data_1RD3
#
_model_server_result.job_id            vrC33JMrVx6FChIdw_HnLg 
_model_server_result.datetime_utc      '2024-12-27 00:43:59' 
_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          1rd3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":253}' 
#
_entry.id    1RD3 
#
_exptl.entry_id    1RD3 
_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    6 
_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            1RD3 
_cell.length_a            73.23 
_cell.length_b            107.62 
_cell.length_c            136.03 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1RD3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? tetrameric 4 author_defined_assembly 1 
PISA,PQS dimeric 2 software_defined_assembly 2 
PISA,PQS dimeric 2 software_defined_assembly 3 
#
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,G,H,I,J,K,L,M,N,O,P,Q,R,S 1 1 
A,B,E,G,H,I,J,K,L,M,P,Q 2 1 
C,D,F,N,O,R,S 3 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 I N N 
? 6 J N N 
? 6 K N N 
? 6 L N N 
? 6 M N N 
? 6 O N N 
#
loop_
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
3 oligosaccharide 
4 oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 3 2 1 NDG NAG C1 O1 . O4 HO4 . sing 
2 ? 3 3 2 BMA NDG C1 O1 . O4 HO4 . sing 
3 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . sing 
4 ? 3 5 1 FUC NAG C1 O1 . O6 HO6 . sing 
5 ? 4 2 1 NDG NAG C1 O1 . O4 HO4 . sing 
6 ? 4 3 1 FUC NAG C1 O1 . O6 HO6 . sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
3 n E NAG 1 E 1 NAG X 1 NAG 
3 n E NDG 2 E 2 NDG X 3 NAG 
3 n E BMA 3 E 3 BMA X 4 MAN 
3 n E MAN 4 E 4 MAN X 5 MAN 
3 n E FUC 5 E 5 FUC X 2 FUC 
4 n F NAG 1 F 1 NAG Z 1 NAG 
4 n F NDG 2 F 2 NDG Z 3 NAG 
4 n F FUC 3 F 3 FUC Z 2 FUC 
#
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 9 A CYS 1 1_555 B SG CYS 119 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf2 B SG CYS 28 B CYS 42 1_555 B SG CYS 44 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf3 B SG CYS 173 B CYS 168 1_555 B SG CYS 187 B CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf4 B SG CYS 201 B CYS 191 1_555 B SG CYS 231 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf5 C SG CYS 9 C CYS 1 1_555 D SG CYS 119 D CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf6 D SG CYS 28 D CYS 42 1_555 D SG CYS 44 D CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf7 D SG CYS 173 D CYS 168 1_555 D SG CYS 187 D CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf8 D SG CYS 201 D CYS 191 1_555 D SG CYS 231 D CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
covale ? covale1 B ND2 ASN 53 B ASN 60 1_555 E C1 NAG . E NAG 1 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale2 D ND2 ASN 53 D ASN 60 1_555 F C1 NAG . F NAG 1 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale3 E O4 NAG . E NAG 1 1_555 E C1 NDG . E NDG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? 
covale ? covale4 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? 
covale ? covale5 E O4 NDG . E NDG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? 
covale ? covale6 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? 
covale ? covale7 F O4 NAG . F NAG 1 1_555 F C1 NDG . F NDG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? 
covale ? covale8 F O6 NAG . F NAG 1 1_555 F C1 FUC . F FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? 
#
_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 176 n n 
C1 C2 GOL sing 177 n n 
C1 H11 GOL sing 178 n n 
C1 H12 GOL sing 179 n n 
O1 HO1 GOL sing 180 n n 
C2 O2 GOL sing 181 n n 
C2 C3 GOL sing 182 n n 
C2 H2 GOL sing 183 n n 
O2 HO2 GOL sing 184 n n 
C3 O3 GOL sing 185 n n 
C3 H31 GOL sing 186 n n 
C3 H32 GOL sing 187 n n 
O3 HO3 GOL sing 188 n n 
#
_atom_sites.entry_id                     1RD3 
_atom_sites.fract_transf_matrix[1][1]    0.013656 
_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]    0.009292 
_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]    0.007351 
_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
G 5 PO4 B 1 248 1 PO4 PO4 . 
