data_8VMG # _model_server_result.job_id 3RNhN5AVdSUmpYRFOKqvnw _model_server_result.datetime_utc '2024-11-29 01:13:19' _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 8vmg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":422}' # _entry.id 8VMG # _exptl.entry_id 8VMG _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 39 _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 120 _cell.entry_id 8VMG _cell.length_a 195.585 _cell.length_b 195.585 _cell.length_c 152.204 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VMG _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall 'P 65 2 (x,y,z+1/12)' _symmetry.space_group_name_H-M 'P 65 2 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,WB,XB,YB,ZB,AC,BC,CC,EC,GC 1 1 B,D,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,DC,FC,HC 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 ? 4 F N N ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 O N N ? 4 Q N N ? 4 S N N ? 4 T N N ? 4 U N N ? 4 V N N ? 4 Y N N ? 4 Z N N ? 4 AA N N ? 4 BA N N ? 4 DA N N ? 4 UA N N ? 4 VA N N ? 4 WA N N ? 4 XA N N ? 4 YA N N ? 4 ZA N N ? 4 AB N N ? 4 BB N N ? 4 CB N N ? 4 DB N N ? 4 EB N N ? 4 FB N N ? 4 GB N N ? 4 HB N N ? 4 IB N N ? 4 JB N N ? 4 KB N N ? 4 LB N N ? 4 MB N N ? 4 WB N N ? 4 XB N N ? 4 YB N N ? 4 ZB 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 metalc ? metalc1 A OD1 ASN 161 A ASN 186 1_555 NA MG MG . A MG 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc2 A OD2 ASP 175 A ASP 200 1_555 NA MG MG . A MG 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc3 E O3A ADP . A ADP 401 1_555 NA MG MG . A MG 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc4 NA MG MG . A MG 436 1_555 EC O HOH . A HOH 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? # _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 127 n n C1 C2 EDO sing 128 n n C1 H11 EDO sing 129 n n C1 H12 EDO sing 130 n n O1 HO1 EDO sing 131 n n C2 O2 EDO sing 132 n n C2 H21 EDO sing 133 n n C2 H22 EDO sing 134 n n O2 HO2 EDO sing 135 n n # _atom_sites.entry_id 8VMG _atom_sites.fract_transf_matrix[1][1] 0.005113 _atom_sites.fract_transf_matrix[1][2] 0.002952 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005904 _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] 0.00657 _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 ADP A 1 401 401 ADP ADP . F 4 EDO A 1 402 404 EDO EDO . G 4 EDO A 1 403 407 EDO EDO . H 4 EDO A 1 404 409 EDO EDO . I 4 EDO A 1 405 410 EDO EDO . J 4 EDO A 1 406 411 EDO EDO . K 5 NO3 A 1 407 412 NO3 NO3 . L 5 NO3 A 1 408 417 NO3 NO3 . M 5 NO3 A 1 409 419 NO3 NO3 . N 6 GOL A 1 410 420 GOL GOL . O 4 EDO A 1 411 421 EDO EDO . P 5 NO3 A 1 