf ? disulf2 B SG CYS 23 B CYS 23 1_555 B SG CYS 88 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
disulf ? disulf3 B SG CYS 134 B CYS 134 1_555 B SG CYS 194 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
disulf ? disulf4 C SG CYS 3 C CYS 28 1_555 C SG CYS 93 C CYS 118 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc1 C O THR 50 C THR 75 1_555 G K K . C K 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.09 ? 
metalc ? metalc2 C OG1 THR 50 C THR 75 1_555 G K K . C K 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? 
metalc ? metalc3 C O THR 50 C THR 75 1_555 G K K . C K 2004 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.09 ? 
metalc ? metalc4 C OG1 THR 50 C THR 75 1_555 G K K . C K 2004 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? 
metalc ? metalc5 C O THR 50 C THR 75 1_555 H K K . C K 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc6 C O THR 50 C THR 75 1_555 H K K . C K 2005 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc7 C O VAL 51 C VAL 76 1_555 H K K . C K 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.926 ? 
metalc ? metalc8 C O VAL 51 C VAL 76 1_555 H K K . C K 2005 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.926 ? 
metalc ? metalc9 C O VAL 51 C VAL 76 1_555 I K K . C K 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.906 ? 
metalc ? metalc10 C O VAL 51 C VAL 76 1_555 I K K . C K 2006 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.906 ? 
metalc ? metalc11 C O GLY 52 C GLY 77 1_555 I K K . C K 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? 
metalc ? metalc12 C O GLY 52 C GLY 77 1_555 I K K . C K 2006 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? 
metalc ? metalc13 C O GLY 52 C GLY 77 1_555 J K K . C K 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.108 ? 
metalc ? metalc14 C O GLY 52 C GLY 77 1_555 J K K . C K 2007 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.108 ? 
metalc ? metalc15 C O TYR 53 C TYR 78 1_555 J K K . C K 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? 
metalc ? metalc16 C O TYR 53 C TYR 78 1_555 J K K . C K 2007 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? 
metalc ? metalc17 L K K . C K 2009 1_555 O O HOH . C HOH 2118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.291 ? 
metalc ? metalc18 L K K . C K 2009 1_555 O O HOH . C HOH 2118 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.291 ? 
#
_chem_comp.formula           'C9 H20 O' 
_chem_comp.formula_weight    144.254 
_chem_comp.id                F09 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              NONAN-1-OL 
_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 F09 sing 163 n n 
C1 H11 F09 sing 164 n n 
C1 H12 F09 sing 165 n n 
C1 H13 F09 sing 166 n n 
C2 C3 F09 sing 167 n n 
C2 H21 F09 sing 168 n n 
C2 H22 F09 sing 169 n n 
C3 C4 F09 sing 170 n n 
C3 H31 F09 sing 171 n n 
C3 H32 F09 sing 172 n n 
C4 C5 F09 sing 173 n n 
C4 H41 F09 sing 174 n n 
C4 H42 F09 sing 175 n n 
C5 C6 F09 sing 176 n n 
C5 H51 F09 sing 177 n n 
C5 H52 F09 sing 178 n n 
C6 C7 F09 sing 179 n n 
C6 H61 F09 sing 180 n n 
C6 H62 F09 sing 181 n n 
C7 C8 F09 sing 182 n n 
C7 H71 F09 sing 183 n n 
C7 H72 F09 sing 184 n n 
C8 C9 F09 sing 185 n n 
C8 H81 F09 sing 186 n n 
C8 H82 F09 sing 187 n n 
C9 OXT F09 sing 188 n n 
C9 H91 F09 sing 189 n n 
C9 H92 F09 sing 190 n n 
OXT HXT F09 sing 191 n n 
#
_atom_sites.entry_id                     5VK6 
_atom_sites.fract_transf_matrix[1][1]    0.006388 
_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]    0.006388 
_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]    0.013402 
_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 F09 C 1 2001 2001 F09 F09 . 
