data_8C3V
#
_model_server_result.job_id            7X0GsUSIz-_lH4fuRYXzhA 
_model_server_result.datetime_utc      '2024-10-19 11:31:58' 
_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          8c3v 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"CA","auth_seq_id":602}' 
#
_entry.id    8C3V 
#
_exptl.entry_id    8C3V 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          8 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    14 
_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            8C3V 
_cell.length_a            105.925 
_cell.length_b            160.817 
_cell.length_c            172.455 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8C3V 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_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 
? tetrameric 4 author_defined_assembly 2 
? tetrameric 4 author_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,M,P,Q,R,S,T,U 1 1 
E,F,I,J,N,V,W,X,Y,Z,AA,GA 2 1 
G,H,K,L,O,BA,CA,DA,EA,FA 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
? 8 P N N 
? 8 Q N N 
? 8 S N N 
? 8 T N N 
? 8 U N N 
? 8 V N N 
? 8 W N N 
? 8 Y N N 
? 8 Z N N 
? 8 BA N N 
? 8 CA N N 
? 8 EA N N 
? 8 FA N N 
? 8 GA N N 
#
loop_
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
5 oligosaccharide 
6 oligosaccharide 
7 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
3 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . sing 
4 ? 5 5 1 FUC NAG C1 O1 . O6 HO6 . sing 
5 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
6 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
7 ? 6 4 1 FUC NAG C1 O1 . O6 HO6 . sing 
8 ? 7 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
9 ? 7 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
10 ? 7 4 3 MAN BMA C1 O1 . O6 HO6 . sing 
11 ? 7 5 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
5 n M NAG 1 E 1 NAG R 602 NAG 
5 n M NAG 2 E 2 NAG R 603 NAG 
5 n M BMA 3 E 3 BMA R 604 BMA 
5 n M MAN 4 E 4 MAN R 605 MAN 
5 n M FUC 5 E 5 FUC R 601 FUC 
6 n N NAG 1 F 1 NAG X 602 NAG 
6 n N NAG 2 F 2 NAG X 603 NAG 
6 n N BMA 3 F 3 BMA X 604 BMA 
6 n N FUC 4 F 4 FUC X 601 FUC 
7 n O NAG 1 G 1 NAG Y 602 NAG 
7 n O NAG 2 G 2 NAG Y 603 NAG 
7 n O BMA 3 G 3 BMA Y 604 BMA 
7 n O MAN 4 G 4 MAN Y 605 MAN 
7 n O FUC 5 G 5 FUC Y 601 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 22 H CYS 22 1_555 A SG CYS 98 H CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf2 A SG CYS 153 H CYS 153 1_555 A SG CYS 209 H CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf3 B SG CYS 23 L CYS 23 1_555 B SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf4 B SG CYS 133 L CYS 133 1_555 B SG CYS 193 L CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf5 C SG CYS 10 R CYS 336 1_555 C SG CYS 35 R CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf6 C SG CYS 53 R CYS 379 1_555 C SG CYS 106 R CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf7 C SG CYS 65 R CYS 391 1_555 C SG CYS 199 R CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf8 C SG CYS 154 R CYS 480 1_555 C SG CYS 162 R CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf9 D SG CYS 22 I CYS 22 1_555 D SG CYS 96 I CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf10 E SG CYS 10 X CYS 336 1_555 E SG CYS 35 X CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf11 E SG CYS 53 X CYS 379 1_555 E SG CYS 106 X CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf12 E SG CYS 65 X CYS 391 1_555 E SG CYS 199 X CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf13 E SG CYS 154 X CYS 480 1_555 E SG CYS 162 X CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf14 F SG CYS 22 J CYS 22 1_555 F SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf15 G SG CYS 10 Y CYS 336 1_555 G SG CYS 35 Y CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf16 G SG CYS 53 Y CYS 379 1_555 G SG CYS 106 Y CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf17 G SG CYS 65 Y CYS 391 1_555 G SG CYS 199 Y CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf18 G SG CYS 154 Y CYS 480 1_555 G SG CYS 162 Y CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf19 H SG CYS 22 K CYS 22 1_555 H SG CYS 96 K CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf20 I SG CYS 22 A CYS 22 1_555 I SG CYS 98 A CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf21 I SG CYS 153 A CYS 153 1_555 I SG CYS 209 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf22 J SG CYS 23 B CYS 23 1_555 J SG CYS 88 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf23 J SG CYS 133 B CYS 133 1_555 J SG CYS 193 B CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf24 K SG CYS 22 C CYS 22 1_555 K SG CYS 98 C CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf25 K SG CYS 153 C CYS 153 1_555 K SG CYS 209 C CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf26 L SG CYS 23 D CYS 23 1_555 L SG CYS 88 D CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf27 L SG CYS 133 D CYS 133 1_555 L SG CYS 193 D CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
covale ? covale1 C ND2 ASN 17 R ASN 343 1_555 M C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale2 E ND2 ASN 17 X ASN 343 1_555 N C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? 
