data_3VKM # _model_server_result.job_id 8BfsMQ9X4-wHAe83m_khQg _model_server_result.datetime_utc '2025-08-31 10:36:02' _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 3vkm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":409}' # _entry.id 3VKM # _exptl.entry_id 3VKM _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 24 _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 3VKM _cell.length_a 74.133 _cell.length_b 80.713 _cell.length_c 129.296 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VKM _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G,H,I,J,K,L,M,N,O,P,Q,EA 1 1 B,E,F,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,FA 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 G N N ? 4 H N N ? 4 I N N ? 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 ? 4 T N N ? 4 U N N ? 4 V N N ? 4 W N N ? 4 X N N ? 4 Y N N ? 4 Z N N ? 4 AA N N ? 4 BA N N ? 4 CA N N ? 4 DA N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 GAL BGC C1 O1 . O4 HO4 . sing 2 ? 2 3 2 SIA GAL C2 O2 . O3 HO3 . sing 3 ? 3 2 1 GAL BGC C1 O1 . O4 HO4 . 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 BGC 1 C 1 BGC A 403 BGC 2 n C GAL 2 C 2 GAL A 402 GAL 2 n C SIA 3 C 3 SIA A 401 SIA 3 n D BGC 1 D 1 BGC A 405 BGC 3 n D GAL 2 D 2 GAL A 404 GAL 2 n E BGC 1 E 1 BGC B 403 BGC 2 n E GAL 2 E 2 GAL B 402 GAL 2 n E SIA 3 E 3 SIA B 401 SIA 3 n F BGC 1 F 1 BGC B 405 BGC 3 n F GAL 2 F 2 GAL B 404 GAL # 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 C O4 BGC . C BGC 1 1_555 C C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale2 C O3 GAL . C GAL 2 1_555 C C2 SIA . C SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale3 D O4 BGC . D BGC 1 1_555 D C1 GAL . D GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale4 E O4 BGC . E BGC 1 1_555 E C1 GAL . E GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale5 E O3 GAL . E GAL 2 1_555 E C2 SIA . E SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale6 F O4 BGC . F BGC 1 1_555 F C1 GAL . F GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? # _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 107 n n C1 C2 EDO sing 108 n n C1 H11 EDO sing 109 n n C1 H12 EDO sing 110 n n O1 HO1 EDO sing 111 n n C2 O2 EDO sing 112 n n C2 H21 EDO sing 113 n n C2 H22 EDO sing 114 n n O2 HO2 EDO sing 115 n n # _atom_sites.entry_id 3VKM _atom_sites.fract_transf_matrix[1][1] 0.013489 _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] 0.01239 _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] 0.007734 _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 G 4 EDO A 1 406 406 EDO EDO . H 4 EDO A 1 407 407 EDO EDO . I 4 EDO A 1 408 408 EDO EDO . J 4 EDO A 1 409 409 EDO EDO . K 4 EDO A 1 410 410 EDO EDO . L 4 EDO A 1 411 411 EDO EDO . M 4 EDO A 1 412 412 EDO EDO . N 4 EDO A 1 413 413 