data_1DE4
#
_model_server_result.job_id            -D2cLnlTFDfShiJYlEZAiA 
_model_server_result.datetime_utc      '2024-11-24 21:12:55' 
_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          1de4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":309}' 
#
_entry.id    1DE4 
#
_exptl.entry_id    1DE4 
_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    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          93.6 
_cell.angle_gamma         90 
_cell.entry_id            1DE4 
_cell.length_a            110.4 
_cell.length_b            144.4 
_cell.length_c            327.1 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1DE4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 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 hexameric 6 author_and_software_defined_assembly 1 
? hexameric 6 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,J,K,L,M,Q,R 1 1 
G,H,I,N,O,P,S 2 1,2 
#
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_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 89.861221 0 326.454543 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             N 
_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 102 A CYS 102 1_555 A SG CYS 165 A CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
disulf ? disulf2 A SG CYS 203 A CYS 203 1_555 A SG CYS 260 A CYS 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf4 C SG CYS 233 C CYS 353 1_555 C SG CYS 243 C CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf5 C SG CYS 436 C CYS 556 1_555 C SG CYS 438 C CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf6 D SG CYS 102 D CYS 102 1_555 D SG CYS 165 D CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf7 D SG CYS 203 D CYS 203 1_555 D SG CYS 260 D CYS 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf8 E SG CYS 25 E CYS 25 1_555 E SG CYS 80 E CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf9 F SG CYS 233 F CYS 353 1_555 F SG CYS 243 F CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf10 F SG CYS 436 F CYS 556 1_555 F SG CYS 438 F CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf11 G SG CYS 102 G CYS 102 1_555 G SG CYS 165 G CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf12 G SG CYS 203 G CYS 203 1_555 G SG CYS 260 G CYS 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf13 H SG CYS 25 H CYS 25 1_555 H SG CYS 80 H CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf14 I SG CYS 233 I CYS 353 1_555 I SG CYS 243 I CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf15 I SG CYS 436 I CYS 556 1_555 I SG CYS 438 I CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
covale ? covale1 C ND2 ASN 197 C ASN 317 1_555 J C1 NAG . C NAG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? 
covale ? covale2 F ND2 ASN 197 F ASN 317 1_555 L C1 NAG . F NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? 
covale ? covale3 I ND2 ASN 197 I ASN 317 1_555 O C1 NAG . I NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
metalc ? metalc1 C O THR 190 C THR 310 1_555 K CA CA . C CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc2 C OG1 THR 190 C THR 310 1_555 K CA CA . C CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? 
metalc ? metalc3 C O PHE 193 C PHE 313 1_555 K CA CA . C CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? 
metalc ? metalc4 C OE1 GLU 345 C GLU 465 1_555 K CA CA . C CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? 
metalc ? metalc5 C OE2 GLU 345 C GLU 465 1_555 K CA CA . C CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? 
metalc ? metalc6 C OE1 GLU 348 C GLU 468 1_555 K CA CA . C CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc7 F O THR 190 F THR 310 1_555 M CA CA . F CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? 
metalc ? metalc8 F OG1 THR 190 F THR 310 1_555 M CA CA . F CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? 
metalc ? metalc9 F O PHE 193 F PHE 313 1_555 M CA CA . F CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc10 F OE1 GLU 345 F GLU 465 1_555 M CA CA . F CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc11 F OE2 GLU 345 F GLU 465 1_555 M CA CA . F CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? 
metalc ? metalc12 F OE1 GLU 348 F GLU 468 1_555 M CA CA . F CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc13 I OG1 THR 190 I THR 310 1_555 P CA CA . I CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? 
metalc ? metalc14 I O THR 190 I THR 310 1_555 P CA CA . I CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc15 I O PHE 193 I PHE 313 1_555 P CA CA . I CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc16 I OE2 GLU 345 I GLU 465 1_555 P CA CA . I CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? 
metalc ? metalc17 I OE1 GLU 345 I GLU 465 1_555 P CA CA . I CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc18 I OE1 GLU 348 I GLU 468 1_555 P CA CA . I CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? 
#
_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                     1DE4 
_atom_sites.fract_transf_matrix[1][1]    0.009058 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00057 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006925 
_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]    0.003063 
_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
J 4 NAG C 1 900 900 NAG NAG . 
K 5 CA C 1 801 1 CA CA . 
L 4 NAG F 1 901 901 NAG NAG . 
M 5 CA F 1 802 2 CA CA . 
N 6 GOL G 1 309 309 GOL CRY . 
O 4 NAG I 1 902 902 NAG NAG . 
P 5 CA I 1 803 3 CA CA . 
Q 7 HOH C 1 1 1 HOH TIP . 
Q 7 HOH C 2 2 2 HOH TIP . 
Q 7 HOH C 3 5 5 HOH TIP . 
Q 7 HOH C 4 6 6 HOH TIP . 
R 7 HOH F 1 7 7 HOH TIP . 
R 7 HOH F 2 8 8 HOH TIP . 
S 7 HOH I 1 3 3 HOH TIP . 
S 7 HOH I 2 4 4 HOH TIP . 
S 7 HOH I 3 9 9 HOH TIP . 
#
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 . . . N 6 55.334 60.654 190.556 1 52.23 ? C1 GOL 309 G 1 
HETATM 2 O O1 GOL . . . N 6 54.16 61.432 190.767 1 59.63 ? O1 GOL 309 G 1 
HETATM 3 C C2 GOL . . . N 6 54.962 59.748 189.402 1 69.06 ? C2 GOL 309 G 1 
HETATM 4 O O2 GOL . . . N 6 53.694 59.022 189.805 1 76.96 ? O2 GOL 309 G 1 
HETATM 5 C C3 GOL . . . N 6 56.134 58.694 189.144 1 62.65 ? C3 GOL 309 G 1 
HETATM 6 O O3 GOL . . . N 6 55.496 57.376 189.416 1 62.81 ? O3 GOL 309 G 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    32 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           6 
#