data_3SRD # _model_server_result.job_id 5oS2GrJG15TggRsyori2nA _model_server_result.datetime_utc '2025-04-03 12:31:03' _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 3srd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":534}' # _entry.id 3SRD # _exptl.entry_id 3SRD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 113.56 _cell.angle_gamma 90 _cell.entry_id 3SRD _cell.length_a 95.05 _cell.length_b 117.37 _cell.length_c 110.46 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SRD _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA _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 ? 6 I N N ? 6 M N N ? 6 R N N ? 6 W N N ? 6 X 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 OD1 ASN 95 A ASN 75 1_555 G K K . A K 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc2 A OG SER 97 A SER 77 1_555 G K K . A K 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.346 ? metalc ? metalc3 A OD2 ASP 133 A ASP 113 1_555 G K K . A K 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc4 A O THR 134 A THR 114 1_555 G K K . A K 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc5 A OE2 GLU 292 A GLU 272 1_555 H MG MG . A MG 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc6 A OD2 ASP 316 A ASP 296 1_555 H MG MG . A MG 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc7 E O4 OXL . A OXL 533 1_555 H MG MG . A MG 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc8 E O1 OXL . A OXL 533 1_555 H MG MG . A MG 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? metalc ? metalc9 H MG MG . A MG 535 1_555 Y O HOH . A HOH 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc10 B OE2 GLU 292 B GLU 272 1_555 K MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc11 B OD2 ASP 316 B ASP 296 1_555 K MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc12 J O1 OXL . B OXL 533 1_555 K MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc13 J O4 OXL . B OXL 533 1_555 K MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? metalc ? metalc14 C OD1 ASN 95 C ASN 75 1_555 Q K K . C K 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.252 ? metalc ? metalc15 C OG SER 97 C SER 77 1_555 Q K K . C K 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.5 ? metalc ? metalc16 C OD2 ASP 133 C ASP 113 1_555 Q K K . C K 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.91 ? metalc ? metalc17 C O THR 134 C THR 114 1_555 Q K K . C K 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc18 C OE2 GLU 292 C GLU 272 1_555 P MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc19 C OD2 ASP 316 C ASP 296 1_555 P MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc20 O O3 OXL . C OXL 533 1_555 P MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc21 O O2 OXL . C OXL 533 1_555 P MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc22 AA O HOH . C HOH 544 1_555 Q K K . C K 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.039 ? metalc ? metalc23 D OD1 ASN 95 D ASN 75 1_555 V K K . D K 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc24 D OG SER 97 D SER 77 1_555 V K K . D K 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.179 ? metalc ? metalc25 