E 5 1EM C 1 2002 1001 1EM DGA . 
F 6 K C 1 2003 1 K K . 
G 6 K C 1 2004 2 K K . 
H 6 K C 1 2005 3 K K . 
I 6 K C 1 2006 4 K K . 
J 6 K C 1 2007 5 K K . 
K 6 K C 1 2008 6 K K . 
L 6 K C 1 2009 7 K K . 
M 7 HOH A 1 301 90 HOH HOH . 
M 7 HOH A 2 302 72 HOH HOH . 
M 7 HOH A 3 303 97 HOH HOH . 
M 7 HOH A 4 304 74 HOH HOH . 
M 7 HOH A 5 305 28 HOH HOH . 
M 7 HOH A 6 306 87 HOH HOH . 
M 7 HOH A 7 307 39 HOH HOH . 
M 7 HOH A 8 308 31 HOH HOH . 
M 7 HOH A 9 309 19 HOH HOH . 
M 7 HOH A 10 310 18 HOH HOH . 
M 7 HOH A 11 311 91 HOH HOH . 
M 7 HOH A 12 312 15 HOH HOH . 
M 7 HOH A 13 313 56 HOH HOH . 
M 7 HOH A 14 314 66 HOH HOH . 
M 7 HOH A 15 315 55 HOH HOH . 
M 7 HOH A 16 316 75 HOH HOH . 
M 7 HOH A 17 317 34 HOH HOH . 
M 7 HOH A 18 318 59 HOH HOH . 
M 7 HOH A 19 319 51 HOH HOH . 
M 7 HOH A 20 320 73 HOH HOH . 
M 7 HOH A 21 321 68 HOH HOH . 
M 7 HOH A 22 322 50 HOH HOH . 
M 7 HOH A 23 323 60 HOH HOH . 
M 7 HOH A 24 324 4 HOH HOH . 
M 7 HOH A 25 325 33 HOH HOH . 
M 7 HOH A 26 326 65 HOH HOH . 
M 7 HOH A 27 327 10 HOH HOH . 
M 7 HOH A 28 328 92 HOH HOH . 
M 7 HOH A 29 329 40 HOH HOH . 
M 7 HOH A 30 330 94 HOH HOH . 
M 7 HOH A 31 331 79 HOH HOH . 
M 7 HOH A 32 332 99 HOH HOH . 
N 7 HOH B 1 301 47 HOH HOH . 
N 7 HOH B 2 302 82 HOH HOH . 
N 7 HOH B 3 303 14 HOH HOH . 
N 7 HOH B 4 304 80 HOH HOH . 
N 7 HOH B 5 305 16 HOH HOH . 
N 7 HOH B 6 306 95 HOH HOH . 
N 7 HOH B 7 307 53 HOH HOH . 
N 7 HOH B 8 308 71 HOH HOH . 
N 7 HOH B 9 309 25 HOH HOH . 
N 7 HOH B 10 310 67 HOH HOH . 
N 7 HOH B 11 311 12 HOH HOH . 
N 7 HOH B 12 312 8 HOH HOH . 
N 7 HOH B 13 313 83 HOH HOH . 
N 7 HOH B 14 314 81 HOH HOH . 
N 7 HOH B 15 315 32 HOH HOH . 
N 7 HOH B 16 316 26 HOH HOH . 
N 7 HOH B 17 317 52 HOH HOH . 
N 7 HOH B 18 318 24 HOH HOH . 
N 7 HOH B 19 319 70 HOH HOH . 
N 7 HOH B 20 320 61 HOH HOH . 
N 7 HOH B 21 321 29 HOH HOH . 
N 7 HOH B 22 322 21 HOH HOH . 
N 7 HOH B 23 323 22 HOH HOH . 
N 7 HOH B 24 324 42 HOH HOH . 
N 7 HOH B 25 325 58 HOH HOH . 
N 7 HOH B 26 326 2 HOH HOH . 
N 7 HOH B 27 327 89 HOH HOH . 
