data_8VCX
#
_model_server_result.job_id            Lxc9Lo8LoOCjlOq-Ef60dw 
_model_server_result.datetime_utc      '2024-11-16 11:04:59' 
_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          8vcx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":201}' 
#
_entry.id    8VCX 
#
_exptl.entry_id    8VCX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          9 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    5 
_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            8VCX 
_cell.length_a            64.651 
_cell.length_b            64.818 
_cell.length_c            255.896 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8VCX 
_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' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_pdbx_struct_assembly.details               author_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,P,Q,R,S 
_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
? 9 J N N 
? 9 K N N 
? 9 L N N 
? 9 M N N 
? 9 N N N 
#
loop_
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
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 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 6 3 1 FUC NAG C1 O1 . O6 HO6 . sing 
3 ? 7 2 1 NAG NAG C1 O1 . O4 HO4 . 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
6 n F NAG 1 F 1 NAG A 201 NAG 
6 n F NAG 2 F 2 NAG A 204 NAG 
6 n F FUC 3 F 3 FUC A 205 FUC 
7 n G NAG 1 G 1 NAG A 202 NAG 
7 n G NAG 2 G 2 NAG A 206 NAG 
7 n H NAG 1 H 1 NAG B 201 NAG 
7 n H NAG 2 H 2 NAG B 204 NAG 
#
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 21 D CYS 23 1_555 A SG CYS 87 D CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 A SG CYS 157 D CYS 174 1_555 B SG CYS 166 E CYS 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf3 B SG CYS 21 E CYS 23 1_555 B SG CYS 89 E CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf4 B SG CYS 140 E CYS 155 1_555 B SG CYS 205 E CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf5 C SG CYS 75 A CYS 72 1_555 E SG CYS 14 C CYS 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf6 C SG CYS 110 A CYS 107 1_555 C SG CYS 166 A CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf7 D SG CYS 15 B CYS 15 1_555 D SG CYS 79 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf8 D SG CYS 117 B CYS 117 1_555 D SG CYS 173 B CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
covale ? covale1 C ND2 ASN 81 A ASN 78 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale2 C ND2 ASN 121 A ASN 118 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale3 D ND2 ASN 19 B ASN 19 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale4 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale5 F O6 NAG . F NAG 1 1_555 F C1 FUC . F FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale6 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale7 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
#
_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 152 n n 
C1 C2 GOL sing 153 n n 
C1 H11 GOL sing 154 n n 
C1 H12 GOL sing 155 n n 
O1 HO1 GOL sing 156 n n 
C2 O2 GOL sing 157 n n 
C2 C3 GOL sing 158 n n 
C2 H2 GOL sing 159 n n 
O2 HO2 GOL sing 160 n n 
C3 O3 GOL sing 161 n n 
C3 H31 GOL sing 162 n n 
C3 H32 GOL sing 163 n n 
O3 HO3 GOL sing 164 n n 
#
_atom_sites.entry_id                     8VCX 
_atom_sites.fract_transf_matrix[1][1]    0.015468 
_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]    0.015428 
_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]    0.003908 
_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
I 8 PO4 D 1 301 1 PO4 PO4 . 
J 9 GOL D 1 302 203 GOL GOL . 
K 9 GOL D 1 303 204 GOL GOL . 
L 9 GOL E 1 301 301 GOL GOL . 
M 9 GOL E 1 302 314 GOL GOL . 
N 9 GOL B 1 201 203 GOL GOL . 
O 10 HOH D 1 401 55 HOH HOH . 
O 10 HOH D 2 402 38 HOH HOH . 
O 10 HOH D 3 403 29 HOH HOH . 
O 10 HOH D 4 404 33 HOH HOH . 
O 10 HOH D 5 405 8 HOH HOH . 
O 10 HOH D 6 406 5 HOH HOH . 
O 10 HOH D 7 407 48 HOH HOH . 
O 10 HOH D 8 408 81 HOH HOH . 
O 10 HOH D 9 409 57 HOH HOH . 
O 10 HOH D 10 410 71 HOH HOH . 
O 10 HOH D 11 411 17 HOH HOH . 
O 10 HOH D 12 412 56 HOH HOH . 
O 10 HOH D 13 413 31 HOH HOH . 
P 10 HOH E 1 401 28 HOH HOH . 
P 10 HOH E 2 402 46 HOH HOH . 
P 10 HOH E 3 403 14 HOH HOH . 
P 10 HOH E 4 404 42 HOH HOH . 
P 10 HOH E 5 405 51 HOH HOH . 
P 10 HOH E 6 406 70 HOH HOH . 
P 10 HOH E 7 407 36 HOH HOH . 