412 423 NO3 NO3 . Q 4 EDO A 1 413 424 EDO EDO . R 6 GOL A 1 414 428 GOL GOL . S 4 EDO A 1 415 431 EDO EDO . T 4 EDO A 1 416 433 EDO EDO . U 4 EDO A 1 417 435 EDO EDO . V 4 EDO A 1 418 438 EDO EDO . W 6 GOL A 1 419 440 GOL GOL . X 5 NO3 A 1 420 452 NO3 NO3 . Y 4 EDO A 1 421 453 EDO EDO . Z 4 EDO A 1 422 454 EDO EDO . AA 4 EDO A 1 423 455 EDO EDO . BA 4 EDO A 1 424 456 EDO EDO . CA 6 GOL A 1 425 457 GOL GOL . DA 4 EDO A 1 426 458 EDO EDO . EA 5 NO3 A 1 427 459 NO3 NO3 . FA 5 NO3 A 1 428 460 NO3 NO3 . GA 5 NO3 A 1 429 461 NO3 NO3 . HA 7 SO4 A 1 430 1 SO4 SO4 . IA 7 SO4 A 1 431 2 SO4 SO4 . JA 7 SO4 A 1 432 11 SO4 SO4 . KA 7 SO4 A 1 433 15 SO4 SO4 . LA 7 SO4 A 1 434 17 SO4 SO4 . MA 7 SO4 A 1 435 19 SO4 SO4 . NA 8 MG A 1 436 1 MG MG . OA 9 CL A 1 437 9 CL CL . PA 9 CL A 1 438 10 CL CL . QA 9 CL A 1 439 15 CL CL . RA 9 CL A 1 440 20 CL CL . SA 9 CL A 1 441 23 CL CL . TA 10 MES B 1 401 401 MES MES . UA 4 EDO B 1 402 403 EDO EDO . VA 4 EDO B 1 403 405 EDO EDO . WA 4 EDO B 1 404 406 EDO EDO . XA 4 EDO B 1 405 408 EDO EDO . YA 4 EDO B 1 406 410 EDO EDO . ZA 4 EDO B 1 407 414 EDO EDO . AB 4 EDO B 1 408 415 EDO EDO . BB 4 EDO B 1 409 416 EDO EDO . CB 4 EDO B 1 410 423 EDO EDO . DB 4 EDO B 1 411 424 EDO EDO . EB 4 EDO B 1 412 425 EDO EDO . FB 4 EDO B 1 413 426 EDO EDO . GB 4 EDO B 1 414 428 EDO EDO . HB 4 EDO B 1 415 429 EDO EDO . IB 4 EDO B 1 416 430 EDO EDO . JB 4 EDO B 1 417 431 EDO EDO . KB 4 EDO B 1 418 432 EDO EDO . LB 4 EDO B 1 419 433 EDO EDO . MB 4 EDO B 1 420 501 EDO EDO . NB 7 SO4 B 1 421 3 SO4 SO4 . OB 7 SO4 B 1 422 16 SO4 SO4 . PB 9 CL B 1 423 5 CL CL . QB 9 CL B 1 424 6 CL CL . RB 9 CL B 1 425 12 CL CL . SB 9 CL B 1 426 16 CL CL . TB 9 CL B 1 427 19 CL CL . UB 9 CL B 1 428 21 CL CL . VB 9 CL B 1 429 22 CL CL . WB 4 EDO C 1 501 416 EDO EDO . XB 4 EDO C 1 502 501 EDO EDO . YB 4 EDO C 1 503 502 EDO EDO . ZB 4 EDO C 1 504 503 EDO EDO . AC 7 SO4 C 1 505 18 SO4 SO4 . BC 9 CL C 1 506 13 CL CL . CC 9 CL C 1 507 14 CL CL . DC 9 CL D 1 501 7 CL CL . EC 11 HOH A 1 501 288 HOH HOH . EC 11 HOH A 2 502 123 HOH HOH . EC 11 HOH A 3 503 22 HOH HOH . EC 11 HOH A 4 504 182 HOH HOH . EC 11 HOH A 5 505 164 HOH HOH . EC 11 HOH A 6 506 255 HOH HOH . EC 11 HOH A 7 507 61 HOH HOH . EC 11 HOH A 8 508 170 HOH HOH . EC 11 HOH A 9 509 171 HOH HOH . EC 11 HOH A 10 510 106 HOH HOH . EC 11 HOH A 11 511 112 HOH HOH . EC 11 HOH A 12 512 29 HOH HOH . EC 11 HOH A 13 513 30 HOH HOH . EC 11 HOH A 14 514 260 HOH HOH . EC 11 HOH A 15 515 127 HOH HOH . EC 11 HOH A 16 516 185 HOH HOH . EC 11 HOH A 17 517 72 HOH HOH . EC 11 HOH A 18 518 259 HOH HOH . EC 11 HOH A 19 519 57 HOH HOH . EC 11 HOH A 20 520 269 HOH HOH . EC 11 HOH A 21 521 167 HOH HOH . EC 