EDO EDO . O 4 EDO A 1 414 415 EDO EDO . P 4 EDO A 1 415 416 EDO EDO . Q 4 EDO A 1 416 417 EDO EDO . R 4 EDO B 1 406 406 EDO EDO . S 4 EDO B 1 407 407 EDO EDO . T 4 EDO B 1 408 408 EDO EDO . U 4 EDO B 1 409 409 EDO EDO . V 4 EDO B 1 410 410 EDO EDO . W 4 EDO B 1 411 411 EDO EDO . X 4 EDO B 1 412 412 EDO EDO . Y 4 EDO B 1 413 414 EDO EDO . Z 4 EDO B 1 414 415 EDO EDO . AA 4 EDO B 1 415 417 EDO EDO . BA 4 EDO B 1 416 419 EDO EDO . CA 4 EDO B 1 417 420 EDO EDO . DA 4 EDO B 1 418 422 EDO EDO . EA 5 HOH A 1 501 501 HOH HOH . EA 5 HOH A 2 502 502 HOH HOH . EA 5 HOH A 3 503 503 HOH HOH . EA 5 HOH A 4 504 504 HOH HOH . EA 5 HOH A 5 505 505 HOH HOH . EA 5 HOH A 6 506 506 HOH HOH . EA 5 HOH A 7 507 507 HOH HOH . EA 5 HOH A 8 508 508 HOH HOH . EA 5 HOH A 9 509 509 HOH HOH . EA 5 HOH A 10 510 510 HOH HOH . EA 5 HOH A 11 511 511 HOH HOH . EA 5 HOH A 12 512 512 HOH HOH . EA 5 HOH A 13 513 513 HOH HOH . EA 5 HOH A 14 514 514 HOH HOH . EA 5 HOH A 15 515 515 HOH HOH . EA 5 HOH A 16 516 516 HOH HOH . EA 5 HOH A 17 517 517 HOH HOH . EA 5 HOH A 18 518 518 HOH HOH . EA 5 HOH A 19 519 519 HOH HOH . EA 5 HOH A 20 520 520 HOH HOH . EA 5 HOH A 21 521 521 HOH HOH . EA 5 HOH A 22 522 522 HOH HOH . EA 5 HOH A 23 523 523 HOH HOH . EA 5 HOH A 24 524 524 HOH HOH . EA 5 HOH A 25 525 525 HOH HOH . EA 5 HOH A 26 526 526 HOH HOH . EA 5 HOH A 27 527 527 HOH HOH . EA 5 HOH A 28 528 528 HOH HOH . EA 5 HOH A 29 529 529 HOH HOH . EA 5 HOH A 30 530 530 HOH HOH . EA 5 HOH A 31 531 531 HOH HOH . EA 5 HOH A 32 532 532 HOH HOH . EA 5 HOH A 33 533 533 HOH HOH . EA 5 HOH A 34 534 534 HOH HOH . EA 5 HOH A 35 535 535 HOH HOH . EA 5 HOH A 36 536 536 HOH HOH . EA 5 HOH A 37 537 537 HOH HOH . EA 5 HOH A 38 538 538 HOH HOH . EA 5 HOH A 39 539 539 HOH HOH . EA 5 HOH A 40 540 540 HOH HOH . EA 5 HOH A 41 541 541 HOH HOH . EA 5 HOH A 42 542 542 HOH HOH . EA 5 HOH A 43 543 543 HOH HOH . EA 5 HOH A 44 544 544 HOH HOH . EA 5 HOH A 45 545 545 HOH HOH . EA 5 HOH A 46 546 546 HOH HOH . EA 5 HOH A 47 547 547 HOH HOH . EA 5 HOH A 48 548 548 HOH HOH . EA 5 HOH A 49 549 549 HOH HOH . EA 5 HOH A 50 550 550 HOH HOH . EA 5 HOH A 51 551 551 HOH HOH . EA 5 HOH A 52 552 552 HOH HOH . EA 5 HOH A 53 553 553 HOH HOH . EA 5 HOH A 54 554 554 HOH HOH . EA 5 HOH A 55 555 555 HOH HOH . EA 5 HOH A 56 556 556 HOH HOH . EA 5 HOH A 57 557 557 HOH HOH . EA 5 HOH A 58 558 558 HOH HOH . EA 5 HOH A 59 559 559 HOH HOH . EA 5 HOH A 60 560 560 HOH HOH . EA 5 HOH A 61 561 561 HOH HOH . EA 5 HOH A 62 562 562 HOH HOH . FA 5 HOH B 1 501 501 HOH HOH . FA 5 HOH B 2 502 502 HOH HOH . FA 5 HOH B 3 503 503 HOH HOH . FA 5 HOH B 4 504 504 HOH HOH . FA 5 HOH B 5 505 505 HOH HOH . FA 5 HOH B 6 506 506 HOH HOH . FA 5 HOH B 7 507 507 HOH HOH . FA 5 HOH B 8 508 508 HOH HOH . FA 5 HOH B 9 509 509 HOH HOH . FA 5 HOH B 10 510 510 HOH HOH . FA 5 