data_3DNM
#
_model_server_result.job_id            i1N_OrECmrdytTgP8aPrtg 
_model_server_result.datetime_utc      '2025-03-06 03:33:52' 
_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          3dnm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":325}' 
#
_entry.id    3DNM 
#
_exptl.entry_id    3DNM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              78.133 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            BETA-MERCAPTOETHANOL 
_entity.pdbx_number_of_molecules    4 
_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            3DNM 
_cell.length_a            117.321 
_cell.length_b            126.828 
_cell.length_c            233.393 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DNM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        24 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
PISA tetrameric 4 software_defined_assembly 5 
PISA tetrameric 4 software_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G,W 1 1 
B,H,I,J,K,L,M,N,O,X 2 1 
C,P,Q,R,Y 3 1 
D,S,T,U,V,Z 4 1 
D,S,T,U,V,Z 5 1,2 
A,E,F,G,W 5 3,4 
B,C,H,I,J,K,L,M,N,O,P,Q,R,X,Y 6 1,5 
#
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' 6_565 -x,-y+3/2,z -1 0 0 0 -1 0 0 0 1 0 190.242 0 
3 'crystal symmetry operation' 2_564 -x+1/2,-y+1,z-1/2 -1 0 0 0 -1 0 0 0 1 58.6605 126.828 -116.6965 
4 'crystal symmetry operation' 5_454 x-1/2,y+1/2,z-1/2 1 0 0 0 1 0 0 0 1 -58.6605 63.414 -116.6965 
5 'crystal symmetry operation' 6_555 -x,-y+1/2,z -1 0 0 0 -1 0 0 0 1 0 63.414 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 H N N 
? 2 P N N 
? 2 S N N 
#
_chem_comp.formula           'C2 H6 O S' 
_chem_comp.formula_weight    78.133 
_chem_comp.id                BME 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              BETA-MERCAPTOETHANOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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 C2 BME sing 70 n n 
C1 O1 BME sing 71 n n 
C1 H11 BME sing 72 n n 
C1 H12 BME sing 73 n n 
C2 S2 BME sing 74 n n 
C2 H21 BME sing 75 n n 
C2 H22 BME sing 76 n n 
O1 HO1 BME sing 77 n n 
S2 HS2 BME sing 78 n n 
#
_atom_sites.entry_id                     3DNM 
_atom_sites.fract_transf_matrix[1][1]    0.008524 
_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]    0.007885 
_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]    0.004285 
_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 2 BME A 1 325 1 BME BME . 
F 3 SO4 A 1 323 1 SO4 SO4 . 
G 3 SO4 A 1 324 6 SO4 SO4 . 
H 2 BME B 1 330 2 BME BME . 
I 3 SO4 B 1 323 2 SO4 SO4 . 
J 3 SO4 B 1 324 5 SO4 SO4 . 
K 3 SO4 B 1 325 7 SO4 SO4 . 
L 3 SO4 B 1 326 9 SO4 SO4 . 
M 3 SO4 B 1 327 10 SO4 SO4 . 
N 3 SO4 B 1 328 12 SO4 SO4 . 
O 3 SO4 B 1 329 13 SO4 SO4 . 
P 2 BME C 1 325 3 BME BME . 
Q 3 SO4 C 1 323 3 SO4 SO4 . 
R 3 SO4 C 1 324 16 SO4 SO4 . 
S 2 BME D 1 326 4 BME BME . 
T 3 SO4 D 1 323 4 SO4 SO4 . 
U 3 SO4 D 1 324 14 SO4 SO4 . 
V 3 SO4 D 1 325 15 SO4 SO4 . 
W 4 HOH A 1 326 2 HOH TIP . 
W 4 HOH A 2 327 3 HOH TIP . 
W 4 HOH A 3 328 7 HOH TIP . 
W 4 HOH A 4 329 8 HOH TIP . 
W 4 HOH A 5 330 14 HOH TIP . 
W 4 HOH A 6 331 18 HOH TIP . 
W 4 HOH A 7 332 20 HOH TIP . 
W 4 HOH A 8 333 24 HOH TIP . 
W 4 HOH A 9 334 26 HOH TIP . 
