data_4DW1 # _model_server_result.job_id 9yaal_ITy-irleRgEHdkJQ _model_server_result.datetime_utc '2024-12-03 18:59:38' _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 4dw1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":509}' # _entry.id 4DW1 # _exptl.entry_id 4DW1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 120 _cell.entry_id 4DW1 _cell.length_a 128.791 _cell.length_b 128.791 _cell.length_c 252.074 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DW1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 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 # _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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O3 HO3 . sing 5 ? 2 6 3 MAN BMA C1 O1 . O6 HO6 . 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 B NAG 1 B 1 NAG A 501 NAG 2 n B NAG 2 B 2 NAG A 502 NAG 2 n B BMA 3 B 3 BMA A 503 BMA 2 n B MAN 4 B 4 MAN A 505 MAN 2 n B MAN 5 B 5 MAN A 506 MAN 2 n B MAN 6 B 6 MAN A 504 MAN # 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 94 A CYS 119 1_555 A SG CYS 143 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf2 A SG CYS 104 A CYS 129 1_555 A SG CYS 127 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 110 A CYS 135 1_555 A SG CYS 137 A CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 195 A CYS 220 1_555 A SG CYS 205 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf5 A SG CYS 239 A CYS 264 1_555 A SG CYS 248 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 88 A ASN 113 1_555 C C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale2 A ND2 ASN 188 A ASN 213 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale4 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale5 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale6 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 B O3 MAN . B MAN 4 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 GOL sing 202 n n C1 C2 GOL sing 203 n n C1 H11 GOL sing 204 n n C1 H12 GOL sing 205 n n O1 HO1 GOL sing 206 n n C2 O2 GOL sing 207 n n C2 C3 GOL sing 208 n n C2 H2 GOL sing 209 n n O2 HO2 GOL sing 210 n n C3 O3 GOL sing 211 n n C3 H31 GOL sing 212 n n C3 H32 GOL sing 213 n n O3 HO3 GOL sing 214 n n # _atom_sites.entry_id 4DW1 _atom_sites.fract_transf_matrix[1][1] 0.007765 _atom_sites.fract_transf_matrix[1][2] 0.004483 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008966 _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] 0.003967 _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 C 3 NAG A 1 507 511 NAG NAG . D 4 ATP A 1 508 1 ATP ATP . E 5 GOL A 1 509 1 GOL GOL . F 5 GOL A 1 510 2 GOL GOL . G 6 HOH A 1 601 1 HOH HOH . G 6 HOH A 2 602 2 HOH HOH . G 6 HOH A 3 603 3 HOH HOH . G 6 HOH A 4 604 4 HOH HOH . G 6 HOH A 5 605 5 HOH HOH . G 6 HOH A 6 606 6 HOH HOH . G 6 HOH A 7 607 7 HOH HOH . G 6 HOH A 8 608 8 HOH HOH . G 6 HOH A 9 609 9 HOH HOH . G 6 HOH A 10 610 10 HOH HOH . G 6 HOH A 11 611 11 HOH HOH . G 6 HOH A 12 612 