data_6B1V # _model_server_result.job_id wZ9vUSVJLr6zAQjfArbtMg _model_server_result.datetime_utc '2024-11-05 00:34:25' _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 6b1v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":510}' # _entry.id 6B1V # _exptl.entry_id 6B1V _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 1 _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 6B1V _cell.length_a 130.44 _cell.length_b 130.44 _cell.length_c 229.754 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6B1V _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type 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 DGS G4S C1 O1 . O3 HO3 . sing 2 ? 2 3 2 G4S DGS C1 O1 . O4 HO4 . sing 3 ? 2 4 3 DGS G4S C1 O1 . O3 HO3 . 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 D G4S 1 D 1 G4S E 1 G4S 2 n D DGS 2 D 2 DGS E 2 DGS 2 n D G4S 3 D 3 G4S E 3 G4S 2 n D DGS 4 D 4 DGS E 4 DGS 2 n E G4S 1 E 1 G4S J 1 G4S 2 n E DGS 2 E 2 DGS J 2 DGS 2 n E G4S 3 E 3 G4S J 3 G4S 2 n E DGS 4 E 4 DGS J 4 DGS 2 n F G4S 1 F 1 G4S D 1 G4S 2 n F DGS 2 F 2 DGS D 2 DGS 2 n F G4S 3 F 3 G4S D 3 G4S 2 n F DGS 4 F 4 DGS D 4 DGS 2 n G G4S 1 G 1 G4S H 1 G4S 2 n G DGS 2 G 2 DGS H 2 DGS 2 n G G4S 3 G 3 G4S H 3 G4S 2 n G DGS 4 G 4 DGS H 4 DGS 2 n H G4S 1 H 1 G4S F 1 G4S 2 n H DGS 2 H 2 DGS F 2 DGS 2 n H G4S 3 H 3 G4S F 3 G4S 2 n H DGS 4 H 4 DGS F 4 DGS # 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 D O3 G4S . D G4S 1 1_555 D C1 DGS . D DGS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 D O4 DGS . D DGS 2 1_555 D C1 G4S . D G4S 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale3 D O3 G4S . D G4S 3 1_555 D C1 DGS . D DGS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 E O3 G4S . E G4S 1 1_555 E C1 DGS . E DGS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 E O4 DGS . E DGS 2 1_555 E C1 G4S . E G4S 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale6 E O3 G4S . E G4S 3 1_555 E C1 DGS . E DGS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale7 F O3 G4S . F G4S 1 1_555 F C1 DGS . F DGS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale8 F O4 DGS . F DGS 2 1_555 F C1 G4S . F G4S 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale9 F O3 G4S . F G4S 3 1_555 F C1 DGS . F DGS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale10 G O3 G4S . G G4S 1 1_555 G C1 DGS . G DGS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale11 G O4 DGS . G DGS 2 1_555 G C1 G4S . G G4S 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale12 G O3 G4S . G G4S 3 1_555 G C1 DGS . G DGS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale13 H O3 G4S . H G4S 1 1_555 H C1 DGS . H DGS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale14 H O4 DGS . H DGS 2 1_555 H C1 G4S . H G4S 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale15 H O3 G4S . H G4S 3 1_555 H C1 DGS . H DGS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? metalc ? metalc1 A OD1 ASP 11 A ASP 38 1_555 I CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc2 A OD1 ASP 12 A ASP 39 1_555 I CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc3 A OD1 ASP 264 A ASP 291 1_555 I CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc4 A OD2 ASP 264 A ASP 291 1_555 I CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc5 A OD1 ASN 265 A ASN 292 1_555 I CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc6 I CA CA . A CA 505 1_555 D O8 G4S . D G4S 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc7 B OD1 ASP 11 B ASP 38 1_555 K CA CA . B CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc8 B OD1 ASP 12 B ASP 39 1_555 K CA CA . B CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc9 B OD1 ASP 264 B ASP 291 1_555 K CA CA . B CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? metalc ? metalc10 B OD2 ASP 264 B ASP 291 1_555 K CA CA . B CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc11 B OD1 ASN 265 B ASN 292 1_555 K CA CA . B CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc12 K CA CA . B CA 505 1_555 F O9 G4S . F G4S 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc13 C OD1 ASP 11 C ASP 38 1_555 L CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc14 C OD1 ASP 12 C ASP 39 1_555 L CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc15 C OD1 ASP 264 C ASP 291 1_555 L CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? metalc ? metalc16 C OD2 ASP 264 C ASP 291 1_555 L CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc17 C OD1 ASN 265 C ASN 292 1_555 L CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc18 L CA CA . C CA 501 1_555 H O8 G4S . H G4S 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? # _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 96 n n C1 C2 EDO sing 97 n n C1 H11 EDO sing 98 n n C1 H12 EDO sing 99 n n O1 HO1 EDO sing 100 n n C2 O2 EDO sing 101 n n C2 H21 EDO sing 102 n n C2 H22 EDO sing 103 n n O2 HO2 EDO sing 104 n n # _atom_sites.entry_id 6B1V _atom_sites.fract_transf_matrix[1][1] 0.007666 _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] 0.007666 _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] 0.004352 _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 I 3 CA A 1 505 3 CA CA . J 4 EDO A 1 510 1 EDO EDO . K 3 CA B 1 505 2 CA CA . L 3 CA C 1 501 1 CA CA . M 5 HOH A 1 601 25 HOH HOH . M 5 HOH A 2 602 43 HOH HOH . M 5 HOH A 3 603 64 HOH HOH . M 5 HOH A 4 604 83 HOH HOH . M 5 HOH A 5 605 65 HOH HOH . M 5 HOH A 6 606 7 HOH HOH . M 5 HOH A 7 607 71 HOH HOH . M 5 HOH A 8 608 12 HOH HOH . M 5 HOH A 9 609 6 HOH HOH . M 5 HOH A 10 610 73 HOH HOH . M 5 HOH A 11 611 24 HOH HOH . M 5 HOH A 12 612 68 HOH HOH . M 5 HOH A 13 613 8 HOH HOH . M 5 HOH A 14 614 72 HOH HOH . M 5 HOH A 15 615 75 HOH HOH . M 5 HOH A 16 616 94 HOH HOH . M 5 HOH A 17 617 55 HOH HOH . M 5 HOH A 18 618 69 HOH HOH . M 5 HOH A 19 619 63 HOH HOH . M 5 HOH A 20 620 67 HOH HOH . N 5 HOH B 1 601 53 HOH HOH . N 5 HOH B 2 602 26 HOH HOH . N 5 HOH B 3 603 3 HOH HOH . N 5 HOH B 4 604 4 HOH HOH . N 5 HOH B 5 605 81 HOH HOH . N 5 HOH B 6 606 76 HOH HOH . N 5 HOH B 7 607 23 HOH HOH . N 5 HOH B 8 608 17 HOH HOH . N 5 HOH B 9 609 49 HOH HOH . N 5 HOH B 10 610 91 HOH HOH . N 5 HOH B 11 611 9 HOH HOH . N 5 HOH B 12 612 77 HOH HOH . N 5 HOH B 13 613 87 HOH HOH . N 5 HOH B 14 614 1 HOH HOH . N 5 HOH B 15 615 88 HOH HOH . N 5 HOH B 16 616 51 HOH HOH . N 5 HOH B 17 617 56 HOH HOH . N 5 HOH B 18 618 78 HOH HOH . N 5 HOH B 19 619 80 HOH HOH . N 5 HOH B 20 620 50 HOH HOH . N 5 HOH B 21 621 57 HOH HOH . N 5 HOH B 22 622 39 HOH HOH . O 5 HOH C 1 601 22 HOH HOH . O 5 HOH C 2 602 27 HOH HOH . O 5 HOH C 3 603 10 HOH HOH . O 5 HOH C 4 604 13 HOH HOH . O 5 HOH C 5 605 31 HOH HOH . O 5 HOH C 6 606 16 HOH HOH . O 5 HOH C 7 607 93 HOH HOH . O 5 HOH C 8 608 30 HOH HOH . O 5 HOH C 9 609 28 HOH HOH . O 5 HOH C 10 610 11 HOH HOH . O 5 HOH C 11 611 14 HOH HOH . O 5 HOH C 12 612 95 HOH HOH . O 5 HOH C 13 613 37 HOH HOH . O 5 HOH C 14 614 2 HOH HOH . O 5 HOH C 15 615 34 HOH HOH . O 5 HOH C 16 616 5 HOH HOH . O 5 HOH C 17 617 60 HOH HOH . O 5 HOH C 18 618 38 HOH HOH . O 5 HOH C 19 619 59 HOH HOH . O 5 HOH C 20 620 58 HOH HOH . O 5 HOH C 21 621 35 HOH HOH . O 5 HOH C 22 622 18 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 -25.059 -37.501 47.508 1 63.42 ? C1 EDO 510 A 1 HETATM 2 O O1 EDO . . . J 4 -25.786 -36.433 46.873 1 65.12 ? O1 EDO 510 A 1 HETATM 3 C C2 EDO . . . J 4 -23.676 -37.031 47.99 1 65.17 ? C2 EDO 510 A 1 HETATM 4 O O2 EDO . . . J 4 -22.945 -36.331 46.963 1 62.44 ? O2 EDO 510 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 4 #