data_5WAV # _model_server_result.job_id RJOuWvN8nw6jEWvOzBl_iQ _model_server_result.datetime_utc '2024-11-28 19:38:12' _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 5wav # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":510}' # _entry.id 5WAV # _exptl.entry_id 5WAV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 3 _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 5WAV _cell.length_a 49.532 _cell.length_b 79.977 _cell.length_c 139.658 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WAV _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 3 E N N ? 3 F N N ? 3 G 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 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN MAN C1 O1 . O3 HO3 . sing 4 ? 2 5 4 NAG MAN C1 O1 . O2 HO2 . sing 5 ? 2 6 3 MAN MAN C1 O1 . O6 HO6 . sing 6 ? 2 7 6 NAG MAN C1 O1 . O2 HO2 . sing 7 ? 2 8 1 FUC NAG 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 C NAG 1 C 1 NAG A 501 NAG 2 n C NAG 2 C 2 NAG A 502 NAG 2 n C MAN 3 C 3 MAN A 503 MAN 2 n C MAN 4 C 4 MAN A 507 MAN 2 n C NAG 5 C 5 NAG A 508 NAG 2 n C MAN 6 C 6 MAN A 504 MAN 2 n C NAG 7 C 7 NAG A 505 NAG 2 n C FUC 8 C 8 FUC A 511 FUC 2 n D NAG 1 D 1 NAG B 501 NAG 2 n D NAG 2 D 2 NAG B 502 NAG 2 n D MAN 3 D 3 MAN B 503 MAN 2 n D MAN 4 D 4 MAN B 507 MAN 2 n D NAG 5 D 5 NAG B 508 NAG 2 n D MAN 6 D 6 MAN B 504 MAN 2 n D NAG 7 D 7 NAG B 505 NAG 2 n D FUC 8 D 8 FUC B 509 FUC # 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 35 A CYS 261 1_555 A SG CYS 95 A CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf2 A SG CYS 141 A CYS 367 1_555 A SG CYS 199 A CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 B SG CYS 35 B CYS 261 1_555 B SG CYS 95 B CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf4 B SG CYS 141 B CYS 367 1_555 B SG CYS 199 B CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 A ND2 ASN 71 A ASN 297 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 B ND2 ASN 71 B ASN 297 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale5 C O4 NAG . C NAG 2 1_555 C C1 MAN . C MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale6 C O3 MAN . C MAN 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale7 C O6 MAN . C MAN 3 1_555 C C1 MAN . C MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale8 C O2 MAN . C MAN 4 1_555 C C1 NAG . C NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale9 C O2 MAN . C MAN 6 1_555 C C1 NAG . C NAG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale11 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale12 D O4 NAG . D NAG 2 1_555 D C1 MAN . D MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale13 D O3 MAN . D MAN 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale14 D O6 MAN . D MAN 3 1_555 D C1 MAN . D MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale15 D O2 MAN . D MAN 4 1_555 D C1 NAG . D NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale16 D O2 MAN . D MAN 6 1_555 D C1 NAG . D NAG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? # _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 152 n n C1 C2 GOL sing 153 n n C1 H11 GOL sing 154 n n C1 H12 GOL sing 155 n n O1 HO1 GOL sing 156 n n C2 O2 GOL sing 157 n n C2 C3 GOL sing 158 n n C2 H2 GOL sing 159 n n O2 HO2 GOL sing 160 n n C3 O3 GOL sing 161 n n C3 H31 GOL sing 162 n n C3 H32 GOL sing 163 n n O3 HO3 GOL sing 164 n n # _atom_sites.entry_id 5WAV _atom_sites.fract_transf_matrix[1][1] 0.020189 _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] 0.012504 _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] 0.00716 _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 GOL A 1 509 2 GOL GOL . F 3 GOL A 1 510 3 GOL GOL . G 3 GOL B 1 509 1 GOL GOL . H 4 HOH A 1 601 113 HOH HOH . H 4 HOH A 2 602 83 HOH HOH . H 4 HOH A 3 603 96 HOH HOH . H 4 HOH A 4 604 235 HOH HOH . H 4 HOH A 5 605 10 HOH HOH . H 4 HOH A 6 606 3 HOH HOH . H 4 HOH A 7 607 229 HOH HOH . H 4 HOH A 8 608 29 HOH HOH . H 4 HOH A 9 609 21 HOH HOH . H 4 HOH A 10 610 169 HOH HOH . H 4 HOH A 11 611 234 HOH HOH . H 4 HOH A 12 612 231 HOH HOH . H 4 HOH A 13 613 28 HOH HOH . H 4 HOH A 14 614 129 HOH HOH . H 4 HOH A 15 615 200 HOH HOH . H 4 HOH A 16 616 135 HOH HOH . H 4 HOH A 17 617 124 HOH HOH . H 4 HOH A 18 618 122 HOH HOH . H 4 HOH A 19 619 36 HOH HOH . H 4 HOH A 20 620 89 HOH HOH . H 4 HOH A 21 621 136 HOH HOH . H 4 HOH A 22 622 19 HOH HOH . H 4 HOH A 23 623 44 HOH HOH . H 4 HOH A 24 624 49 HOH HOH . H 4 HOH A 25 625 222 HOH HOH . H 4 HOH A 26 626 243 HOH HOH . H 4 HOH A 27 627 155 HOH HOH . H 4 HOH A 28 628 125 HOH HOH . H 4 HOH A 29 629 111 HOH HOH . H 4 HOH A 30 630 148 HOH HOH . H 4 HOH A 31 631 39 HOH HOH . H 4 HOH A 32 632 167 HOH HOH . H 4 HOH A 33 633 127 HOH HOH . H 4 HOH A 34 634 202 HOH HOH . H 4 HOH A 35 635 15 HOH HOH . H 4 HOH A 36 636 130 HOH HOH . H 4 HOH A 37 637 69 HOH HOH . H 4 HOH A 38 638 194 HOH HOH . H 4 HOH A 39 639 128 HOH HOH . H 4 HOH A 40 640 144 HOH HOH . H 4 HOH A 41 641 218 HOH HOH . H 4 HOH A 42 642 201 HOH HOH . H 4 HOH A 43 643 203 HOH HOH . H 4 HOH A 44 644 168 HOH HOH . H 4 HOH A 45 645 248 HOH HOH . H 4 HOH A 46 646 51 HOH HOH . H 4 HOH A 47 647 190 HOH HOH . H 4 HOH A 48 648 182 HOH HOH . H 4 HOH A 49 649 245 HOH HOH . H 4 HOH A 50 650 180 HOH HOH . H 4 HOH A 51 651 121 HOH HOH . H 4 HOH A 52 652 131 HOH HOH . H 4 HOH A 53 653 164 HOH HOH . H 4 HOH A 54 654 11 HOH HOH . H 4 HOH A 55 655 77 HOH HOH . H 4 HOH A 56 656 45 HOH HOH . H 4 HOH A 57 657 181 HOH HOH . H 4 HOH A 58 658 100 HOH HOH . H 4 HOH A 59 659 71 HOH HOH . H 4 HOH A 60 660 244 HOH HOH . H 4 HOH A 61 661 158 HOH HOH . H 4 HOH A 62 662 240 HOH HOH . H 4 HOH A 63 663 33 HOH HOH . H 4 HOH A 64 664 40 HOH HOH . H 4 HOH A 65 665 62 HOH HOH . H 4 HOH A 66 666 25 HOH HOH . H 4 HOH A 67 667 140 HOH HOH . H 4 HOH A 68 668 43 HOH HOH . H 4 HOH A 69 669 58 HOH HOH . H 4 HOH A 70 670 141 HOH HOH . H 4 HOH A 71 671 116 HOH HOH . H 4 HOH A 72 672 81 HOH HOH . H 4 HOH A 73 673 157 HOH HOH . H 4 HOH A 74 674 171 HOH HOH . H 4 HOH A 75 675 80 HOH HOH . H 4 HOH A 76 676 214 HOH HOH . H 4 HOH A 77 677 162 HOH HOH . H 4 HOH A 78 678 226 HOH HOH . H 4 HOH A 79 679 232 HOH HOH . H 4 HOH A 80 680 227 HOH HOH . H 4 HOH A 81 681 34 HOH HOH . I 4 HOH B 1 601 133 HOH HOH . I 4 HOH B 2 602 230 HOH HOH . I 4 HOH B 3 603 147 HOH HOH . I 4 HOH B 4 604 117 HOH HOH . I 4 HOH B 5 605 87 HOH HOH . I 4 HOH B 6 606 112 HOH HOH . I 4 HOH B 7 607 37 HOH HOH . I 4 HOH B 8 608 237 HOH HOH . I 4 HOH B 9 609 134 HOH HOH . I 4 HOH B 10 610 146 HOH HOH . I 4 HOH B 11 611 149 HOH HOH . I 4 HOH B 12 612 160 HOH HOH . I 4 HOH B 13 613 213 HOH HOH . I 4 HOH B 14 614 23 HOH HOH . I 4 HOH B 15 615 183 HOH HOH . I 4 HOH B 16 616 191 HOH HOH . I 4 HOH B 17 617 79 HOH HOH . I 4 HOH B 18 618 153 HOH HOH . I 4 HOH B 19 619 241 HOH HOH . I 4 HOH B 20 620 137 HOH HOH . I 4 HOH B 21 621 6 HOH HOH . I 4 HOH B 22 622 102 HOH HOH . I 4 HOH B 23 623 118 HOH HOH . I 4 HOH B 24 624 212 HOH HOH . I 4 HOH B 25 625 119 HOH HOH . I 4 HOH B 26 626 189 HOH HOH . I 4 HOH B 27 627 197 HOH HOH . I 4 HOH B 28 628 123 HOH HOH . I 4 HOH B 29 629 242 HOH HOH . I 4 HOH B 30 630 27 HOH HOH . I 4 HOH B 31 631 55 HOH HOH . I 4 HOH B 32 632 120 HOH HOH . I 4 HOH B 33 633 238 HOH HOH . I 4 HOH B 34 634 4 HOH HOH . I 4 HOH B 35 635 236 HOH HOH . I 4 HOH B 36 636 1 HOH HOH . I 4 HOH B 37 637 246 HOH HOH . I 4 HOH B 38 638 225 HOH HOH . I 4 HOH B 39 639 104 HOH HOH . I 4 HOH B 40 640 188 HOH HOH . I 4 HOH B 41 641 193 HOH HOH . I 4 HOH B 42 642 217 HOH HOH . I 4 HOH B 43 643 247 HOH HOH . I 4 HOH B 44 644 239 HOH HOH . I 4 HOH B 45 645 233 HOH HOH . I 4 HOH B 46 646 143 HOH HOH . I 4 HOH B 47 647 126 HOH HOH . I 4 HOH B 48 648 224 HOH HOH . I 4 HOH B 49 649 223 HOH HOH . I 4 HOH B 50 650 110 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 . . . F 3 -3.858 5.941 7.92 1 94.96 ? C1 GOL 510 A 1 HETATM 2 O O1 GOL . . . F 3 -3.494 6.01 9.304 1 97.33 ? O1 GOL 510 A 1 HETATM 3 C C2 GOL . . . F 3 -2.647 5.507 7.064 1 92.78 ? C2 GOL 510 A 1 HETATM 4 O O2 GOL . . . F 3 -2.451 6.403 5.951 1 79.65 ? O2 GOL 510 A 1 HETATM 5 C C3 GOL . . . F 3 -2.748 4.033 6.625 1 92.58 ? C3 GOL 510 A 1 HETATM 6 O O3 GOL . . . F 3 -4.042 3.694 6.095 1 88.96 ? O3 GOL 510 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 447 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 6 #