data_5VNW
#
_model_server_result.job_id            gWvoM3zTGCbylzIdziEdUw 
_model_server_result.datetime_utc      '2024-11-08 22:27:46' 
_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          5vnw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":201}' 
#
_entry.id    5VNW 
#
_exptl.entry_id    5VNW 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         96.14 
_cell.angle_beta          104.6 
_cell.angle_gamma         104.02 
_cell.entry_id            5VNW 
_cell.length_a            66.338 
_cell.length_b            72.15 
_cell.length_c            108.513 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VNW 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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
? dimeric 2 author_defined_assembly 1 
? dimeric 2 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,D,E,F,G,H,I,M,P 1 1 
B,C,J,K,L,N,O 2 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
? 3 E N N 
? 3 F N N 
? 3 G N N 
? 3 L 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 53 A CYS 53 1_555 A SG CYS 62 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 A SG CYS 75 A CYS 75 1_555 A SG CYS 91 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf3 A SG CYS 90 A CYS 90 1_555 A SG CYS 101 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 A SG CYS 124 A CYS 124 1_555 A SG CYS 169 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf5 A SG CYS 168 A CYS 168 1_555 A SG CYS 177 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf6 A SG CYS 200 A CYS 200 1_555 A SG CYS 246 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf7 A SG CYS 245 A CYS 245 1_555 A SG CYS 253 A CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf8 A SG CYS 265 A CYS 265 1_555 A SG CYS 279 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf9 A SG CYS 278 A CYS 278 1_555 A SG CYS 289 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf10 A SG CYS 316 A CYS 316 1_555 A SG CYS 361 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf11 A SG CYS 360 A CYS 360 1_555 A SG CYS 369 A CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf12 A SG CYS 392 A CYS 392 1_555 A SG CYS 438 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf13 A SG CYS 437 A CYS 437 1_555 A SG CYS 448 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf14 A SG CYS 461 A CYS 461 1_555 A SG CYS 477 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf15 A SG CYS 476 A CYS 476 1_555 A SG CYS 487 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf16 A SG CYS 514 A CYS 514 1_555 A SG CYS 559 A CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf17 A SG CYS 558 A CYS 558 1_555 A SG CYS 567 A CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf18 B SG CYS 53 B CYS 53 1_555 B SG CYS 62 B CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf19 B SG CYS 75 B CYS 75 1_555 B SG CYS 91 B CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf20 B SG CYS 90 B CYS 90 1_555 B SG CYS 101 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf21 B SG CYS 124 B CYS 124 1_555 B SG CYS 169 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf22 B SG CYS 168 B CYS 168 1_555 B SG CYS 177 B CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf23 B SG CYS 200 B CYS 200 1_555 B SG CYS 246 B CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf24 B SG CYS 245 B CYS 245 1_555 B SG CYS 253 B CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf25 B SG CYS 265 B CYS 265 1_555 B SG CYS 279 B CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf26 B SG CYS 278 B CYS 278 1_555 B SG CYS 289 B CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf27 B SG CYS 316 B CYS 316 1_555 B SG CYS 361 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf28 B SG CYS 360 B CYS 360 1_555 B SG CYS 369 B CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf29 B SG CYS 392 B CYS 392 1_555 B SG CYS 438 B CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf30 B SG CYS 437 B CYS 437 1_555 B SG CYS 448 B CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf31 B SG CYS 461 B CYS 461 1_555 B SG CYS 477 B CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf32 B SG CYS 476 B CYS 476 1_555 B SG CYS 487 B CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf33 B SG CYS 514 B CYS 514 1_555 B SG CYS 559 B CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf34 B SG CYS 558 B CYS 558 1_555 B SG CYS 567 B CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf35 C SG CYS 22 C CYS 22 1_555 C SG CYS 95 C CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf36 D SG CYS 22 D CYS 22 1_555 D SG CYS 95 D CYS 95 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 179 n n 
C1 C2 GOL sing 180 n n 
C1 H11 GOL sing 181 n n 
C1 H12 GOL sing 182 n n 
O1 HO1 GOL sing 183 n n 
C2 O2 GOL sing 184 n n 
C2 C3 GOL sing 185 n n 
C2 H2 GOL sing 186 n n 
O2 HO2 GOL sing 187 n n 
C3 O3 GOL sing 188 n n 
C3 H31 GOL sing 189 n n 
C3 H32 GOL sing 190 n n 
O3 HO3 GOL sing 191 n n 
#
_atom_sites.entry_id                     5VNW 
_atom_sites.fract_transf_matrix[1][1]    0.015074 
_atom_sites.fract_transf_matrix[1][2]    0.003765 
_atom_sites.fract_transf_matrix[1][3]    0.004676 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014286 
_atom_sites.fract_transf_matrix[2][3]    0.002598 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.009679 
_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
E 3 GOL A 1 601 70 GOL GOL . 
F 3 GOL A 1 602 71 GOL GOL . 
G 3 GOL A 1 603 72 GOL GOL . 
H 4 PLM A 1 604 73 PLM PLM . 
I 5 DAO A 1 605 75 DAO DAO . 
J 4 PLM B 1 601 74 PLM PLM . 