D OD2 ASP 133 D ASP 113 1_555 V K K . D K 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? metalc ? metalc26 D O THR 134 D THR 114 1_555 V K K . D K 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.802 ? metalc ? metalc27 D OE2 GLU 292 D GLU 272 1_555 U MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc28 D OD2 ASP 316 D ASP 296 1_555 U MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc29 T O1 OXL . D OXL 533 1_555 U MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? metalc ? metalc30 T O4 OXL . D OXL 533 1_555 U MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? # _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 163 n n C1 C2 GOL sing 164 n n C1 H11 GOL sing 165 n n C1 H12 GOL sing 166 n n O1 HO1 GOL sing 167 n n C2 O2 GOL sing 168 n n C2 C3 GOL sing 169 n n C2 H2 GOL sing 170 n n O2 HO2 GOL sing 171 n n C3 O3 GOL sing 172 n n C3 H31 GOL sing 173 n n C3 H32 GOL sing 174 n n O3 HO3 GOL sing 175 n n # _atom_sites.entry_id 3SRD _atom_sites.fract_transf_matrix[1][1] 0.010521 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004588 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00852 _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] 0.009876 _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 2 OXL A 1 533 533 OXL OXL . F 3 FBP A 1 532 532 FBP FBP . G 4 K A 1 534 1 K K . H 5 MG A 1 535 1 MG MG . I 6 GOL A 1 536 1 GOL GOL . J 2 OXL B 1 533 533 OXL OXL . K 5 MG B 1 602 602 MG MG . L 3 FBP B 1 532 532 FBP FBP . M 6 GOL B 1 534 1 GOL GOL . N 3 FBP C 1 532 532 FBP FBP . O 2 OXL C 1 533 533 OXL OXL . P 5 MG C 1 603 603 MG MG . Q 4 K C 1 703 703 K K . R 6 GOL C 1 534 1 GOL GOL . S 3 FBP D 1 532 532 FBP FBP . T 2 OXL D 1 533 533 OXL OXL . U 5 MG D 1 604 604 MG MG . V 4 K D 1 704 704 K K . W 6 GOL D 1 534 1 GOL GOL . X 6 GOL D 1 535 1 GOL GOL . Y 7 HOH A 1 537 1 HOH HOH . Y 7 HOH A 2 538 18 HOH HOH . Y 7 HOH A 3 539 21 HOH HOH . Y 7 HOH A 4 540 24 HOH HOH . Y 7 HOH A 5 541 39 HOH HOH . Y 7 HOH A 6 542 40 HOH HOH . Y 7 HOH A 7 543 43 HOH HOH . Y 7 HOH A 8 544 46 HOH HOH . Y 7 HOH A 9 545 48 HOH HOH . Y 7 HOH A 10 546 50 HOH HOH . Y 7 HOH A 11 547 54 HOH HOH . Y 7 HOH A 12 548 58 HOH HOH . Y 7 HOH A 13 549 61 HOH HOH . Y 7 HOH A 14 550 87 HOH HOH . Y 7 HOH A 15 551 105 HOH HOH . Y 7 HOH A 16 552 125 HOH HOH . Y 7 HOH A 17 553 139 HOH HOH . Y 7 HOH A 18 554 143 HOH HOH . Y 7 HOH A 19 555 152 HOH HOH . Y 7 HOH A 20 556 155 HOH HOH . Y 7 HOH A 21 557 161 HOH HOH . Y 7 HOH A 22 558 164 HOH HOH . Y 7 HOH A 23 559 168 HOH HOH . Y 7 HOH A 24 560 170 HOH HOH . Y 7 HOH A 25 561 171 HOH HOH . Y 7 HOH A 26 562 172 HOH HOH . Y 7 HOH A 27 563 175 HOH HOH . Y 7 HOH A 28 564 199 HOH HOH . Y 7 HOH A 29 565 208 HOH HOH . Y 7 HOH A 30 566 211 HOH HOH . Y 7 HOH A 31 567 216 HOH HOH . Y 7 HOH A 32 568 217 HOH HOH . Y 7 HOH A 33 569 228 HOH HOH . Y 7 HOH A 34 570 237 HOH HOH . Z 7 HOH B 1 535 7 HOH HOH . Z 7 HOH B 2 536 12 HOH HOH . Z 7 HOH B 3 537 15 HOH HOH . Z 7 HOH B 4 538 17 HOH HOH . Z 7 HOH B 5 539 20 HOH HOH . Z 7 HOH B 6 540 23 HOH HOH . Z 7 HOH B 7 541 27 HOH HOH . Z 7 HOH B 8 542 28 HOH HOH . Z 7 HOH B 9 543 31 HOH HOH . Z 7 HOH B 10 544 