12 HOH HOH . G 6 HOH A 13 613 13 HOH HOH . G 6 HOH A 14 614 14 HOH HOH . G 6 HOH A 15 615 15 HOH HOH . G 6 HOH A 16 616 16 HOH HOH . G 6 HOH A 17 617 17 HOH HOH . G 6 HOH A 18 618 18 HOH HOH . G 6 HOH A 19 619 19 HOH HOH . G 6 HOH A 20 620 20 HOH HOH . G 6 HOH A 21 621 21 HOH HOH . G 6 HOH A 22 622 22 HOH HOH . G 6 HOH A 23 623 23 HOH HOH . G 6 HOH A 24 624 24 HOH HOH . G 6 HOH A 25 625 25 HOH HOH . G 6 HOH A 26 626 26 HOH HOH . G 6 HOH A 27 627 27 HOH HOH . G 6 HOH A 28 628 28 HOH HOH . G 6 HOH A 29 629 29 HOH HOH . G 6 HOH A 30 630 30 HOH HOH . G 6 HOH A 31 631 31 HOH HOH . G 6 HOH A 32 632 32 HOH HOH . G 6 HOH A 33 633 33 HOH HOH . G 6 HOH A 34 634 34 HOH HOH . G 6 HOH A 35 635 35 HOH HOH . G 6 HOH A 36 636 36 HOH HOH . G 6 HOH A 37 637 37 HOH HOH . G 6 HOH A 38 638 38 HOH HOH . G 6 HOH A 39 639 39 HOH HOH . G 6 HOH A 40 640 40 HOH HOH . G 6 HOH A 41 641 41 HOH HOH . G 6 HOH A 42 642 42 HOH HOH . G 6 HOH A 43 643 43 HOH HOH . G 6 HOH A 44 644 44 HOH HOH . G 6 HOH A 45 645 45 HOH HOH . G 6 HOH A 46 646 46 HOH HOH . G 6 HOH A 47 647 47 HOH HOH . G 6 HOH A 48 648 48 HOH HOH . G 6 HOH A 49 649 49 HOH HOH . G 6 HOH A 50 650 50 HOH HOH . G 6 HOH A 51 651 51 HOH HOH . G 6 HOH A 52 652 52 HOH HOH . G 6 HOH A 53 653 53 HOH HOH . G 6 HOH A 54 654 54 HOH HOH . G 6 HOH A 55 655 55 HOH HOH . G 6 HOH A 56 656 56 HOH HOH . G 6 HOH A 57 657 57 HOH HOH . G 6 HOH A 58 658 58 HOH HOH . G 6 HOH A 59 659 59 HOH HOH . G 6 HOH A 60 660 60 HOH HOH . G 6 HOH A 61 661 61 HOH HOH . G 6 HOH A 62 662 62 HOH HOH . G 6 HOH A 63 663 63 HOH HOH . G 6 HOH A 64 664 64 HOH HOH . G 6 HOH A 65 665 65 HOH HOH . G 6 HOH A 66 666 66 HOH HOH . G 6 HOH A 67 667 67 HOH HOH . G 6 HOH A 68 668 68 HOH HOH . G 6 HOH A 69 669 69 HOH HOH . G 6 HOH A 70 670 70 HOH HOH . G 6 HOH A 71 671 71 HOH HOH . G 6 HOH A 72 672 72 HOH HOH . G 6 HOH A 73 673 73 HOH HOH . G 6 HOH A 74 674 74 HOH HOH . G 6 HOH A 75 675 75 HOH HOH . G 6 HOH A 76 676 76 HOH HOH . G 6 HOH A 77 677 77 HOH HOH . G 6 HOH A 78 678 78 HOH HOH . G 6 HOH A 79 679 82 HOH HOH . G 6 HOH A 80 680 83 HOH HOH . G 6 HOH A 81 681 84 HOH HOH . G 6 HOH A 82 682 85 HOH HOH . G 6 HOH A 83 683 86 HOH HOH . G 6 HOH A 84 684 87 HOH HOH . G 6 HOH A 85 685 88 HOH HOH . G 6 HOH A 86 686 89 HOH HOH . G 6 HOH A 87 687 90 HOH HOH . G 6 HOH A 88 688 91 HOH HOH . G 6 HOH A 89 689 92 HOH HOH . G 6 HOH A 90 690 93 HOH HOH . G 6 HOH A 91 691 94 HOH HOH . G 6 HOH A 92 692 95 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 GOL . . . E 5 -16.184 -1.803 53.64 1 70.36 ? C1 GOL 509 A 1 HETATM 2 O O1 GOL . . . E 5 -17.096 -1.567 52.595 1 68.82 ? O1 GOL 509 A 1 HETATM 3 C C2 GOL . . . E 5 -15.858 -3.289 53.647 1 74.48 ? C2 GOL 509 A 1 HETATM 4 O O2 GOL . . . E 5 -14.689 -3.552 52.894 1 72.2 ? O2 GOL 509 A 1 HETATM 5 C C3 GOL . . . E 5 -17.065 -4.046 53.097 1 71.83 ? C3 GOL 509 A 1 HETATM 6 O O3 GOL . . . E 5 -18.136 -3.775 53.973 1 72.75 ? O3 GOL 509 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 6 #