HOH B 11 511 511 HOH HOH . FA 5 HOH B 12 512 512 HOH HOH . FA 5 HOH B 13 513 513 HOH HOH . FA 5 HOH B 14 514 514 HOH HOH . FA 5 HOH B 15 515 515 HOH HOH . FA 5 HOH B 16 516 516 HOH HOH . FA 5 HOH B 17 517 517 HOH HOH . FA 5 HOH B 18 518 518 HOH HOH . FA 5 HOH B 19 519 519 HOH HOH . FA 5 HOH B 20 520 520 HOH HOH . FA 5 HOH B 21 521 521 HOH HOH . FA 5 HOH B 22 522 522 HOH HOH . FA 5 HOH B 23 523 523 HOH HOH . FA 5 HOH B 24 524 524 HOH HOH . FA 5 HOH B 25 525 525 HOH HOH . FA 5 HOH B 26 526 526 HOH HOH . FA 5 HOH B 27 527 527 HOH HOH . FA 5 HOH B 28 528 528 HOH HOH . FA 5 HOH B 29 529 529 HOH HOH . FA 5 HOH B 30 530 530 HOH HOH . FA 5 HOH B 31 531 531 HOH HOH . FA 5 HOH B 32 532 532 HOH HOH . FA 5 HOH B 33 533 533 HOH HOH . FA 5 HOH B 34 534 534 HOH HOH . FA 5 HOH B 35 535 535 HOH HOH . FA 5 HOH B 36 536 536 HOH HOH . FA 5 HOH B 37 537 537 HOH HOH . FA 5 HOH B 38 538 538 HOH HOH . FA 5 HOH B 39 539 539 HOH HOH . FA 5 HOH B 40 540 540 HOH HOH . FA 5 HOH B 41 541 541 HOH HOH . FA 5 HOH B 42 542 542 HOH HOH . FA 5 HOH B 43 543 543 HOH HOH . FA 5 HOH B 44 544 544 HOH HOH . FA 5 HOH B 45 545 545 HOH HOH . FA 5 HOH B 46 546 546 HOH HOH . FA 5 HOH B 47 547 547 HOH HOH . FA 5 HOH B 48 548 548 HOH HOH . FA 5 HOH B 49 549 549 HOH HOH . FA 5 HOH B 50 550 550 HOH HOH . FA 5 HOH B 51 551 551 HOH HOH . FA 5 HOH B 52 552 552 HOH HOH . FA 5 HOH B 53 553 553 HOH HOH . FA 5 HOH B 54 554 554 HOH HOH . FA 5 HOH B 55 555 555 HOH HOH . FA 5 HOH B 56 556 556 HOH HOH . FA 5 HOH B 57 557 557 HOH HOH . FA 5 HOH B 58 558 558 HOH HOH . FA 5 HOH B 59 559 559 HOH HOH . FA 5 HOH B 60 560 560 HOH HOH . FA 5 HOH B 61 561 561 HOH HOH . FA 5 HOH B 62 562 562 HOH HOH . FA 5 HOH B 63 563 563 HOH HOH . FA 5 HOH B 64 564 564 HOH HOH . FA 5 HOH B 65 565 565 HOH HOH . FA 5 HOH B 66 566 566 HOH HOH . FA 5 HOH B 67 567 567 HOH HOH . FA 5 HOH B 68 568 568 HOH HOH . FA 5 HOH B 69 569 569 HOH HOH . FA 5 HOH B 70 570 570 HOH HOH . FA 5 HOH B 71 571 571 HOH HOH . FA 5 HOH B 72 572 572 HOH HOH . FA 5 HOH B 73 573 573 HOH HOH . FA 5 HOH B 74 574 574 HOH HOH . FA 5 HOH B 75 575 575 HOH HOH . FA 5 HOH B 76 576 576 HOH HOH . FA 5 HOH B 77 577 577 HOH HOH . FA 5 HOH B 78 578 578 HOH HOH . FA 5 HOH B 79 579 579 HOH HOH . FA 5 HOH B 80 580 580 HOH HOH . FA 5 HOH B 81 581 581 HOH HOH . FA 5 HOH B 82 582 582 HOH HOH . FA 5 HOH B 83 583 583 HOH HOH . FA 5 HOH B 84 584 584 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 4 12.015 -45.041 -8.12 1 59.26 ? C1 EDO 409 A 1 HETATM 2 O O1 EDO . . . J 4 13.34 -44.768 -7.685 1 58.84 ? O1 EDO 409 A 1 HETATM 3 C C2 EDO . . . J 4 11.082 -45.214 -6.912 1 59.93 ? C2 EDO 409 A 1 HETATM 4 O O2 EDO . . . J 4 10.787 -43.953 -6.321 1 58.6 ? O2 EDO 409 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 506 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 4 #