covale ? covale3 G ND2 ASN 17 Y ASN 343 1_555 O C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? 
covale ? covale4 M O4 NAG . E NAG 1 1_555 M C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? 
covale ? covale5 M O6 NAG . E NAG 1 1_555 M C1 FUC . E FUC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale6 M O4 NAG . E NAG 2 1_555 M C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
covale ? covale7 M O3 BMA . E BMA 3 1_555 M C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale8 N O4 NAG . F NAG 1 1_555 N C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
covale ? covale9 N O6 NAG . F NAG 1 1_555 N C1 FUC . F FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale10 N O4 NAG . F NAG 2 1_555 N C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
covale ? covale11 O O4 NAG . G NAG 1 1_555 O C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale12 O O6 NAG . G NAG 1 1_555 O C1 FUC . G FUC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale13 O O4 NAG . G NAG 2 1_555 O C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
covale ? covale14 O O6 BMA . G BMA 3 1_555 O C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
#
_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                     8C3V 
_atom_sites.fract_transf_matrix[1][1]    0.009441 
_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]    0.006218 
_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]    0.005799 
_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
P 8 GOL R 1 601 608 GOL GOL . 
Q 8 GOL R 1 602 609 GOL GOL . 
R 9 PG0 R 1 603 610 PG0 PG0 . 
S 8 GOL I 1 201 201 GOL GOL . 
T 8 GOL I 1 202 202 GOL GOL . 
U 8 GOL I 1 203 203 GOL GOL . 
V 8 GOL X 1 601 606 GOL GOL . 
W 8 GOL X 1 602 609 GOL GOL . 
X 10 PG4 X 1 603 610 PG4 PG4 . 
Y 8 GOL J 1 201 606 GOL GOL . 
Z 8 GOL J 1 202 607 GOL GOL . 
AA 9 PG0 J 1 203 201 PG0 PG0 . 
BA 8 GOL Y 1 601 615 GOL GOL . 
CA 8 GOL Y 1 602 617 GOL GOL . 
DA 10 PG4 Y 1 603 618 PG4 PG4 . 
EA 8 GOL K 1 201 201 GOL GOL . 
FA 8 GOL K 1 202 202 GOL GOL . 
GA 8 GOL A 1 301 301 GOL GOL . 
#
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 . . . CA 8 47.364 54.088 60.83 1 67.32 ? C1 GOL 602 Y 1 
HETATM 2 O O1 GOL . . . CA 8 46.521 53.075 60.342 1 74.98 ? O1 GOL 602 Y 1 
HETATM 3 C C2 GOL . . . CA 8 47.394 55.194 59.751 1 64.19 ? C2 GOL 602 Y 1 
HETATM 4 O O2 GOL . . . CA 8 46.946 56.428 60.234 1 64.18 ? O2 GOL 602 Y 1 
HETATM 5 C C3 GOL . . . CA 8 48.867 55.239 59.291 1 63.84 ? C3 GOL 602 Y 1 
HETATM 6 O O3 GOL . . . CA 8 49.025 56.446 58.602 1 63.66 ? O3 GOL 602 Y 1 
#
_model_server_stats.io_time_ms              52 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#