K 6 BUA B 1 602 77 BUA BUA . 
L 3 GOL C 1 201 76 GOL GOL . 
M 7 HOH A 1 701 10 HOH HOH . 
M 7 HOH A 2 702 58 HOH HOH . 
M 7 HOH A 3 703 59 HOH HOH . 
M 7 HOH A 4 704 11 HOH HOH . 
M 7 HOH A 5 705 60 HOH HOH . 
M 7 HOH A 6 706 7 HOH HOH . 
M 7 HOH A 7 707 15 HOH HOH . 
M 7 HOH A 8 708 52 HOH HOH . 
M 7 HOH A 9 709 42 HOH HOH . 
M 7 HOH A 10 710 61 HOH HOH . 
M 7 HOH A 11 711 14 HOH HOH . 
M 7 HOH A 12 712 3 HOH HOH . 
M 7 HOH A 13 713 30 HOH HOH . 
M 7 HOH A 14 714 1 HOH HOH . 
M 7 HOH A 15 715 53 HOH HOH . 
M 7 HOH A 16 716 54 HOH HOH . 
M 7 HOH A 17 717 34 HOH HOH . 
M 7 HOH A 18 718 62 HOH HOH . 
M 7 HOH A 19 719 41 HOH HOH . 
M 7 HOH A 20 720 55 HOH HOH . 
M 7 HOH A 21 721 33 HOH HOH . 
M 7 HOH A 22 722 69 HOH HOH . 
M 7 HOH A 23 723 67 HOH HOH . 
M 7 HOH A 24 724 9 HOH HOH . 
M 7 HOH A 25 725 50 HOH HOH . 
M 7 HOH A 26 726 22 HOH HOH . 
M 7 HOH A 27 727 32 HOH HOH . 
M 7 HOH A 28 728 16 HOH HOH . 
M 7 HOH A 29 729 45 HOH HOH . 
M 7 HOH A 30 730 51 HOH HOH . 
M 7 HOH A 31 731 66 HOH HOH . 
M 7 HOH A 32 732 35 HOH HOH . 
N 7 HOH B 1 701 5 HOH HOH . 
N 7 HOH B 2 702 2 HOH HOH . 
N 7 HOH B 3 703 6 HOH HOH . 
N 7 HOH B 4 704 27 HOH HOH . 
N 7 HOH B 5 705 47 HOH HOH . 
N 7 HOH B 6 706 25 HOH HOH . 
N 7 HOH B 7 707 31 HOH HOH . 
N 7 HOH B 8 708 17 HOH HOH . 
N 7 HOH B 9 709 26 HOH HOH . 
N 7 HOH B 10 710 38 HOH HOH . 
N 7 HOH B 11 711 46 HOH HOH . 
N 7 HOH B 12 712 68 HOH HOH . 
N 7 HOH B 13 713 36 HOH HOH . 
N 7 HOH B 14 714 49 HOH HOH . 
N 7 HOH B 15 715 56 HOH HOH . 
N 7 HOH B 16 716 37 HOH HOH . 
N 7 HOH B 17 717 12 HOH HOH . 
N 7 HOH B 18 718 29 HOH HOH . 
N 7 HOH B 19 719 28 HOH HOH . 
O 7 HOH C 1 301 23 HOH HOH . 
O 7 HOH C 2 302 63 HOH HOH . 
O 7 HOH C 3 303 8 HOH HOH . 
O 7 HOH C 4 304 64 HOH HOH . 
O 7 HOH C 5 305 20 HOH HOH . 
O 7 HOH C 6 306 44 HOH HOH . 
O 7 HOH C 7 307 4 HOH HOH . 
O 7 HOH C 8 308 19 HOH HOH . 
O 7 HOH C 9 309 13 HOH HOH . 
O 7 HOH C 10 310 18 HOH HOH . 
O 7 HOH C 11 311 24 HOH HOH . 
O 7 HOH C 12 312 48 HOH HOH . 
O 7 HOH C 13 313 21 HOH HOH . 
P 7 HOH D 1 201 65 HOH HOH . 
P 7 HOH D 2 202 43 HOH HOH . 
P 7 HOH D 3 203 39 HOH HOH . 
P 7 HOH D 4 204 57 HOH HOH . 
P 7 HOH D 5 205 40 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 3 -74.788 17.092 45.565 1 127.93 ? C1 GOL 201 C 1 
HETATM 2 O O1 GOL . . . L 3 -73.93 16.822 44.45 1 131.65 ? O1 GOL 201 C 1 
HETATM 3 C C2 GOL . . . L 3 -74.599 16.014 46.626 1 128.49 ? C2 GOL 201 C 1 
HETATM 4 O O2 GOL . . . L 3 -74.273 14.776 45.984 1 126.4 ? O2 GOL 201 C 1 
HETATM 5 C C3 GOL . . . L 3 -73.464 16.405 47.564 1 124.44 ? C3 GOL 201 C 1 
HETATM 6 O O3 GOL . . . L 3 -73.399 15.477 48.653 1 121.81 ? O3 GOL 201 C 1 
#
_model_server_stats.io_time_ms              45 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           338 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           6 
#