11 HOH A 22 522 78 HOH HOH . EC 11 HOH A 23 523 289 HOH HOH . EC 11 HOH A 24 524 277 HOH HOH . EC 11 HOH A 25 525 13 HOH HOH . EC 11 HOH A 26 526 217 HOH HOH . EC 11 HOH A 27 527 215 HOH HOH . EC 11 HOH A 28 528 94 HOH HOH . EC 11 HOH A 29 529 46 HOH HOH . EC 11 HOH A 30 530 10 HOH HOH . EC 11 HOH A 31 531 47 HOH HOH . EC 11 HOH A 32 532 190 HOH HOH . EC 11 HOH A 33 533 136 HOH HOH . EC 11 HOH A 34 534 53 HOH HOH . EC 11 HOH A 35 535 12 HOH HOH . EC 11 HOH A 36 536 45 HOH HOH . EC 11 HOH A 37 537 175 HOH HOH . EC 11 HOH A 38 538 179 HOH HOH . EC 11 HOH A 39 539 240 HOH HOH . EC 11 HOH A 40 540 114 HOH HOH . EC 11 HOH A 41 541 283 HOH HOH . EC 11 HOH A 42 542 84 HOH HOH . EC 11 HOH A 43 543 274 HOH HOH . EC 11 HOH A 44 544 130 HOH HOH . EC 11 HOH A 45 545 98 HOH HOH . EC 11 HOH A 46 546 267 HOH HOH . EC 11 HOH A 47 547 70 HOH HOH . EC 11 HOH A 48 548 157 HOH HOH . EC 11 HOH A 49 549 23 HOH HOH . EC 11 HOH A 50 550 139 HOH HOH . EC 11 HOH A 51 551 264 HOH HOH . EC 11 HOH A 52 552 181 HOH HOH . EC 11 HOH A 53 553 119 HOH HOH . EC 11 HOH A 54 554 109 HOH HOH . EC 11 HOH A 55 555 25 HOH HOH . EC 11 HOH A 56 556 102 HOH HOH . EC 11 HOH A 57 557 304 HOH HOH . EC 11 HOH A 58 558 279 HOH HOH . EC 11 HOH A 59 559 298 HOH HOH . EC 11 HOH A 60 560 40 HOH HOH . EC 11 HOH A 61 561 121 HOH HOH . EC 11 HOH A 62 562 138 HOH HOH . EC 11 HOH A 63 563 97 HOH HOH . EC 11 HOH A 64 564 226 HOH HOH . EC 11 HOH A 65 565 209 HOH HOH . EC 11 HOH A 66 566 120 HOH HOH . EC 11 HOH A 67 567 18 HOH HOH . EC 11 HOH A 68 568 302 HOH HOH . EC 11 HOH A 69 569 241 HOH HOH . EC 11 HOH A 70 570 247 HOH HOH . EC 11 HOH A 71 571 126 HOH HOH . EC 11 HOH A 72 572 142 HOH HOH . EC 11 HOH A 73 573 258 HOH HOH . EC 11 HOH A 74 574 198 HOH HOH . EC 11 HOH A 75 575 297 HOH HOH . EC 11 HOH A 76 576 95 HOH HOH . EC 11 HOH A 77 577 110 HOH HOH . EC 11 HOH A 78 578 225 HOH HOH . EC 11 HOH A 79 579 34 HOH HOH . EC 11 HOH A 80 580 301 HOH HOH . EC 11 HOH A 81 581 174 HOH HOH . EC 11 HOH A 82 582 234 HOH HOH . EC 11 HOH A 83 583 270 HOH HOH . EC 11 HOH A 84 584 49 HOH HOH . EC 11 HOH A 85 585 290 HOH HOH . EC 11 HOH A 86 586 230 HOH HOH . EC 11 HOH A 87 587 228 HOH HOH . EC 11 HOH A 88 588 244 HOH HOH . EC 11 HOH A 89 589 275 HOH HOH . EC 11 HOH A 90 590 303 HOH HOH . EC 11 HOH A 91 591 99 HOH HOH . EC 11 HOH A 92 592 223 HOH HOH . EC 11 HOH A 93 593 143 HOH HOH . EC 11 HOH A 94 594 216 HOH HOH . EC 11 HOH A 95 595 156 HOH HOH . EC 11 HOH A 96 596 227 HOH HOH . FC 11 HOH B 1 501 204 HOH HOH . FC 11 HOH B 2 502 141 HOH HOH . FC 11 HOH B 3 503 64 HOH HOH . FC 11 HOH B 4 504 166 HOH HOH . FC 11 HOH B 5 505 268 HOH HOH . FC 11 HOH B 6 506 257 HOH HOH . FC 11 HOH B 7 