N 7 HOH B 28 328 44 HOH HOH . 
N 7 HOH B 29 329 62 HOH HOH . 
N 7 HOH B 30 330 96 HOH HOH . 
N 7 HOH B 31 331 5 HOH HOH . 
N 7 HOH B 32 332 45 HOH HOH . 
N 7 HOH B 33 333 20 HOH HOH . 
N 7 HOH B 34 334 57 HOH HOH . 
N 7 HOH B 35 335 63 HOH HOH . 
N 7 HOH B 36 336 98 HOH HOH . 
N 7 HOH B 37 337 88 HOH HOH . 
N 7 HOH B 38 338 84 HOH HOH . 
N 7 HOH B 39 339 85 HOH HOH . 
N 7 HOH B 40 340 69 HOH HOH . 
N 7 HOH B 41 341 100 HOH HOH . 
N 7 HOH B 42 342 93 HOH HOH . 
N 7 HOH B 43 343 43 HOH HOH . 
N 7 HOH B 44 344 86 HOH HOH . 
N 7 HOH B 45 345 35 HOH HOH . 
N 7 HOH B 46 346 23 HOH HOH . 
N 7 HOH B 47 347 76 HOH HOH . 
N 7 HOH B 48 348 41 HOH HOH . 
N 7 HOH B 49 349 54 HOH HOH . 
N 7 HOH B 50 350 77 HOH HOH . 
O 7 HOH C 1 2101 104 HOH HOH . 
O 7 HOH C 2 2102 6 HOH HOH . 
O 7 HOH C 3 2103 1 HOH HOH . 
O 7 HOH C 4 2104 9 HOH HOH . 
O 7 HOH C 5 2105 64 HOH HOH . 
O 7 HOH C 6 2106 27 HOH HOH . 
O 7 HOH C 7 2107 49 HOH HOH . 
O 7 HOH C 8 2108 3 HOH HOH . 
O 7 HOH C 9 2109 37 HOH HOH . 
O 7 HOH C 10 2110 36 HOH HOH . 
O 7 HOH C 11 2111 38 HOH HOH . 
O 7 HOH C 12 2112 46 HOH HOH . 
O 7 HOH C 13 2113 13 HOH HOH . 
O 7 HOH C 14 2114 17 HOH HOH . 
O 7 HOH C 15 2115 30 HOH HOH . 
O 7 HOH C 16 2116 48 HOH HOH . 
O 7 HOH C 17 2117 78 HOH HOH . 
O 7 HOH C 18 2118 102 HOH HOH . 
O 7 HOH C 19 2119 103 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 F09 . . . D 4 1.383 24.877 19.111 1 77.68 ? C1 F09 2001 C 1 
HETATM 2 C C2 F09 . . . D 4 0.466 25.548 20.141 1 80.34 ? C2 F09 2001 C 1 
HETATM 3 C C3 F09 . . . D 4 0.928 25.218 21.556 1 72.09 ? C3 F09 2001 C 1 
HETATM 4 C C4 F09 . . . D 4 -0.268 24.961 22.471 1 73.47 ? C4 F09 2001 C 1 
HETATM 5 C C5 F09 . . . D 4 0.258 24.375 23.783 1 74.13 ? C5 F09 2001 C 1 
HETATM 6 C C6 F09 . . . D 4 -0.761 24.582 24.895 1 80.07 ? C6 F09 2001 C 1 
HETATM 7 C C7 F09 . . . D 4 -0.051 24.509 26.245 1 84.42 ? C7 F09 2001 C 1 
HETATM 8 C C8 F09 . . . D 4 0.66 23.166 26.386 1 85.74 ? C8 F09 2001 C 1 
HETATM 9 C C9 F09 . . . D 4 1.022 22.95 27.856 1 86 ? C9 F09 2001 C 1 
HETATM 10 O OXT F09 . . . D 4 1.633 21.701 28.024 1 85.15 ? OXT F09 2001 C 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           10 
#