data_5VNB
#
_model_server_result.job_id            iUHYjMePNFDqvhCDhK-YUw 
_model_server_result.datetime_utc      '2024-11-22 21:48:52' 
_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          5vnb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":201}' 
#
_entry.id    5VNB 
#
_exptl.entry_id    5VNB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              62.068 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-ETHANEDIOL 
_entity.pdbx_number_of_molecules    7 
_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            5VNB 
_cell.length_a            70.79 
_cell.length_b            80.305 
_cell.length_c            121.663 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VNB 
_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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,F,G,R 1 1 
B,H,I,J,K,L,M,N,O,P,S 2 1 
C,Q,T 3 1 
D,E,U 4 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 F N N 
? 3 H N N 
? 3 I N N 
? 3 J N N 
? 3 K N N 
? 3 L N N 
? 3 M 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
covale ? covale1 E C THR 2 K THR 22 1_555 E N ALY 3 K ALY 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 E C ALY 3 K ALY 23 1_555 E N ALA 4 K ALA 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale3 E C ARG 6 K ARG 26 1_555 E N ALY 7 K ALY 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale4 E C ALY 7 K ALY 27 1_555 E N SER 8 K SER 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
#
_chem_comp.formula           'C2 H6 O2' 
_chem_comp.formula_weight    62.068 
_chem_comp.id                EDO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,2-ETHANEDIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'ETHYLENE GLYCOL' 
#
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 EDO sing 98 n n 
C1 C2 EDO sing 99 n n 
C1 H11 EDO sing 100 n n 
C1 H12 EDO sing 101 n n 
O1 HO1 EDO sing 102 n n 
C2 O2 EDO sing 103 n n 
C2 H21 EDO sing 104 n n 
C2 H22 EDO sing 105 n n 
O2 HO2 EDO sing 106 n n 
#
_atom_sites.entry_id                     5VNB 
_atom_sites.fract_transf_matrix[1][1]    0.014126 
_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]    0.012453 
_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]    0.008219 
_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 3 EDO A 1 201 1 EDO EDO . 
G 4 SO4 A 1 202 4 SO4 SO4 . 
H 3 EDO B 1 201 2 EDO EDO . 
I 3 EDO B 1 202 3 EDO EDO . 
J 3 EDO B 1 203 4 EDO EDO . 
K 3 EDO B 1 204 5 EDO EDO . 
L 3 EDO B 1 205 6 EDO EDO . 
M 3 EDO B 1 206 7 EDO EDO . 
N 4 SO4 B 1 207 1 SO4 SO4 . 
O 4 SO4 B 1 208 2 SO4 SO4 . 
P 4 SO4 B 1 209 3 SO4 SO4 . 
Q 4 SO4 C 1 201 5 SO4 SO4 . 
R 5 HOH A 1 301 81 HOH HOH . 
R 5 HOH A 2 302 56 HOH HOH . 
R 5 HOH A 3 303 65 HOH HOH . 
R 5 HOH A 4 304 30 HOH HOH . 
R 5 HOH A 5 305 113 HOH HOH . 
R 5 HOH A 6 306 122 HOH HOH . 
R 5 HOH A 7 307 94 HOH HOH . 
R 5 HOH A 8 308 102 HOH HOH . 
R 5 HOH A 9 309 105 HOH HOH . 
R 5 HOH A 10 310 62 HOH HOH . 
R 5 HOH A 11 311 55 HOH HOH . 
R 5 HOH A 12 312 114 HOH HOH . 
R 5 HOH A 13 313 108 HOH HOH . 
R 5 HOH A 14 314 60 HOH HOH . 
R 5 HOH A 15 315 99 HOH HOH . 
R 5 HOH A 16 316 100 HOH HOH . 
R 5 HOH A 17 317 38 HOH HOH . 
R 5 HOH A 18 318 54 HOH HOH . 
R 5 HOH A 19 319 59 HOH HOH . 
R 5 HOH A 20 320 40 HOH HOH . 
R 5 HOH A 21 321 106 HOH HOH . 
R 5 HOH A 22 322 10 HOH HOH . 
R 5 HOH A 23 323 110 HOH HOH . 
R 5 HOH A 24 324 98 HOH HOH . 
R 5 HOH A 25 325 53 HOH HOH . 
R 5 HOH A 26 326 70 HOH HOH . 
R 5 HOH A 27 327 50 HOH HOH . 
R 5 HOH A 28 328 28 HOH HOH . 
R 5 HOH A 29 329 58 HOH HOH . 
R 5 HOH A 30 330 61 HOH HOH . 
R 5 HOH A 31 331 66 HOH HOH . 
R 5 HOH A 32 332 129 HOH HOH . 
R 5 HOH A 33 333 73 HOH HOH . 
R 5 HOH A 34 334 8 HOH HOH . 
R 5 HOH A 35 335 18 HOH HOH . 
R 5 HOH A 36 336 3 HOH HOH . 
R 5 HOH A 37 337 112 HOH HOH . 
R 5 HOH A 38 338 64 HOH HOH . 
R 5 HOH A 39 339 63 HOH HOH . 
R 5 HOH A 40 340 57 HOH HOH . 
R 5 HOH A 41 341 46 HOH HOH . 
R 5 HOH A 42 342 109 HOH HOH . 
R 5 HOH A 43 343 82 HOH HOH . 
R 5 HOH A 44 344 68 HOH HOH . 
R 5 HOH A 45 345 69 HOH HOH . 
R 5 HOH A 46 346 49 HOH HOH . 
R 5 HOH A 47 347 45 HOH HOH . 
R 5 HOH A 48 348 120 HOH HOH . 