507 103 HOH HOH . FC 11 HOH B 8 508 27 HOH HOH . FC 11 HOH B 9 509 21 HOH HOH . FC 11 HOH B 10 510 71 HOH HOH . FC 11 HOH B 11 511 36 HOH HOH . FC 11 HOH B 12 512 281 HOH HOH . FC 11 HOH B 13 513 276 HOH HOH . FC 11 HOH B 14 514 184 HOH HOH . FC 11 HOH B 15 515 20 HOH HOH . FC 11 HOH B 16 516 299 HOH HOH . FC 11 HOH B 17 517 266 HOH HOH . FC 11 HOH B 18 518 210 HOH HOH . FC 11 HOH B 19 519 193 HOH HOH . FC 11 HOH B 20 520 221 HOH HOH . FC 11 HOH B 21 521 81 HOH HOH . FC 11 HOH B 22 522 77 HOH HOH . FC 11 HOH B 23 523 50 HOH HOH . FC 11 HOH B 24 524 38 HOH HOH . FC 11 HOH B 25 525 26 HOH HOH . FC 11 HOH B 26 526 177 HOH HOH . FC 11 HOH B 27 527 14 HOH HOH . FC 11 HOH B 28 528 73 HOH HOH . FC 11 HOH B 29 529 273 HOH HOH . FC 11 HOH B 30 530 31 HOH HOH . FC 11 HOH B 31 531 173 HOH HOH . FC 11 HOH B 32 532 79 HOH HOH . FC 11 HOH B 33 533 63 HOH HOH . FC 11 HOH B 34 534 214 HOH HOH . FC 11 HOH B 35 535 183 HOH HOH . FC 11 HOH B 36 536 92 HOH HOH . FC 11 HOH B 37 537 86 HOH HOH . FC 11 HOH B 38 538 24 HOH HOH . FC 11 HOH B 39 539 191 HOH HOH . FC 11 HOH B 40 540 39 HOH HOH . FC 11 HOH B 41 541 285 HOH HOH . FC 11 HOH B 42 542 250 HOH HOH . FC 11 HOH B 43 543 105 HOH HOH . FC 11 HOH B 44 544 176 HOH HOH . FC 11 HOH B 45 545 203 HOH HOH . FC 11 HOH B 46 546 295 HOH HOH . FC 11 HOH B 47 547 80 HOH HOH . FC 11 HOH B 48 548 87 HOH HOH . FC 11 HOH B 49 549 201 HOH HOH . FC 11 HOH B 50 550 208 HOH HOH . FC 11 HOH B 51 551 196 HOH HOH . GC 11 HOH C 1 601 271 HOH HOH . GC 11 HOH C 2 602 169 HOH HOH . GC 11 HOH C 3 603 280 HOH HOH . GC 11 HOH C 4 604 296 HOH HOH . GC 11 HOH C 5 605 205 HOH HOH . GC 11 HOH C 6 606 96 HOH HOH . GC 11 HOH C 7 607 93 HOH HOH . GC 11 HOH C 8 608 286 HOH HOH . GC 11 HOH C 9 609 189 HOH HOH . GC 11 HOH C 10 610 233 HOH HOH . HC 11 HOH D 1 601 251 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 . . . Z 4 -82.699 42.051 -39.586 1 96.11 ? C1 EDO 422 A 1 HETATM 2 O O1 EDO . . . Z 4 -81.698 42.996 -39.974 1 103.99 ? O1 EDO 422 A 1 HETATM 3 C C2 EDO . . . Z 4 -82.341 40.668 -40.139 1 100.07 ? C2 EDO 422 A 1 HETATM 4 O O2 EDO . . . Z 4 -80.946 40.325 -40.036 1 77.34 ? O2 EDO 422 A 1 HETATM 5 H H11 EDO . . . Z 4 -83.672 42.363 -39.971 1 115.24 ? H11 EDO 422 A 1 HETATM 6 H H12 EDO . . . Z 4 -82.767 42.008 -38.497 1 115.24 ? H12 EDO 422 A 1 HETATM 7 H HO1 EDO . . . Z 4 -82.121 43.826 -40.234 1 124.69 ? HO1 EDO 422 A 1 HETATM 8 H H21 EDO . . . Z 4 -82.632 40.628 -41.19 1 119.98 ? H21 EDO 422 A 1 HETATM 9 H H22 EDO . . . Z 4 -82.924 39.917 -39.601 1 119.98 ? H22 EDO 422 A 1 HETATM 10 H HO2 EDO . . . Z 4 -80.832 39.381 -40.212 1 92.71 ? HO2 EDO 422 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 10 #