W 4 HOH A 10 335 28 HOH TIP . 
W 4 HOH A 11 336 30 HOH TIP . 
W 4 HOH A 12 337 32 HOH TIP . 
W 4 HOH A 13 338 37 HOH TIP . 
W 4 HOH A 14 339 38 HOH TIP . 
W 4 HOH A 15 340 44 HOH TIP . 
W 4 HOH A 16 341 45 HOH TIP . 
W 4 HOH A 17 342 46 HOH TIP . 
W 4 HOH A 18 343 48 HOH TIP . 
W 4 HOH A 19 344 50 HOH TIP . 
W 4 HOH A 20 345 55 HOH TIP . 
W 4 HOH A 21 346 58 HOH TIP . 
W 4 HOH A 22 347 63 HOH TIP . 
W 4 HOH A 23 348 64 HOH TIP . 
W 4 HOH A 24 349 67 HOH TIP . 
W 4 HOH A 25 350 75 HOH TIP . 
W 4 HOH A 26 351 77 HOH TIP . 
W 4 HOH A 27 352 80 HOH TIP . 
W 4 HOH A 28 353 81 HOH TIP . 
W 4 HOH A 29 354 83 HOH TIP . 
W 4 HOH A 30 355 84 HOH TIP . 
W 4 HOH A 31 356 86 HOH TIP . 
W 4 HOH A 32 357 90 HOH TIP . 
W 4 HOH A 33 358 91 HOH TIP . 
W 4 HOH A 34 359 95 HOH TIP . 
W 4 HOH A 35 360 97 HOH TIP . 
W 4 HOH A 36 361 101 HOH TIP . 
W 4 HOH A 37 362 104 HOH TIP . 
W 4 HOH A 38 363 106 HOH TIP . 
W 4 HOH A 39 364 109 HOH TIP . 
W 4 HOH A 40 365 113 HOH TIP . 
W 4 HOH A 41 366 118 HOH TIP . 
W 4 HOH A 42 367 119 HOH TIP . 
W 4 HOH A 43 368 125 HOH TIP . 
W 4 HOH A 44 369 132 HOH TIP . 
W 4 HOH A 45 370 137 HOH TIP . 
W 4 HOH A 46 371 138 HOH TIP . 
W 4 HOH A 47 372 145 HOH TIP . 
W 4 HOH A 48 373 147 HOH TIP . 
W 4 HOH A 49 374 149 HOH TIP . 
W 4 HOH A 50 375 168 HOH TIP . 
W 4 HOH A 51 376 176 HOH TIP . 
W 4 HOH A 52 377 177 HOH TIP . 
W 4 HOH A 53 378 178 HOH TIP . 
W 4 HOH A 54 379 179 HOH TIP . 
W 4 HOH A 55 380 180 HOH TIP . 
W 4 HOH A 56 381 181 HOH TIP . 
W 4 HOH A 57 382 182 HOH TIP . 
W 4 HOH A 58 383 183 HOH TIP . 
W 4 HOH A 59 384 184 HOH TIP . 
W 4 HOH A 60 385 185 HOH TIP . 
W 4 HOH A 61 386 186 HOH TIP . 
W 4 HOH A 62 387 187 HOH TIP . 
W 4 HOH A 63 388 188 HOH TIP . 
X 4 HOH B 1 331 1 HOH TIP . 
X 4 HOH B 2 332 11 HOH TIP . 
X 4 HOH B 3 333 15 HOH TIP . 
X 4 HOH B 4 334 16 HOH TIP . 
X 4 HOH B 5 335 17 HOH TIP . 
X 4 HOH B 6 336 19 HOH TIP . 
X 4 HOH B 7 337 21 HOH TIP . 
X 4 HOH B 8 338 25 HOH TIP . 
X 4 HOH B 9 339 31 HOH TIP . 
X 4 HOH B 10 340 35 HOH TIP . 
X 4 HOH B 11 341 36 HOH TIP . 
X 4 HOH B 12 342 39 HOH TIP . 
X 4 HOH B 13 343 41 HOH TIP . 
X 4 HOH B 14 344 43 HOH TIP . 
X 4 HOH B 15 345 54 HOH TIP . 