R 5 HOH A 49 349 51 HOH HOH . 
R 5 HOH A 50 350 52 HOH HOH . 
S 5 HOH B 1 301 20 HOH HOH . 
S 5 HOH B 2 302 31 HOH HOH . 
S 5 HOH B 3 303 25 HOH HOH . 
S 5 HOH B 4 304 115 HOH HOH . 
S 5 HOH B 5 305 14 HOH HOH . 
S 5 HOH B 6 306 34 HOH HOH . 
S 5 HOH B 7 307 123 HOH HOH . 
S 5 HOH B 8 308 76 HOH HOH . 
S 5 HOH B 9 309 19 HOH HOH . 
S 5 HOH B 10 310 11 HOH HOH . 
S 5 HOH B 11 311 17 HOH HOH . 
S 5 HOH B 12 312 32 HOH HOH . 
S 5 HOH B 13 313 23 HOH HOH . 
S 5 HOH B 14 314 2 HOH HOH . 
S 5 HOH B 15 315 6 HOH HOH . 
S 5 HOH B 16 316 26 HOH HOH . 
S 5 HOH B 17 317 74 HOH HOH . 
S 5 HOH B 18 318 42 HOH HOH . 
S 5 HOH B 19 319 39 HOH HOH . 
S 5 HOH B 20 320 43 HOH HOH . 
S 5 HOH B 21 321 118 HOH HOH . 
S 5 HOH B 22 322 7 HOH HOH . 
S 5 HOH B 23 323 78 HOH HOH . 
S 5 HOH B 24 324 33 HOH HOH . 
S 5 HOH B 25 325 36 HOH HOH . 
S 5 HOH B 26 326 96 HOH HOH . 
S 5 HOH B 27 327 75 HOH HOH . 
S 5 HOH B 28 328 44 HOH HOH . 
S 5 HOH B 29 329 4 HOH HOH . 
S 5 HOH B 30 330 41 HOH HOH . 
S 5 HOH B 31 331 107 HOH HOH . 
S 5 HOH B 32 332 80 HOH HOH . 
S 5 HOH B 33 333 79 HOH HOH . 
T 5 HOH C 1 301 47 HOH HOH . 
T 5 HOH C 2 302 87 HOH HOH . 
T 5 HOH C 3 303 67 HOH HOH . 
T 5 HOH C 4 304 90 HOH HOH . 
T 5 HOH C 5 305 89 HOH HOH . 
T 5 HOH C 6 306 71 HOH HOH . 
T 5 HOH C 7 307 101 HOH HOH . 
T 5 HOH C 8 308 15 HOH HOH . 
T 5 HOH C 9 309 97 HOH HOH . 
T 5 HOH C 10 310 86 HOH HOH . 
T 5 HOH C 11 311 5 HOH HOH . 
T 5 HOH C 12 312 111 HOH HOH . 
T 5 HOH C 13 313 116 HOH HOH . 
T 5 HOH C 14 314 85 HOH HOH . 
T 5 HOH C 15 315 104 HOH HOH . 
T 5 HOH C 16 316 91 HOH HOH . 
T 5 HOH C 17 317 128 HOH HOH . 
T 5 HOH C 18 318 125 HOH HOH . 
T 5 HOH C 19 319 103 HOH HOH . 
T 5 HOH C 20 320 72 HOH HOH . 
T 5 HOH C 21 321 126 HOH HOH . 
T 5 HOH C 22 322 95 HOH HOH . 
T 5 HOH C 23 323 48 HOH HOH . 
T 5 HOH C 24 324 84 HOH HOH . 
T 5 HOH C 25 325 117 HOH HOH . 
T 5 HOH C 26 326 24 HOH HOH . 
T 5 HOH C 27 327 83 HOH HOH . 
T 5 HOH C 28 328 127 HOH HOH . 
T 5 HOH C 29 329 92 HOH HOH . 
T 5 HOH C 30 330 119 HOH HOH . 
T 5 HOH C 31 331 124 HOH HOH . 
T 5 HOH C 32 332 27 HOH HOH . 
T 5 HOH C 33 333 88 HOH HOH . 
U 5 HOH D 1 201 13 HOH HOH . 
U 5 HOH D 2 202 29 HOH HOH . 
U 5 HOH D 3 203 131 HOH HOH . 
U 5 HOH D 4 204 121 HOH HOH . 
U 5 HOH D 5 205 16 HOH HOH . 
U 5 HOH D 6 206 130 HOH HOH . 
U 5 HOH D 7 207 93 HOH HOH . 
U 5 HOH D 8 208 1 HOH HOH . 
U 5 HOH D 9 209 35 HOH HOH . 
U 5 HOH D 10 210 37 HOH HOH . 
U 5 HOH D 11 211 12 HOH HOH . 
U 5 HOH D 12 212 77 HOH HOH . 
U 5 HOH D 13 213 21 HOH HOH . 
U 5 HOH D 14 214 22 HOH HOH . 
U 5 HOH D 15 215 9 HOH HOH . 
U 5 HOH D 16 216 132 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 EDO . . . H 3 -11.768 12.052 -39.19 1 78.45 ? C1 EDO 201 B 1 
HETATM 2 O O1 EDO . . . H 3 -13.005 11.326 -39.084 1 71.81 ? O1 EDO 201 B 1 
HETATM 3 C C2 EDO . . . H 3 -11.943 13.497 -38.72 1 86.01 ? C2 EDO 201 B 1 
HETATM 4 O O2 EDO . . . H 3 -11.642 13.64 -37.308 1 88.07 ? O2 EDO 201 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           39 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           346 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           4 
#