data_6VM7
#
_model_server_result.job_id            0n-nrVCTchKuzUmusl2XlQ 
_model_server_result.datetime_utc      '2024-11-04 23:16:01' 
_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          6vm7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":301}' 
#
_entry.id    6VM7 
#
_exptl.entry_id    6VM7 
_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    3 
_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            6VM7 
_cell.length_a            68.118 
_cell.length_b            94.403 
_cell.length_c            143.849 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VM7 
_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        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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
C,D,E,F,G,H,K,L,M 1 1 
A,B,I,J 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' 4_545 x+1/2,-y-1/2,-z 1 0 0 0 -1 0 0 0 -1 34.059 -47.2015 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 
#
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 24 D CYS 24 1_555 A SG CYS 92 D CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 A SG CYS 137 D CYS 137 1_555 A SG CYS 187 D CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf3 A SG CYS 162 D CYS 162 1_555 B SG CYS 170 E CYS 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf4 B SG CYS 22 E CYS 22 1_555 B SG CYS 90 E CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf5 B SG CYS 144 E CYS 144 1_555 B SG CYS 209 E CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf6 C SG CYS 101 A CYS 101 1_555 C SG CYS 164 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf7 C SG CYS 203 A CYS 203 1_555 C SG CYS 259 A CYS 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf8 D SG CYS 26 B CYS 26 1_555 D SG CYS 81 B CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
#
_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                     6VM7 
_atom_sites.fract_transf_matrix[1][1]    0.01468 
_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]    0.010593 
_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]    0.006952 
_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 A 1 301 1 GOL GOL . 
G 6 GOL B 1 201 3 GOL GOL . 
H 6 GOL B 1 202 4 GOL GOL . 
I 7 HOH D 1 301 16 HOH HOH . 
I 7 HOH D 2 302 154 HOH HOH . 
I 7 HOH D 3 303 30 HOH HOH . 
I 7 HOH D 4 304 46 HOH HOH . 
I 7 HOH D 5 305 35 HOH HOH . 
I 7 HOH D 6 306 29 HOH HOH . 
I 7 HOH D 7 307 9 HOH HOH . 
I 7 HOH D 8 308 39 HOH HOH . 
I 7 HOH D 9 309 44 HOH HOH . 
I 7 HOH D 10 310 68 HOH HOH . 
I 7 HOH D 11 311 61 HOH HOH . 
I 7 HOH D 12 312 11 HOH HOH . 
I 7 HOH D 13 313 157 HOH HOH . 
I 7 HOH D 14 314 84 HOH HOH . 
I 7 HOH D 15 315 50 HOH HOH . 
I 7 HOH D 16 316 76 HOH HOH . 
I 7 HOH D 17 317 159 HOH HOH . 
I 7 HOH D 18 318 155 HOH HOH . 
I 7 HOH D 19 319 156 HOH HOH . 
J 7 HOH E 1 301 145 HOH HOH . 
J 7 HOH E 2 302 158 HOH HOH . 
J 7 HOH E 3 303 162 HOH HOH . 
J 7 HOH E 4 304 5 HOH HOH . 
J 7 HOH E 5 305 33 HOH HOH . 
J 7 HOH E 6 306 153 HOH HOH . 
J 7 HOH E 7 307 103 HOH HOH . 
J 7 HOH E 8 308 59 HOH HOH . 
J 7 HOH E 9 309 161 HOH HOH . 
J 7 HOH E 10 310 28 HOH HOH . 
J 7 HOH E 11 311 85 HOH HOH . 
J 7 HOH E 12 312 107 HOH HOH . 
J 7 HOH E 13 313 62 HOH HOH . 
J 7 HOH E 14 314 74 HOH HOH . 
J 7 HOH E 15 315 19 HOH HOH . 
J 7 HOH E 16 316 40 HOH HOH . 
J 7 HOH E 17 317 63 HOH HOH . 
J 7 HOH E 18 318 12 HOH HOH . 
J 7 HOH E 19 319 31 HOH HOH . 
J 7 HOH E 20 320 70 HOH HOH . 
J 7 HOH E 21 321 135 HOH HOH . 
J 7 HOH E 22 322 56 HOH HOH . 
J 7 HOH E 23 323 102 HOH HOH . 
J 7 HOH E 24 324 1 HOH HOH . 
J 7 HOH E 25 325 7 HOH HOH . 
J 7 HOH E 26 326 72 HOH HOH . 
J 7 HOH E 27 327 53 HOH HOH . 