45 HOH HOH . Z 7 HOH B 11 545 66 HOH HOH . Z 7 HOH B 12 546 72 HOH HOH . Z 7 HOH B 13 547 75 HOH HOH . Z 7 HOH B 14 548 76 HOH HOH . Z 7 HOH B 15 549 78 HOH HOH . Z 7 HOH B 16 550 85 HOH HOH . Z 7 HOH B 17 551 88 HOH HOH . Z 7 HOH B 18 552 91 HOH HOH . Z 7 HOH B 19 553 94 HOH HOH . Z 7 HOH B 20 554 97 HOH HOH . Z 7 HOH B 21 555 111 HOH HOH . Z 7 HOH B 22 556 114 HOH HOH . Z 7 HOH B 23 557 116 HOH HOH . Z 7 HOH B 24 558 118 HOH HOH . Z 7 HOH B 25 559 121 HOH HOH . Z 7 HOH B 26 560 136 HOH HOH . Z 7 HOH B 27 561 156 HOH HOH . Z 7 HOH B 28 562 176 HOH HOH . Z 7 HOH B 29 563 196 HOH HOH . Z 7 HOH B 30 564 201 HOH HOH . Z 7 HOH B 31 565 224 HOH HOH . Z 7 HOH B 32 566 225 HOH HOH . Z 7 HOH B 33 567 226 HOH HOH . Z 7 HOH B 34 568 238 HOH HOH . AA 7 HOH C 1 535 6 HOH HOH . AA 7 HOH C 2 536 11 HOH HOH . AA 7 HOH C 3 537 16 HOH HOH . AA 7 HOH C 4 538 19 HOH HOH . AA 7 HOH C 5 539 22 HOH HOH . AA 7 HOH C 6 540 25 HOH HOH . AA 7 HOH C 7 541 29 HOH HOH . AA 7 HOH C 8 542 32 HOH HOH . AA 7 HOH C 9 543 35 HOH HOH . AA 7 HOH C 10 544 44 HOH HOH . AA 7 HOH C 11 545 47 HOH HOH . AA 7 HOH C 12 546 51 HOH HOH . AA 7 HOH C 13 547 64 HOH HOH . AA 7 HOH C 14 548 73 HOH HOH . AA 7 HOH C 15 549 74 HOH HOH . AA 7 HOH C 16 550 77 HOH HOH . AA 7 HOH C 17 551 86 HOH HOH . AA 7 HOH C 18 552 92 HOH HOH . AA 7 HOH C 19 553 106 HOH HOH . AA 7 HOH C 20 554 108 HOH HOH . AA 7 HOH C 21 555 115 HOH HOH . AA 7 HOH C 22 556 120 HOH HOH . AA 7 HOH C 23 557 123 HOH HOH . AA 7 HOH C 24 558 131 HOH HOH . AA 7 HOH C 25 559 137 HOH HOH . AA 7 HOH C 26 560 153 HOH HOH . AA 7 HOH C 27 561 158 HOH HOH . AA 7 HOH C 28 562 166 HOH HOH . AA 7 HOH C 29 563 193 HOH HOH . AA 7 HOH C 30 564 198 HOH HOH . AA 7 HOH C 31 565 222 HOH HOH . BA 7 HOH D 1 536 2 HOH HOH . BA 7 HOH D 2 537 4 HOH HOH . BA 7 HOH D 3 538 5 HOH HOH . BA 7 HOH D 4 539 9 HOH HOH . BA 7 HOH D 5 540 13 HOH HOH . BA 7 HOH D 6 541 36 HOH HOH . BA 7 HOH D 7 542 55 HOH HOH . BA 7 HOH D 8 543 57 HOH HOH . BA 7 HOH D 9 544 59 HOH HOH . BA 7 HOH D 10 545 62 HOH HOH . BA 7 HOH D 11 546 63 HOH HOH . BA 7 HOH D 12 547 65 HOH HOH . BA 7 HOH D 13 548 71 HOH HOH . BA 7 HOH D 14 549 83 HOH HOH . BA 7 HOH D 15 550 93 HOH HOH . BA 7 HOH D 16 551 98 HOH HOH . BA 7 HOH D 17 552 122 HOH HOH . BA 7 HOH D 18 553 145 HOH HOH . BA 7 HOH D 19 554 147 HOH HOH . BA 7 HOH D 20 555 150 HOH HOH . BA 7 HOH D 21 556 177 HOH HOH . BA 7 HOH D 22 557 178 HOH HOH . BA 7 HOH D 23 558 183 HOH HOH . BA 7 HOH D 24 559 189 HOH HOH . BA 7 HOH D 25 560 192 HOH HOH . BA 7 HOH D 26 561 220 HOH HOH . BA 7 HOH D 27 562 235 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 . . . R 6 9.652 -9.257 -2.492 1 72.58 ? C1 GOL 534 C 1 HETATM 2 O O1 GOL . . . R 6 9.801 -7.875 -2.236 1 72.33 ? O1 GOL 534 C 1 HETATM 3 C C2 GOL . . . R 6 10.916 -10.001 -2.064 1 73.04 ? C2 GOL 534 C 1 HETATM 4 O O2 GOL . . . R 6 11.555 -10.559 -3.188 1 73.29 ? O2 GOL 534 C 1 HETATM 5 C C3 GOL . . . R 6 10.579 -11.124 -1.095 1 72.98 ? C3 GOL 534 C 1 HETATM 6 O O3 GOL . . . R 6 9.751 -12.07 -1.727 1 73.58 ? O3 GOL 534 C 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 412 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #