data_8CMD
#
_model_server_result.job_id            8lb6UmITET8mLMSFetsccQ 
_model_server_result.datetime_utc      '2025-07-18 17:19:48' 
_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          8cmd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":201}' 
#
_entry.id    8CMD 
#
_exptl.entry_id    8CMD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              62.068 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-ETHANEDIOL 
_entity.pdbx_number_of_molecules    10 
_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            8CMD 
_cell.length_a            113.023 
_cell.length_b            156.12 
_cell.length_c            164.852 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8CMD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    'C 2c 2' 
_symmetry.space_group_name_H-M     'C 2 2 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
? trimeric 3 author_defined_assembly 1 
? trimeric 3 author_defined_assembly 2 
? trimeric 3 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,J,K,L,M,N,T,U,V 1 1 
D,E,F,O,P,Q,R,W,X 2 1 
G,H,I,S,Y,Z,AA 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
? 4 J N N 
? 4 K N N 
? 4 L N N 
? 4 M N N 
? 4 N N N 
? 4 O N N 
? 4 P N N 
? 4 Q N N 
? 4 R N N 
? 4 S 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 108 A CYS 107 1_555 A SG CYS 164 A CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf2 B SG CYS 19 B CYS 15 1_555 B SG CYS 83 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf3 B SG CYS 121 B CYS 117 1_555 B SG CYS 177 B CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 D SG CYS 108 D CYS 107 1_555 D SG CYS 164 D CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf5 E SG CYS 19 E CYS 15 1_555 E SG CYS 83 E CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
disulf ? disulf6 E SG CYS 121 E CYS 117 1_555 E SG CYS 177 E CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf7 G SG CYS 108 G CYS 107 1_555 G SG CYS 164 G CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf8 H SG CYS 19 H CYS 15 1_555 H SG CYS 83 H CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf9 H SG CYS 121 H CYS 117 1_555 H SG CYS 177 H CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
#
_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 83 n n 
C1 C2 EDO sing 84 n n 
C1 H11 EDO sing 85 n n 
C1 H12 EDO sing 86 n n 
O1 HO1 EDO sing 87 n n 
C2 O2 EDO sing 88 n n 
C2 H21 EDO sing 89 n n 
C2 H22 EDO sing 90 n n 
O2 HO2 EDO sing 91 n n 
#
_atom_sites.entry_id                     8CMD 
_atom_sites.fract_transf_matrix[1][1]    0.008848 
_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]    0.006405 
_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]    0.006066 
_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
J 4 EDO A 1 201 4 EDO EDO . 
K 4 EDO A 1 202 5 EDO EDO . 
L 4 EDO B 1 201 2 EDO EDO . 
M 4 EDO B 1 202 6 EDO EDO . 
N 4 EDO B 1 203 10 EDO EDO . 
O 4 EDO E 1 201 1 EDO EDO . 
P 4 EDO E 1 202 7 EDO EDO . 
Q 4 EDO E 1 203 8 EDO EDO . 
R 4 EDO E 1 204 9 EDO EDO . 
S 4 EDO G 1 201 3 EDO EDO . 
T 5 HOH A 1 301 108 HOH HOH . 
T 5 HOH A 2 302 13 HOH HOH . 
T 5 HOH A 3 303 43 HOH HOH . 
T 5 HOH A 4 304 153 HOH HOH . 
T 5 HOH A 5 305 6 HOH HOH . 
T 5 HOH A 6 306 161 HOH HOH . 
T 5 HOH A 7 307 157 HOH HOH . 
T 5 HOH A 8 308 175 HOH HOH . 
T 5 HOH A 9 309 119 HOH HOH . 
T 5 HOH A 10 310 109 HOH HOH . 
T 5 HOH A 11 311 123 HOH HOH . 
T 5 HOH A 12 312 12 HOH HOH . 
T 5 HOH A 13 313 80 HOH HOH . 
T 5 HOH A 14 314 27 HOH HOH . 
T 5 HOH A 15 315 167 HOH HOH . 
T 5 HOH A 16 316 74 HOH HOH . 
T 5 HOH A 17 317 42 HOH HOH . 
T 5 HOH A 18 318 19 HOH HOH . 
T 5 HOH A 19 319 21 HOH HOH . 
T 5 HOH A 20 320 136 HOH HOH . 
T 5 HOH A 21 321 116 HOH HOH . 
T 5 HOH A 22 322 155 HOH HOH . 
T 5 HOH A 23 323 81 HOH HOH . 
T 5 HOH A 24 324 146 HOH HOH . 
T 5 HOH A 25 325 137 HOH HOH . 