J 7 HOH E 28 328 15 HOH HOH . 
J 7 HOH E 29 329 160 HOH HOH . 
K 7 HOH A 1 401 113 HOH HOH . 
K 7 HOH A 2 402 131 HOH HOH . 
K 7 HOH A 3 403 2 HOH HOH . 
K 7 HOH A 4 404 4 HOH HOH . 
K 7 HOH A 5 405 66 HOH HOH . 
K 7 HOH A 6 406 60 HOH HOH . 
K 7 HOH A 7 407 173 HOH HOH . 
K 7 HOH A 8 408 147 HOH HOH . 
K 7 HOH A 9 409 21 HOH HOH . 
K 7 HOH A 10 410 43 HOH HOH . 
K 7 HOH A 11 411 32 HOH HOH . 
K 7 HOH A 12 412 86 HOH HOH . 
K 7 HOH A 13 413 73 HOH HOH . 
K 7 HOH A 14 414 24 HOH HOH . 
K 7 HOH A 15 415 104 HOH HOH . 
K 7 HOH A 16 416 112 HOH HOH . 
K 7 HOH A 17 417 20 HOH HOH . 
K 7 HOH A 18 418 94 HOH HOH . 
K 7 HOH A 19 419 88 HOH HOH . 
K 7 HOH A 20 420 126 HOH HOH . 
K 7 HOH A 21 421 3 HOH HOH . 
K 7 HOH A 22 422 105 HOH HOH . 
K 7 HOH A 23 423 169 HOH HOH . 
K 7 HOH A 24 424 14 HOH HOH . 
K 7 HOH A 25 425 48 HOH HOH . 
K 7 HOH A 26 426 34 HOH HOH . 
K 7 HOH A 27 427 51 HOH HOH . 
K 7 HOH A 28 428 22 HOH HOH . 
K 7 HOH A 29 429 95 HOH HOH . 
K 7 HOH A 30 430 71 HOH HOH . 
K 7 HOH A 31 431 132 HOH HOH . 
K 7 HOH A 32 432 164 HOH HOH . 
K 7 HOH A 33 433 171 HOH HOH . 
K 7 HOH A 34 434 168 HOH HOH . 
K 7 HOH A 35 435 172 HOH HOH . 
K 7 HOH A 36 436 170 HOH HOH . 
K 7 HOH A 37 437 176 HOH HOH . 
K 7 HOH A 38 438 166 HOH HOH . 
K 7 HOH A 39 439 163 HOH HOH . 
K 7 HOH A 40 440 165 HOH HOH . 
K 7 HOH A 41 441 167 HOH HOH . 
K 7 HOH A 42 442 133 HOH HOH . 
L 7 HOH B 1 301 10 HOH HOH . 
L 7 HOH B 2 302 45 HOH HOH . 
L 7 HOH B 3 303 42 HOH HOH . 
L 7 HOH B 4 304 13 HOH HOH . 
L 7 HOH B 5 305 98 HOH HOH . 
L 7 HOH B 6 306 82 HOH HOH . 
L 7 HOH B 7 307 119 HOH HOH . 
L 7 HOH B 8 308 175 HOH HOH . 
L 7 HOH B 9 309 174 HOH HOH . 
M 7 HOH C 1 101 8 HOH HOH . 
M 7 HOH C 2 102 37 HOH HOH . 
M 7 HOH C 3 103 149 HOH HOH . 
M 7 HOH C 4 104 17 HOH HOH . 
M 7 HOH C 5 105 23 HOH HOH . 
M 7 HOH C 6 106 47 HOH HOH . 
M 7 HOH C 7 107 150 HOH HOH . 
M 7 HOH C 8 108 114 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 . . . F 6 -6.157 -18.076 -1.261 1 63.51 ? C1 GOL 301 A 1 
HETATM 2 O O1 GOL . . . F 6 -5.385 -17.231 -0.45 1 63.53 ? O1 GOL 301 A 1 
HETATM 3 C C2 GOL . . . F 6 -7.018 -17.238 -2.206 1 63.09 ? C2 GOL 301 A 1 
HETATM 4 O O2 GOL . . . F 6 -6.209 -16.653 -3.19 1 63.14 ? O2 GOL 301 A 1 
HETATM 5 C C3 GOL . . . F 6 -8.064 -18.129 -2.872 1 61.58 ? C3 GOL 301 A 1 
HETATM 6 O O3 GOL . . . F 6 -8.996 -18.56 -1.919 1 60.32 ? O3 GOL 301 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           245 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#