X 4 HOH B 16 346 56 HOH TIP . 
X 4 HOH B 17 347 61 HOH TIP . 
X 4 HOH B 18 348 62 HOH TIP . 
X 4 HOH B 19 349 73 HOH TIP . 
X 4 HOH B 20 350 78 HOH TIP . 
X 4 HOH B 21 351 79 HOH TIP . 
X 4 HOH B 22 352 92 HOH TIP . 
X 4 HOH B 23 353 98 HOH TIP . 
X 4 HOH B 24 354 102 HOH TIP . 
X 4 HOH B 25 355 103 HOH TIP . 
X 4 HOH B 26 356 108 HOH TIP . 
X 4 HOH B 27 357 110 HOH TIP . 
X 4 HOH B 28 358 112 HOH TIP . 
X 4 HOH B 29 359 115 HOH TIP . 
X 4 HOH B 30 360 116 HOH TIP . 
X 4 HOH B 31 361 117 HOH TIP . 
X 4 HOH B 32 362 122 HOH TIP . 
X 4 HOH B 33 363 130 HOH TIP . 
X 4 HOH B 34 364 135 HOH TIP . 
X 4 HOH B 35 365 136 HOH TIP . 
X 4 HOH B 36 366 139 HOH TIP . 
X 4 HOH B 37 367 140 HOH TIP . 
X 4 HOH B 38 368 142 HOH TIP . 
X 4 HOH B 39 369 146 HOH TIP . 
X 4 HOH B 40 370 148 HOH TIP . 
X 4 HOH B 41 371 150 HOH TIP . 
X 4 HOH B 42 372 161 HOH TIP . 
X 4 HOH B 43 373 164 HOH TIP . 
X 4 HOH B 44 374 167 HOH TIP . 
X 4 HOH B 45 375 170 HOH TIP . 
X 4 HOH B 46 376 174 HOH TIP . 
X 4 HOH B 47 377 189 HOH TIP . 
X 4 HOH B 48 378 190 HOH TIP . 
X 4 HOH B 49 379 191 HOH TIP . 
X 4 HOH B 50 380 192 HOH TIP . 
X 4 HOH B 51 381 193 HOH TIP . 
X 4 HOH B 52 382 194 HOH TIP . 
X 4 HOH B 53 383 195 HOH TIP . 
X 4 HOH B 54 384 196 HOH TIP . 
X 4 HOH B 55 385 206 HOH TIP . 
X 4 HOH B 56 386 51 HOH TIP . 
Y 4 HOH C 1 326 99 HOH TIP . 
Y 4 HOH C 2 327 4 HOH TIP . 
Y 4 HOH C 3 328 5 HOH TIP . 
Y 4 HOH C 4 329 9 HOH TIP . 
Y 4 HOH C 5 330 10 HOH TIP . 
Y 4 HOH C 6 331 13 HOH TIP . 
Y 4 HOH C 7 332 22 HOH TIP . 
Y 4 HOH C 8 333 23 HOH TIP . 
Y 4 HOH C 9 334 33 HOH TIP . 
Y 4 HOH C 10 335 34 HOH TIP . 
Y 4 HOH C 11 336 40 HOH TIP . 
Y 4 HOH C 12 337 42 HOH TIP . 
Y 4 HOH C 13 338 52 HOH TIP . 
Y 4 HOH C 14 339 53 HOH TIP . 
Y 4 HOH C 15 340 59 HOH TIP . 
Y 4 HOH C 16 341 68 HOH TIP . 
Y 4 HOH C 17 342 69 HOH TIP . 
Y 4 HOH C 18 343 72 HOH TIP . 
Y 4 HOH C 19 344 74 HOH TIP . 
Y 4 HOH C 20 345 88 HOH TIP . 
Y 4 HOH C 21 346 93 HOH TIP . 
Y 4 HOH C 22 347 100 HOH TIP . 
Y 4 HOH C 23 348 105 HOH TIP . 
Y 4 HOH C 24 349 120 HOH TIP . 
Y 4 HOH C 25 350 121 HOH TIP . 
Y 4 HOH C 26 351 123 HOH TIP . 
Y 4 HOH C 27 352 126 HOH TIP . 