T 5 HOH A 26 326 65 HOH HOH . 
T 5 HOH A 27 327 154 HOH HOH . 
T 5 HOH A 28 328 156 HOH HOH . 
U 5 HOH B 1 301 121 HOH HOH . 
U 5 HOH B 2 302 50 HOH HOH . 
U 5 HOH B 3 303 4 HOH HOH . 
U 5 HOH B 4 304 63 HOH HOH . 
U 5 HOH B 5 305 78 HOH HOH . 
U 5 HOH B 6 306 143 HOH HOH . 
U 5 HOH B 7 307 117 HOH HOH . 
U 5 HOH B 8 308 98 HOH HOH . 
U 5 HOH B 9 309 120 HOH HOH . 
U 5 HOH B 10 310 5 HOH HOH . 
U 5 HOH B 11 311 76 HOH HOH . 
U 5 HOH B 12 312 53 HOH HOH . 
U 5 HOH B 13 313 134 HOH HOH . 
U 5 HOH B 14 314 15 HOH HOH . 
U 5 HOH B 15 315 139 HOH HOH . 
U 5 HOH B 16 316 68 HOH HOH . 
U 5 HOH B 17 317 36 HOH HOH . 
U 5 HOH B 18 318 58 HOH HOH . 
U 5 HOH B 19 319 44 HOH HOH . 
U 5 HOH B 20 320 55 HOH HOH . 
U 5 HOH B 21 321 89 HOH HOH . 
U 5 HOH B 22 322 102 HOH HOH . 
U 5 HOH B 23 323 69 HOH HOH . 
U 5 HOH B 24 324 147 HOH HOH . 
V 5 HOH C 1 101 82 HOH HOH . 
V 5 HOH C 2 102 93 HOH HOH . 
V 5 HOH C 3 103 149 HOH HOH . 
W 5 HOH D 1 201 140 HOH HOH . 
W 5 HOH D 2 202 7 HOH HOH . 
W 5 HOH D 3 203 66 HOH HOH . 
W 5 HOH D 4 204 72 HOH HOH . 
W 5 HOH D 5 205 77 HOH HOH . 
W 5 HOH D 6 206 115 HOH HOH . 
W 5 HOH D 7 207 1 HOH HOH . 
W 5 HOH D 8 208 60 HOH HOH . 
W 5 HOH D 9 209 18 HOH HOH . 
W 5 HOH D 10 210 126 HOH HOH . 
W 5 HOH D 11 211 35 HOH HOH . 
W 5 HOH D 12 212 9 HOH HOH . 
W 5 HOH D 13 213 104 HOH HOH . 
W 5 HOH D 14 214 64 HOH HOH . 
W 5 HOH D 15 215 2 HOH HOH . 
W 5 HOH D 16 216 37 HOH HOH . 
W 5 HOH D 17 217 112 HOH HOH . 
W 5 HOH D 18 218 75 HOH HOH . 
W 5 HOH D 19 219 24 HOH HOH . 
W 5 HOH D 20 220 91 HOH HOH . 
W 5 HOH D 21 221 41 HOH HOH . 
W 5 HOH D 22 222 92 HOH HOH . 
W 5 HOH D 23 223 128 HOH HOH . 
W 5 HOH D 24 224 59 HOH HOH . 
W 5 HOH D 25 225 164 HOH HOH . 
W 5 HOH D 26 226 47 HOH HOH . 
W 5 HOH D 27 227 85 HOH HOH . 
W 5 HOH D 28 228 182 HOH HOH . 
W 5 HOH D 29 229 158 HOH HOH . 
W 5 HOH D 30 230 90 HOH HOH . 
X 5 HOH E 1 301 20 HOH HOH . 
X 5 HOH E 2 302 97 HOH HOH . 
X 5 HOH E 3 303 145 HOH HOH . 
X 5 HOH E 4 304 83 HOH HOH . 
X 5 HOH E 5 305 181 HOH HOH . 
X 5 HOH E 6 306 51 HOH HOH . 
X 5 HOH E 7 307 25 HOH HOH . 
X 5 HOH E 8 308 8 HOH HOH . 
X 5 HOH E 9 309 48 HOH HOH . 
X 5 HOH E 10 310 99 HOH HOH . 
X 5 HOH E 11 311 86 HOH HOH . 
X 5 HOH E 12 312 40 HOH HOH . 
X 5 HOH E 13 313 56 HOH HOH . 
X 5 HOH E 14 314 31 HOH HOH . 
X 5 HOH E 15 315 23 HOH HOH . 
X 5 HOH E 16 316 34 HOH HOH . 