H 5 PO4 B 1 249 3 PO4 PO4 . 
I 6 GOL B 1 250 1 GOL GOL . 
J 6 GOL B 1 251 2 GOL GOL . 
K 6 GOL B 1 252 3 GOL GOL . 
L 6 GOL B 1 253 4 GOL GOL . 
M 6 GOL B 1 254 6 GOL GOL . 
N 5 PO4 D 1 248 2 PO4 PO4 . 
O 6 GOL D 1 249 5 GOL GOL . 
P 7 HOH A 1 18 2 HOH HOH . 
P 7 HOH A 2 19 3 HOH HOH . 
Q 7 HOH B 1 255 1 HOH HOH . 
Q 7 HOH B 2 256 4 HOH HOH . 
Q 7 HOH B 3 257 5 HOH HOH . 
Q 7 HOH B 4 258 6 HOH HOH . 
Q 7 HOH B 5 259 7 HOH HOH . 
Q 7 HOH B 6 260 8 HOH HOH . 
Q 7 HOH B 7 261 12 HOH HOH . 
Q 7 HOH B 8 262 14 HOH HOH . 
Q 7 HOH B 9 263 15 HOH HOH . 
Q 7 HOH B 10 264 16 HOH HOH . 
Q 7 HOH B 11 265 18 HOH HOH . 
Q 7 HOH B 12 266 19 HOH HOH . 
Q 7 HOH B 13 267 20 HOH HOH . 
Q 7 HOH B 14 268 21 HOH HOH . 
Q 7 HOH B 15 269 30 HOH HOH . 
Q 7 HOH B 16 270 31 HOH HOH . 
Q 7 HOH B 17 271 32 HOH HOH . 
Q 7 HOH B 18 272 33 HOH HOH . 
Q 7 HOH B 19 273 34 HOH HOH . 
Q 7 HOH B 20 274 35 HOH HOH . 
Q 7 HOH B 21 275 36 HOH HOH . 
Q 7 HOH B 22 276 37 HOH HOH . 
Q 7 HOH B 23 277 38 HOH HOH . 
R 7 HOH C 1 17 10 HOH HOH . 
R 7 HOH C 2 18 22 HOH HOH . 
S 7 HOH D 1 250 9 HOH HOH . 
S 7 HOH D 2 251 11 HOH HOH . 
S 7 HOH D 3 252 13 HOH HOH . 
S 7 HOH D 4 253 17 HOH HOH . 
S 7 HOH D 5 254 23 HOH HOH . 
S 7 HOH D 6 255 24 HOH HOH . 
S 7 HOH D 7 256 25 HOH HOH . 
S 7 HOH D 8 257 26 HOH HOH . 
S 7 HOH D 9 258 27 HOH HOH . 
S 7 HOH D 10 259 28 HOH HOH . 
S 7 HOH D 11 260 29 HOH HOH . 
S 7 HOH D 12 261 39 HOH HOH . 
S 7 HOH D 13 262 40 HOH HOH . 
S 7 HOH D 14 263 41 HOH HOH . 
S 7 HOH D 15 264 42 HOH HOH . 
S 7 HOH D 16 265 43 HOH HOH . 
S 7 HOH D 17 266 44 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 . . . L 6 50.031 36.855 14.085 1 66.69 ? C1 GOL 253 B 1 
HETATM 2 O O1 GOL . . . L 6 48.7 36.914 13.502 1 65.92 ? O1 GOL 253 B 1 
HETATM 3 C C2 GOL . . . L 6 51.022 37.656 13.187 1 66.96 ? C2 GOL 253 B 1 
HETATM 4 O O2 GOL . . . L 6 52.208 38 13.884 1 67.83 ? O2 GOL 253 B 1 
HETATM 5 C C3 GOL . . . L 6 50.416 38.962 12.664 1 67.35 ? C3 GOL 253 B 1 
HETATM 6 O O3 GOL . . . L 6 49.753 39.677 13.683 1 69.05 ? O3 GOL 253 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           6 
#