data_3RX8 # _model_server_result.job_id '_Jx7biTk81MreIKYp1GGiw' _model_server_result.datetime_utc '2025-02-18 06:35:03' _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 3rx8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":603}' # _entry.id 3RX8 # _exptl.entry_id 3RX8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.313 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 2 _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 3RX8 _cell.length_a 85.41 _cell.length_b 129.34 _cell.length_c 49.39 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RX8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F 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 SG CYS 104 A CYS 104 1_555 C ZN ZN . A ZN 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc2 A SG CYS 121 A CYS 121 1_555 C ZN ZN . A ZN 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc3 A ND1 HIS 122 A HIS 122 1_555 C ZN ZN . A ZN 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc4 A NE2 HIS 142 A HIS 142 1_555 C ZN ZN . A ZN 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc5 A OD2 ASP 302 A ASP 302 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc6 A O GLU 304 A GLU 304 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc7 A OD1 ASP 307 A ASP 307 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc8 A OD2 ASP 307 A ASP 307 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc9 A OE2 GLU 308 A GLU 308 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc10 A OE1 GLU 308 A GLU 308 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc11 A O ALA 344 A ALA 344 1_555 B CA CA . A CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? # _chem_comp.formula 'C12 H23 N O8' _chem_comp.formula_weight 309.313 _chem_comp.id 9MR _chem_comp.mon_nstd_flag n _chem_comp.name '(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'CELLOBIOSE-LIKE ISOFAGOMINE;(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucoside;(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl D-glucoside;(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl glucoside' # 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 O2 C2 9MR sing 1 n n O2 HO2 9MR sing 2 n n C2 C1 9MR sing 3 n n C2 C3 9MR sing 4 n n C2 H2 9MR sing 5 n n C3 C4 9MR sing 6 n n C3 O3 9MR sing 7 n n C3 H3 9MR sing 8 n n O3 HO3 9MR sing 9 n n C4 C5 9MR sing 10 n n C4 O4 9MR sing 11 n n C4 H4 9MR sing 12 n n O4 HO4 9MR sing 13 n n C5 C6 9MR sing 14 n n C5 O5 9MR sing 15 n n C5 H5 9MR sing 16 n n C6 O6 9MR sing 17 n n C6 H61 9MR sing 18 n n C6 H62 9MR sing 19 n n O6 HO6 9MR sing 20 n n O5 C1 9MR sing 21 n n C1 O1 9MR sing 22 n n C1 H1 9MR sing 23 n n O1 C3A 9MR sing 24 n n C3A C2A 9MR sing 25 n n C3A C4A 9MR sing 26 n n C3A H3A 9MR sing 27 n n C4A C5M 9MR sing 28 n n C4A O4A 9MR sing 29 n n C4A H4A 9MR sing 30 n n O4A HO4A 9MR sing 31 n n C5M N5A 9MR sing 32 n n C5M H5M1 9MR sing 33 n n C5M H5M2 9MR sing 34 n n N5A C1A 9MR sing 35 n n N5A HN5A 9MR sing 36 n n C1A C2A 9MR sing 37 n n C1A H1A1 9MR sing 38 n n C1A H1A2 9MR sing 39 n n C2A C6A 9MR sing 40 n n C2A H2A 9MR sing 41 n n C6A O6A 9MR sing 42 n n C6A H6A1 9MR sing 43 n n C6A H6A2 9MR sing 44 n n O6A HO6A 9MR sing 45 n n # _atom_sites.entry_id 3RX8 _atom_sites.fract_transf_matrix[1][1] 0.011708 _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] 0.007732 _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] 0.020247 _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 B 2 CA A 1 538 1 CA CA . C 3 ZN A 1 539 2 ZN ZN . D 4 MPD A 1 540 540 MPD MPD . E 5 9MR A 1 603 603 9MR 9MR . F 5 9MR A 1 601 601 9MR 9MR . G 6 HOH A 1 541 1 HOH HOH . G 6 HOH A 2 542 2 HOH HOH . G 6 HOH A 3 543 3 HOH HOH . G 6 HOH A 4 544 4 HOH HOH . G 6 HOH A 5 545 5 HOH HOH . G 6 HOH A 6 546 6 HOH HOH . G 6 HOH A 7 547 7 HOH HOH . G 6 HOH A 8 548 8 HOH HOH . G 6 HOH A 9 549 9 HOH HOH . G 6 HOH A 10 550 10 HOH HOH . G 6 HOH A 11 551 11 HOH HOH . G 6 HOH A 12 552 12 HOH HOH . G 6 HOH A 13 553 13 HOH HOH . G 6 HOH A 14 554 14 HOH HOH . G 6 HOH A 15 555 15 HOH HOH . G 6 HOH A 16 556 16 HOH HOH . G 6 HOH A 17 557 17 HOH HOH . G 6 HOH A 18 558 18 HOH HOH . G 6 HOH A 19 559 19 HOH HOH . G 6 HOH A 20 560 20 HOH HOH . G 6 HOH A 21 561 21 HOH HOH . G 6 HOH A 22 562 22 HOH HOH . G 6 HOH A 23 563 23 HOH HOH . G 6 HOH A 24 564 24 HOH HOH . G 6 HOH A 25 565 25 HOH HOH . G 6 HOH A 26 566 26 HOH HOH . G 6 HOH A 27 567 27 HOH HOH . G 6 HOH A 28 568 28 HOH HOH . G 6 HOH A 29 569 29 HOH HOH . G 6 HOH A 30 570 30 HOH HOH . G 6 HOH A 31 571 31 HOH HOH . G 6 HOH A 32 572 32 HOH HOH . G 6 HOH A 33 573 33 HOH HOH . G 6 HOH A 34 574 34 HOH HOH . G 6 HOH A 35 575 35 HOH HOH . G 6 HOH A 36 576 36 HOH HOH . G 6 HOH A 37 577 37 HOH HOH . G 6 HOH A 38 578 38 HOH HOH . G 6 HOH A 39 579 39 HOH HOH . G 6 HOH A 40 580 40 HOH HOH . G 6 HOH A 41 581 41 HOH HOH . G 6 HOH A 42 582 42 HOH HOH . G 6 HOH A 43 583 43 HOH HOH . G 6 HOH A 44 584 44 HOH HOH . G 6 HOH A 45 585 45 HOH HOH . G 6 HOH A 46 586 46 HOH HOH . G 6 HOH A 47 587 47 HOH HOH . G 6 HOH A 48 588 48 HOH HOH . G 6 HOH A 49 589 49 HOH HOH . G 6 HOH A 50 590 50 HOH HOH . G 6 HOH A 51 591 51 HOH HOH . G 6 HOH A 52 592 52 HOH HOH . G 6 HOH A 53 593 53 HOH HOH . G 6 HOH A 54 594 54 HOH HOH . G 6 HOH A 55 595 55 HOH HOH . G 6 HOH A 56 596 56 HOH HOH . G 6 HOH A 57 597 57 HOH HOH . G 6 HOH A 58 598 58 HOH HOH . G 6 HOH A 59 599 59 HOH HOH . G 6 HOH A 60 600 60 HOH HOH . G 6 HOH A 61 602 61 HOH HOH . G 6 HOH A 62 604 62 HOH HOH . G 6 HOH A 63 605 63 HOH HOH . G 6 HOH A 64 606 64 HOH HOH . G 6 HOH A 65 607 65 HOH HOH . G 6 HOH A 66 608 66 HOH HOH . G 6 HOH A 67 609 67 HOH HOH . G 6 HOH A 68 610 68 HOH HOH . G 6 HOH A 69 611 69 HOH HOH . G 6 HOH A 70 612 70 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 O O2 9MR . . . E 5 -12.706 35.747 -33.709 1 53.51 ? O2 9MR 603 A 1 HETATM 2 C C2 9MR . . . E 5 -14.126 35.842 -33.931 1 54.42 ? C2 9MR 603 A 1 HETATM 3 C C3 9MR . . . E 5 -14.564 36.974 -34.965 1 56.14 ? C3 9MR 603 A 1 HETATM 4 O O3 9MR . . . E 5 -14.511 36.796 -36.434 1 58.66 ? O3 9MR 603 A 1 HETATM 5 C C4 9MR . . . E 5 -15.937 37.724 -34.688 1 56.67 ? C4 9MR 603 A 1 HETATM 6 O O4 9MR . . . E 5 -15.411 38.917 -35.068 1 58.4 ? O4 9MR 603 A 1 HETATM 7 C C5 9MR . . . E 5 -15.976 38.007 -33.174 1 55.45 ? C5 9MR 603 A 1 HETATM 8 C C6 9MR . . . E 5 -16.798 39.138 -32.466 1 52.37 ? C6 9MR 603 A 1 HETATM 9 O O6 9MR . . . E 5 -17.952 39.263 -33.144 1 50.13 ? O6 9MR 603 A 1 HETATM 10 O O5 9MR . . . E 5 -15.959 36.742 -32.481 1 56.06 ? O5 9MR 603 A 1 HETATM 11 C C1 9MR . . . E 5 -14.613 36.233 -32.491 1 54.29 ? C1 9MR 603 A 1 HETATM 12 O O1 9MR . . . E 5 -14.554 35.956 -31.256 1 50.93 ? O1 9MR 603 A 1 HETATM 13 C C3A 9MR . . . E 5 -14.596 35.891 -29.825 1 47.52 ? C3A 9MR 603 A 1 HETATM 14 C C4A 9MR . . . E 5 -15.963 35.2 -29.619 1 44.28 ? C4A 9MR 603 A 1 HETATM 15 O O4A 9MR . . . E 5 -17.033 36.021 -30.053 1 42.24 ? O4A 9MR 603 A 1 HETATM 16 C C5M 9MR . . . E 5 -16.248 34.661 -28.2 1 44.04 ? C5M 9MR 603 A 1 HETATM 17 N N5A 9MR . . . E 5 -15.009 34.255 -27.432 1 47.25 ? N5A 9MR 603 A 1 HETATM 18 C C1A 9MR . . . E 5 -13.635 34.869 -27.737 1 46.5 ? C1A 9MR 603 A 1 HETATM 19 C C2A 9MR . . . E 5 -13.589 34.86 -29.287 1 47.23 ? C2A 9MR 603 A 1 HETATM 20 C C6A 9MR . . . E 5 -12.211 34.597 -29.966 1 45.9 ? C6A 9MR 603 A 1 HETATM 21 O O6A 9MR . . . E 5 -11.28 35.564 -29.688 1 46.06 ? O6A 9MR 603 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 21 #