data_5SVL # _model_server_result.job_id sjDZ5WqbaBgX6-6XEmlYGQ _model_server_result.datetime_utc '2024-11-05 21:07:11' _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 5svl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":408}' # _entry.id 5SVL # _exptl.entry_id 5SVL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _entity.pdbx_number_of_molecules 6 _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 5SVL _cell.length_a 172.14 _cell.length_b 172.14 _cell.length_c 172.14 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SVL _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 3' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Y 1 1 A,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Y 1 2 A,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Y 1 4 B,Q,R,S,T,U,V,W,X,Z 2 1 B,Q,R,S,T,U,V,W,X,Z 2 3 B,Q,R,S,T,U,V,W,X,Z 2 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 6_566 z+1/2,-x+3/2,-y+1 0 0 1 -1 0 0 0 -1 0 86.07 258.21 172.14 4 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 5 'crystal symmetry operation' 12_664 -y+3/2,-z+1,x-1/2 0 -1 0 0 0 -1 1 0 0 258.21 172.14 -86.07 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 H N N ? 5 I N N ? 5 J N N ? 5 K N N ? 5 U N N ? 5 V N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 GLC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C GLC 1 C 1 GLC D 1 MAL 2 n C GLC 2 C 2 GLC D 1 MAL # 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 106 A CYS 107 1_555 A SG CYS 152 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 A SG CYS 121 A CYS 122 1_555 A SG CYS 146 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 202 A CYS 203 1_555 A SG CYS 212 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 246 A CYS 247 1_555 A SG CYS 255 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 106 B CYS 107 1_555 B SG CYS 152 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf7 B SG CYS 115 B CYS 116 1_555 B SG CYS 136 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 B SG CYS 121 B CYS 122 1_555 B SG CYS 146 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf9 B SG CYS 202 B CYS 203 1_555 B SG CYS 212 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf10 B SG CYS 246 B CYS 247 1_555 B SG CYS 255 B CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 169 A ASN 170 1_555 E C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 A ND2 ASN 193 A ASN 194 1_555 F C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale3 A ND2 ASN 289 A ASN 290 1_555 G C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale4 B ND2 ASN 169 B ASN 170 1_555 R C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 B ND2 ASN 193 B ASN 194 1_555 S C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 B ND2 ASN 289 B ASN 290 1_555 T C1 NAG . B NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale7 C O4 GLC . C GLC 1 1_555 C C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 sing metalc ? metalc1 A OD1 ASP 209 A ASP 210 1_555 N NA NA . A NA 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? metalc ? metalc2 D O1G ATP . A ATP 401 1_555 O NA NA . A NA 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc3 D O2G ATP . A ATP 401 1_555 O NA NA . A NA 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.931 ? metalc ? metalc4 N NA NA . A NA 412 1_555 Y O HOH . A HOH 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc5 N NA NA . A NA 412 1_555 Y O HOH . A HOH 547 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc6 O NA NA . A NA 413 1_555 Y O HOH . A HOH 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc7 O NA NA . A NA 413 1_555 Y O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.917 ? metalc ? metalc8 O NA NA . A NA 413 1_555 Y O HOH . A HOH 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc9 B OD2 ASP 157 B ASP 158 1_555 X NA NA . B NA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.923 ? metalc ? metalc10 Q O1G ATP . B ATP 401 1_555 X NA NA . B NA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.033 ? metalc ? metalc11 X NA NA . B NA 408 1_555 Z O HOH . B HOH 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? # _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 138 n n C1 C2 EDO sing 139 n n C1 H11 EDO sing 140 n n C1 H12 EDO sing 141 