X 5 HOH E 17 317 30 HOH HOH . 
X 5 HOH E 18 318 132 HOH HOH . 
X 5 HOH E 19 319 45 HOH HOH . 
X 5 HOH E 20 320 142 HOH HOH . 
X 5 HOH E 21 321 61 HOH HOH . 
X 5 HOH E 22 322 183 HOH HOH . 
Y 5 HOH G 1 301 73 HOH HOH . 
Y 5 HOH G 2 302 152 HOH HOH . 
Y 5 HOH G 3 303 171 HOH HOH . 
Y 5 HOH G 4 304 163 HOH HOH . 
Y 5 HOH G 5 305 176 HOH HOH . 
Y 5 HOH G 6 306 46 HOH HOH . 
Y 5 HOH G 7 307 168 HOH HOH . 
Y 5 HOH G 8 308 11 HOH HOH . 
Y 5 HOH G 9 309 124 HOH HOH . 
Y 5 HOH G 10 310 122 HOH HOH . 
Y 5 HOH G 11 311 62 HOH HOH . 
Y 5 HOH G 12 312 118 HOH HOH . 
Y 5 HOH G 13 313 57 HOH HOH . 
Y 5 HOH G 14 314 38 HOH HOH . 
Y 5 HOH G 15 315 103 HOH HOH . 
Y 5 HOH G 16 316 22 HOH HOH . 
Y 5 HOH G 17 317 26 HOH HOH . 
Y 5 HOH G 18 318 87 HOH HOH . 
Y 5 HOH G 19 319 88 HOH HOH . 
Y 5 HOH G 20 320 17 HOH HOH . 
Y 5 HOH G 21 321 39 HOH HOH . 
Y 5 HOH G 22 322 16 HOH HOH . 
Y 5 HOH G 23 323 29 HOH HOH . 
Y 5 HOH G 24 324 107 HOH HOH . 
Y 5 HOH G 25 325 96 HOH HOH . 
Y 5 HOH G 26 326 95 HOH HOH . 
Y 5 HOH G 27 327 148 HOH HOH . 
Y 5 HOH G 28 328 67 HOH HOH . 
Y 5 HOH G 29 329 70 HOH HOH . 
Y 5 HOH G 30 330 170 HOH HOH . 
Y 5 HOH G 31 331 127 HOH HOH . 
Y 5 HOH G 32 332 113 HOH HOH . 
Z 5 HOH H 1 201 105 HOH HOH . 
Z 5 HOH H 2 202 32 HOH HOH . 
Z 5 HOH H 3 203 125 HOH HOH . 
Z 5 HOH H 4 204 10 HOH HOH . 
Z 5 HOH H 5 205 79 HOH HOH . 
Z 5 HOH H 6 206 14 HOH HOH . 
Z 5 HOH H 7 207 100 HOH HOH . 
Z 5 HOH H 8 208 28 HOH HOH . 
Z 5 HOH H 9 209 3 HOH HOH . 
Z 5 HOH H 10 210 162 HOH HOH . 
Z 5 HOH H 11 211 180 HOH HOH . 
Z 5 HOH H 12 212 135 HOH HOH . 
Z 5 HOH H 13 213 94 HOH HOH . 
Z 5 HOH H 14 214 71 HOH HOH . 
Z 5 HOH H 15 215 49 HOH HOH . 
Z 5 HOH H 16 216 150 HOH HOH . 
Z 5 HOH H 17 217 52 HOH HOH . 
Z 5 HOH H 18 218 84 HOH HOH . 
Z 5 HOH H 19 219 129 HOH HOH . 
Z 5 HOH H 20 220 144 HOH HOH . 
Z 5 HOH H 21 221 138 HOH HOH . 
Z 5 HOH H 22 222 173 HOH HOH . 
Z 5 HOH H 23 223 106 HOH HOH . 
Z 5 HOH H 24 224 141 HOH HOH . 
AA 5 HOH I 1 101 178 HOH HOH . 
AA 5 HOH I 2 102 101 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 . . . O 4 -29.893 -13.141 45.994 1 55.87 ? C1 EDO 201 E 1 
HETATM 2 O O1 EDO . . . O 4 -28.811 -12.376 46.535 1 47.13 ? O1 EDO 201 E 1 
HETATM 3 C C2 EDO . . . O 4 -29.833 -13.107 44.469 1 57.88 ? C2 EDO 201 E 1 
HETATM 4 O O2 EDO . . . O 4 -28.58 -13.642 44.021 1 54.98 ? O2 EDO 201 E 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           245 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           4 
#