Y 4 HOH C 28 353 127 HOH TIP . 
Y 4 HOH C 29 354 128 HOH TIP . 
Y 4 HOH C 30 355 133 HOH TIP . 
Y 4 HOH C 31 356 134 HOH TIP . 
Y 4 HOH C 32 357 152 HOH TIP . 
Y 4 HOH C 33 358 153 HOH TIP . 
Y 4 HOH C 34 359 155 HOH TIP . 
Y 4 HOH C 35 360 156 HOH TIP . 
Y 4 HOH C 36 361 157 HOH TIP . 
Y 4 HOH C 37 362 159 HOH TIP . 
Y 4 HOH C 38 363 162 HOH TIP . 
Y 4 HOH C 39 364 163 HOH TIP . 
Y 4 HOH C 40 365 165 HOH TIP . 
Y 4 HOH C 41 366 169 HOH TIP . 
Y 4 HOH C 42 367 171 HOH TIP . 
Y 4 HOH C 43 368 173 HOH TIP . 
Y 4 HOH C 44 369 175 HOH TIP . 
Y 4 HOH C 45 370 197 HOH TIP . 
Y 4 HOH C 46 371 198 HOH TIP . 
Y 4 HOH C 47 372 199 HOH TIP . 
Y 4 HOH C 48 373 200 HOH TIP . 
Y 4 HOH C 49 374 201 HOH TIP . 
Z 4 HOH D 1 327 6 HOH TIP . 
Z 4 HOH D 2 328 12 HOH TIP . 
Z 4 HOH D 3 329 27 HOH TIP . 
Z 4 HOH D 4 330 29 HOH TIP . 
Z 4 HOH D 5 331 47 HOH TIP . 
Z 4 HOH D 6 332 49 HOH TIP . 
Z 4 HOH D 7 333 57 HOH TIP . 
Z 4 HOH D 8 334 60 HOH TIP . 
Z 4 HOH D 9 335 65 HOH TIP . 
Z 4 HOH D 10 336 66 HOH TIP . 
Z 4 HOH D 11 337 70 HOH TIP . 
Z 4 HOH D 12 338 71 HOH TIP . 
Z 4 HOH D 13 339 76 HOH TIP . 
Z 4 HOH D 14 340 82 HOH TIP . 
Z 4 HOH D 15 341 87 HOH TIP . 
Z 4 HOH D 16 342 89 HOH TIP . 
Z 4 HOH D 17 343 94 HOH TIP . 
Z 4 HOH D 18 344 96 HOH TIP . 
Z 4 HOH D 19 345 107 HOH TIP . 
Z 4 HOH D 20 346 111 HOH TIP . 
Z 4 HOH D 21 347 114 HOH TIP . 
Z 4 HOH D 22 348 124 HOH TIP . 
Z 4 HOH D 23 349 129 HOH TIP . 
Z 4 HOH D 24 350 131 HOH TIP . 
Z 4 HOH D 25 351 141 HOH TIP . 
Z 4 HOH D 26 352 143 HOH TIP . 
Z 4 HOH D 27 353 144 HOH TIP . 
Z 4 HOH D 28 354 151 HOH TIP . 
Z 4 HOH D 29 355 158 HOH TIP . 
Z 4 HOH D 30 356 160 HOH TIP . 
Z 4 HOH D 31 357 166 HOH TIP . 
Z 4 HOH D 32 358 172 HOH TIP . 
Z 4 HOH D 33 359 202 HOH TIP . 
Z 4 HOH D 34 360 203 HOH TIP . 
Z 4 HOH D 35 361 204 HOH TIP . 
Z 4 HOH D 36 362 205 HOH TIP . 
#
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 BME . . . P 2 -5.599 46.518 -2.125 0.3 1 ? C1 BME 325 C 1 
HETATM 2 C C2 BME . . . P 2 -6.341 47.768 -1.723 0.3 1 ? C2 BME 325 C 1 
HETATM 3 O O1 BME . . . P 2 -6.415 45.744 -2.917 0.3 1 ? O1 BME 325 C 1 
HETATM 4 S S2 BME . . . P 2 -5.234 48.835 -0.805 0.3 5.55 ? S2 BME 325 C 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           4 
#