n n O1 HO1 EDO sing 142 n n C2 O2 EDO sing 143 n n C2 H21 EDO sing 144 n n C2 H22 EDO sing 145 n n O2 HO2 EDO sing 146 n n # _atom_sites.entry_id 5SVL _atom_sites.fract_transf_matrix[1][1] 0.005809 _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] 0.005809 _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] 0.005809 _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 D 3 ATP A 1 401 402 ATP ATP . E 4 NAG A 1 402 500 NAG NAG . F 4 NAG A 1 403 501 NAG NAG . G 4 NAG A 1 404 502 NAG NAG . H 5 EDO A 1 406 2 EDO EDO . I 5 EDO A 1 407 4 EDO EDO . J 5 EDO A 1 408 17 EDO EDO . K 5 EDO A 1 409 18 EDO EDO . L 6 ACT A 1 410 1 ACT ACT . M 6 ACT A 1 411 2 ACT ACT . N 7 NA A 1 412 1 NA NA . O 7 NA A 1 413 1 NA NA . P 8 TRS A 1 414 1 TRS TRS . Q 3 ATP B 1 401 402 ATP ATP . R 4 NAG B 1 402 500 NAG NAG . S 4 NAG B 1 403 501 NAG NAG . T 4 NAG B 1 404 502 NAG NAG . U 5 EDO B 1 405 14 EDO EDO . V 5 EDO B 1 406 19 EDO EDO . W 6 ACT B 1 407 3 ACT ACT . X 7 NA B 1 408 1 NA NA . Y 9 HOH A 1 501 338 HOH HOH . Y 9 HOH A 2 502 205 HOH HOH . Y 9 HOH A 3 503 262 HOH HOH . Y 9 HOH A 4 504 18 HOH HOH . Y 9 HOH A 5 505 50 HOH HOH . Y 9 HOH A 6 506 297 HOH HOH . Y 9 HOH A 7 507 336 HOH HOH . Y 9 HOH A 8 508 28 HOH HOH . Y 9 HOH A 9 509 335 HOH HOH . Y 9 HOH A 10 510 332 HOH HOH . Y 9 HOH A 11 511 19 HOH HOH . Y 9 HOH A 12 512 169 HOH HOH . Y 9 HOH A 13 513 20 HOH HOH . Y 9 HOH A 14 514 267 HOH HOH . Y 9 HOH A 15 515 24 HOH HOH . Y 9 HOH A 16 516 293 HOH HOH . Y 9 HOH A 17 517 13 HOH HOH . Y 9 HOH A 18 518 292 HOH HOH . Y 9 HOH A 19 519 206 HOH HOH . Y 9 HOH A 20 520 268 HOH HOH . Y 9 HOH A 21 521 324 HOH HOH . Y 9 HOH A 22 522 216 HOH HOH . Y 9 HOH A 23 523 54 HOH HOH . Y 9 HOH A 24 524 329 HOH HOH . Y 9 HOH A 25 525 242 HOH HOH . Y 9 HOH A 26 526 178 HOH HOH . Y 9 HOH A 27 527 136 HOH HOH . Y 9 HOH A 28 528 4 HOH HOH . Y 9 HOH A 29 529 5 HOH HOH . Y 9 HOH A 30 530 269 HOH HOH . Y 9 HOH A 31 531 240 HOH HOH . Y 9 HOH A 32 532 288 HOH HOH . Y 9 HOH A 33 533 2 HOH HOH . Y 9 HOH A 34 534 7 HOH HOH . Y 9 HOH A 35 535 22 HOH HOH . Y 9 HOH A 36 536 156 HOH HOH . Y 9 HOH A 37 537 298 HOH HOH . Y 9 HOH A 38 538 323 HOH HOH . Y 9 HOH A 39 539 87 HOH HOH . Y 9 HOH A 40 540 310 HOH HOH . Y 9 HOH A 41 541 241 HOH HOH . Y 9 HOH A 42 542 294 HOH HOH . Y 9 HOH A 43 543 259 HOH HOH . Y 9 HOH A 44 544 322 HOH HOH . Y 9 HOH A 45 545 29 HOH HOH . Y 9 HOH A 46 546 181 HOH HOH . Y 9 HOH A 47 547 258 HOH HOH . Y 9 HOH A 48 548 48 HOH HOH . Z 9 HOH B 1 501 264 HOH HOH . Z 9 HOH B 2 502 331 HOH HOH . Z 9 HOH B 3 503 326 HOH HOH . Z 9 HOH B 4 504 280 HOH HOH . Z 9 HOH B 5 505 283 HOH HOH . Z 9 HOH B 6 506 327 HOH HOH . Z 9 HOH B 7 507 271 HOH HOH . Z 9 HOH B 8 508 274 HOH HOH . Z 9 HOH B 9 509 39 HOH HOH . Z 9 HOH B 10 510 150 HOH HOH . Z 9 HOH B 11 511 328 HOH HOH . Z 9 HOH B 12 512 265 HOH HOH . Z 9 HOH B 13 513 147 HOH HOH . Z 9 HOH B 14 514 302 HOH HOH . Z 9 HOH B 15 515 198 HOH HOH . Z 9 HOH B 16 516 72 HOH HOH . Z 9 HOH B 17 517 334 HOH HOH . Z 9 HOH B 18 518 154 HOH HOH . Z 9 HOH B 19 519 146 HOH HOH . Z 9 HOH B 20 520 337 HOH HOH . Z 9 HOH B 21 521 79 HOH HOH . Z 9 HOH B 22 522 325 HOH HOH . Z 9 HOH B 23 523 319 HOH HOH . Z 9 HOH B 24 524 303 HOH HOH . Z 9 HOH B 25 525 301 HOH HOH . Z 9 HOH B 26 526 296 HOH HOH . Z 9 HOH B 27 527 244 HOH HOH . Z 9 HOH B 28 528 320 HOH HOH . Z 9 HOH B 29 529 286 HOH HOH . Z 9 HOH B 30 530 219 HOH HOH . Z 9 HOH B 31 531 308 HOH HOH . Z 9 HOH B 32 532 221 HOH HOH . Z 9 HOH B 33 533 232 HOH HOH . Z 9 HOH B 34 534 36 HOH HOH . Z 9 HOH B 35 535 276 HOH HOH . Z 9 HOH B 36 536 251 HOH HOH . Z 9 HOH B 37 537 249 HOH HOH . Z 9 HOH B 38 538 321 HOH HOH . Z 9 HOH B 39 539 277 HOH HOH . Z 9 HOH B 40 540 138 HOH HOH . Z 9 HOH B 41 541 311 HOH HOH . Z 9 HOH B 42 542 317 HOH HOH . Z 9 HOH B 43 543 313 HOH HOH . Z 9 HOH B 44 544 305 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 . . . J 5 115.946 63.559 98.689 1 123.52 ? C1 EDO 408 A 1 HETATM 2 O O1 EDO . . . J 5 115.033 63.299 97.608 1 121.59 ? O1 EDO 408 A 1 HETATM 3 C C2 EDO . . . J 5 116.545 64.995 98.497 1 118.7 ? C2 EDO 408 A 1 HETATM 4 O O2 EDO . . . J 5 117.646 65.149 99.343 1 115.66 ? O2 EDO 408 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 360 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 4 #