P 10 HOH E 8 408 89 HOH HOH . 
P 10 HOH E 9 409 72 HOH HOH . 
P 10 HOH E 10 410 86 HOH HOH . 
P 10 HOH E 11 411 41 HOH HOH . 
P 10 HOH E 12 412 52 HOH HOH . 
P 10 HOH E 13 413 9 HOH HOH . 
P 10 HOH E 14 414 34 HOH HOH . 
P 10 HOH E 15 415 49 HOH HOH . 
P 10 HOH E 16 416 54 HOH HOH . 
P 10 HOH E 17 417 87 HOH HOH . 
P 10 HOH E 18 418 16 HOH HOH . 
P 10 HOH E 19 419 50 HOH HOH . 
P 10 HOH E 20 420 37 HOH HOH . 
P 10 HOH E 21 421 15 HOH HOH . 
P 10 HOH E 22 422 27 HOH HOH . 
P 10 HOH E 23 423 69 HOH HOH . 
P 10 HOH E 24 424 68 HOH HOH . 
P 10 HOH E 25 425 53 HOH HOH . 
P 10 HOH E 26 426 35 HOH HOH . 
Q 10 HOH A 1 201 21 HOH HOH . 
Q 10 HOH A 2 202 23 HOH HOH . 
Q 10 HOH A 3 203 22 HOH HOH . 
Q 10 HOH A 4 204 73 HOH HOH . 
Q 10 HOH A 5 205 32 HOH HOH . 
Q 10 HOH A 6 206 39 HOH HOH . 
Q 10 HOH A 7 207 24 HOH HOH . 
Q 10 HOH A 8 208 61 HOH HOH . 
Q 10 HOH A 9 209 40 HOH HOH . 
Q 10 HOH A 10 210 59 HOH HOH . 
Q 10 HOH A 11 211 64 HOH HOH . 
Q 10 HOH A 12 212 84 HOH HOH . 
Q 10 HOH A 13 213 60 HOH HOH . 
Q 10 HOH A 14 214 82 HOH HOH . 
Q 10 HOH A 15 215 20 HOH HOH . 
Q 10 HOH A 16 216 65 HOH HOH . 
Q 10 HOH A 17 217 74 HOH HOH . 
Q 10 HOH A 18 218 67 HOH HOH . 
Q 10 HOH A 19 219 66 HOH HOH . 
R 10 HOH B 1 301 10 HOH HOH . 
R 10 HOH B 2 302 30 HOH HOH . 
R 10 HOH B 3 303 3 HOH HOH . 
R 10 HOH B 4 304 18 HOH HOH . 
R 10 HOH B 5 305 79 HOH HOH . 
R 10 HOH B 6 306 11 HOH HOH . 
R 10 HOH B 7 307 25 HOH HOH . 
R 10 HOH B 8 308 58 HOH HOH . 
R 10 HOH B 9 309 47 HOH HOH . 
R 10 HOH B 10 310 77 HOH HOH . 
R 10 HOH B 11 311 80 HOH HOH . 
R 10 HOH B 12 312 76 HOH HOH . 
R 10 HOH B 13 313 75 HOH HOH . 
R 10 HOH B 14 314 26 HOH HOH . 
R 10 HOH B 15 315 78 HOH HOH . 
S 10 HOH C 1 101 85 HOH HOH . 
S 10 HOH C 2 102 88 HOH HOH . 
S 10 HOH C 3 103 13 HOH HOH . 
S 10 HOH C 4 104 12 HOH HOH . 
S 10 HOH C 5 105 62 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 . . . N 9 61.399 207.708 41.378 1 84.48 ? C1 GOL 201 B 1 
HETATM 2 O O1 GOL . . . N 9 62.083 208.416 40.39 1 73.29 ? O1 GOL 201 B 1 
HETATM 3 C C2 GOL . . . N 9 61.859 206.234 41.279 1 74.07 ? C2 GOL 201 B 1 
HETATM 4 O O2 GOL . . . N 9 61.488 205.654 40.074 1 93.54 ? O2 GOL 201 B 1 
HETATM 5 C C3 GOL . . . N 9 61.209 205.533 42.493 1 67.78 ? C3 GOL 201 B 1 
HETATM 6 O O3 GOL . . . N 9 61.521 204.179 42.389 1 76.59 ? O3 GOL 201 B 1 
#
_model_server_stats.io_time_ms              116 
_model_server_stats.parse_time_ms           31 
_model_server_stats.create_model_time_ms    56 
_model_server_stats.query_time_ms           343 
_model_server_stats.encode_time_ms          17 
_model_server_stats.element_count           6 
#