data_3D39
#
_model_server_result.job_id            PIjfzjBd0aEudP1clf7lrQ 
_model_server_result.datetime_utc      '2024-11-04 20:53:43' 
_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          3d39 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":250}' 
#
_entry.id    3D39 
#
_exptl.entry_id    3D39 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.51 
_cell.angle_gamma         90 
_cell.entry_id            3D39 
_cell.length_a            224.245 
_cell.length_b            48.32 
_cell.length_c            93.218 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3D39 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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 
_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 F N N 
? 6 G N N 
? 6 H N N 
? 6 I 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 101 A CYS 101 1_555 A SG CYS 164 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
disulf ? disulf2 A SG CYS 203 A CYS 203 1_555 A SG CYS 259 A CYS 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf3 B SG CYS 26 B CYS 25 1_555 B SG CYS 81 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf4 D SG CYS 22 D CYS 22 1_555 D SG CYS 88 D CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf5 D SG CYS 133 D CYS 139 1_555 D SG CYS 183 D CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
disulf ? disulf6 E SG CYS 23 E CYS 23 1_555 E SG CYS 91 E CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
disulf ? disulf7 E SG CYS 146 E CYS 147 1_555 E SG CYS 211 E CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
covale ? covale1 C C GLY 4 C GLY 4 1_555 C N PFF 5 C PFF 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? 
covale ? covale2 C C PFF 5 C PFF 5 1_555 C N PRO 6 C PRO 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? 
#
_chem_comp.formula           'C3 H8 O3' 
_chem_comp.formula_weight    92.094 
_chem_comp.id                GOL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     GLYCERIN;PROPANE-1,2,3-TRIOL 
#
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 GOL sing 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     3D39 
_atom_sites.fract_transf_matrix[1][1]    0.004459 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00004 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020695 
_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]    0.010728 
_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
F 6 GOL D 1 207 207 GOL GOL . 
G 6 GOL E 1 248 248 GOL GOL . 
H 6 GOL E 1 249 249 GOL GOL . 
I 6 GOL E 1 250 250 GOL GOL . 
J 7 HOH A 1 276 276 HOH HOH . 
J 7 HOH A 2 277 277 HOH HOH . 
J 7 HOH A 3 278 278 HOH HOH . 
J 7 HOH A 4 279 279 HOH HOH . 
J 7 HOH A 5 280 280 HOH HOH . 
J 7 HOH A 6 281 281 HOH HOH . 
J 7 HOH A 7 282 282 HOH HOH . 
J 7 HOH A 8 283 283 HOH HOH . 
J 7 HOH A 9 284 284 HOH HOH . 
J 7 HOH A 10 285 285 HOH HOH . 
J 7 HOH A 11 286 286 HOH HOH . 
J 7 HOH A 12 287 287 HOH HOH . 
J 7 HOH A 13 288 288 HOH HOH . 
J 7 HOH A 14 289 289 HOH HOH . 
J 7 HOH A 15 290 290 HOH HOH . 
J 7 HOH A 16 291 291 HOH HOH . 
J 7 HOH A 17 292 292 HOH HOH . 
J 7 HOH A 18 293 293 HOH HOH . 
K 7 HOH B 1 100 100 HOH HOH . 
K 7 HOH B 2 101 101 HOH HOH . 
K 7 HOH B 3 102 102 HOH HOH . 
K 7 HOH B 4 103 103 HOH HOH . 
K 7 HOH B 5 104 104 HOH HOH . 
K 7 HOH B 6 105 105 HOH HOH . 
K 7 HOH B 7 106 106 HOH HOH . 
K 7 HOH B 8 107 107 HOH HOH . 
K 7 HOH B 9 108 108 HOH HOH . 
K 7 HOH B 10 109 109 HOH HOH . 
K 7 HOH B 11 110 110 HOH HOH . 
K 7 HOH B 12 111 111 HOH HOH . 
K 7 HOH B 13 112 112 HOH HOH . 
L 7 HOH D 1 208 208 HOH HOH . 
L 7 HOH D 2 209 209 HOH HOH . 
L 7 HOH D 3 210 210 HOH HOH . 
L 7 HOH D 4 211 211 HOH HOH . 
L 7 HOH D 5 212 212 HOH HOH . 
L 7 HOH D 6 213 213 HOH HOH . 
L 7 HOH D 7 214 214 HOH HOH . 
L 7 HOH D 8 215 215 HOH HOH . 
M 7 HOH E 1 251 251 HOH HOH . 
M 7 HOH E 2 252 252 HOH HOH . 
M 7 HOH E 3 253 253 HOH HOH . 
M 7 HOH E 4 254 254 HOH HOH . 
M 7 HOH E 5 255 255 HOH HOH . 
M 7 HOH E 6 256 256 HOH HOH . 
M 7 HOH E 7 257 257 HOH HOH . 
M 7 HOH E 8 258 258 HOH HOH . 
M 7 HOH E 9 259 259 HOH HOH . 
M 7 HOH E 10 260 260 HOH HOH . 
M 7 HOH E 11 261 261 HOH HOH . 
M 7 HOH E 12 262 262 HOH HOH . 
M 7 HOH E 13 263 263 HOH HOH . 
M 7 HOH E 14 264 264 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 GOL . . . I 6 5.209 10.99 29.219 1 60.76 ? C1 GOL 250 E 1 
HETATM 2 O O1 GOL . . . I 6 4.781 9.668 29.428 1 59.89 ? O1 GOL 250 E 1 
HETATM 3 C C2 GOL . . . I 6 5.492 11.194 27.739 1 61.82 ? C2 GOL 250 E 1 
HETATM 4 O O2 GOL . . . I 6 4.258 11.277 27.032 1 62.22 ? O2 GOL 250 E 1 
HETATM 5 C C3 GOL . . . I 6 6.351 12.444 27.526 1 61.81 ? C3 GOL 250 E 1 
HETATM 6 O O3 GOL . . . I 6 5.539 13.523 27.106 1 62.2 ? O3 GOL 250 E 1 
#
_model_server_stats.io_time_ms              41 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    38 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           6 
#