data_5MNV # _model_server_result.job_id r7Ot-MVDUsjlFl1z5q7gUA _model_server_result.datetime_utc '2024-10-11 00:23:32' _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 5mnv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":502}' # _entry.id 5MNV # _exptl.entry_id 5MNV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 386.523 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '6-DEOXYERYTHRONOLIDE B' _entity.pdbx_number_of_molecules 9 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 103.9 _cell.angle_beta 104.3 _cell.angle_gamma 114.7 _cell.entry_id 5MNV _cell.length_a 112.5 _cell.length_b 116.7 _cell.length_c 123.3 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MNV _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 PISA monomeric 1 author_and_software_defined_assembly 5 PISA monomeric 1 author_and_software_defined_assembly 6 PISA monomeric 1 author_and_software_defined_assembly 7 PISA monomeric 1 author_and_software_defined_assembly 8 PISA monomeric 1 author_and_software_defined_assembly 9 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,J,K,BA 1 1 B,L,M,CA 2 1 C,N,O,DA 3 1 D,P,Q,EA 4 1 E,R,S,FA 5 1 F,T,U,GA 6 1 G,V,W,HA 7 1 H,X,Y,IA 8 1 I,Z,AA 9 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 K N N ? 3 M N N ? 3 O N N ? 3 Q N N ? 3 S N N ? 3 U N N ? 3 W N N ? 3 Y N N ? 3 AA 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 356 A CYS 356 1_555 J FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc2 J FE HEM . A HEM 501 1_555 BA O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc3 B SG CYS 356 B CYS 356 1_555 L FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc4 C SG CYS 356 C CYS 356 1_555 N FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc5 E SG CYS 356 E CYS 356 1_555 R FE HEM . E HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc6 F SG CYS 356 F CYS 356 1_555 T FE HEM . F HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc7 T FE HEM . F HEM 501 1_555 GA O HOH . F HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? metalc ? metalc8 G SG CYS 356 G CYS 356 1_555 V FE HEM . G HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc9 H SG CYS 356 H CYS 356 1_555 X FE HEM . H HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc10 X FE HEM . H HEM 501 1_555 IA O HOH . H HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? # _chem_comp.formula 'C21 H38 O6' _chem_comp.formula_weight 386.523 _chem_comp.id DEB _chem_comp.mon_nstd_flag . _chem_comp.name '6-DEOXYERYTHRONOLIDE B' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C2 DEB sing 83 n n C1 O16 DEB sing 84 n n C1 O17 DEB doub 85 n n C2 C3 DEB sing 86 n n C2 C18 DEB sing 87 n n C2 H2 DEB sing 88 n n C3 C4 DEB sing 89 n n C3 O19 DEB sing 90 n n C3 H3 DEB sing 91 n n C4 C5 DEB sing 92 n n C4 C20 DEB sing 93 n n C4 H4 DEB sing 94 n n C5 C6 DEB sing 95 n n C5 O21 DEB sing 96 n n C5 H5 DEB sing 97 n n C6 C7 DEB sing 98 n n C6 C22 DEB sing 99 n n C6 H6 DEB sing 100 n n C7 C8 DEB sing 101 n n C7 H71 DEB sing 102 n n C7 H72 DEB sing 103 n n C8 C9 DEB sing 104 n n C8 C23 DEB sing 105 n n C8 H8 DEB sing 106 n n C9 C10 DEB sing 107 n n C9 O24 DEB doub 108 n n C10 C11 DEB sing 109 n n C10 C25 DEB sing 110 n n C10 H10 DEB sing 111 n n C11 C12 DEB sing 112 n n C11 O26 DEB sing 113 n n C11 H11 DEB sing 114 n n C12 C13 DEB sing 115 n n C12 C27 DEB sing 116 n n C12 H12 DEB sing 117 n n C13 C14 DEB sing 118 n n C13 O16 DEB sing 119 n n C13 H13 DEB sing 120 n n C14 C15 DEB sing 121 n n C14 H141 DEB sing 122 n n C14 H142 DEB sing 123 n n C15 H151 DEB sing 124 n n C15 H152 DEB sing 125 n n C15 H153 DEB sing 126 n n C18 H181 DEB sing 127 n n C18 H182 DEB sing 128 n n C18 H183 DEB sing 129 n n O19 HO9 DEB sing 130 n n C20 H201 DEB sing 131 n n C20 H202 DEB sing 132 n n C20 H203 DEB sing 133 n n O21 HO1 DEB sing 134 n n C22 H221 DEB sing 135 n n C22 H222 DEB sing 136 n n C22 H223 DEB sing 137 n n C23 H231 DEB sing 138 n n C23 H232 DEB sing 139 n n C23 H233 DEB sing 140 n n C25 H251 DEB sing 141 n n C25 H252 DEB sing 142 n n C25 H253 DEB sing 143 n n O26 HO6 DEB sing 144 n n C27 H271 DEB sing 145 n n C27 H272 DEB sing 146 n n C27 H273 DEB sing 147 n n # _atom_sites.entry_id 5MNV _atom_sites.fract_transf_matrix[1][1] 0.008889 _atom_sites.fract_transf_matrix[1][2] 0.004088 _atom_sites.fract_transf_matrix[1][3] 0.004193 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009432 _atom_sites.fract_transf_matrix[2][3] 0.003996 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.00909 _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 J 2 HEM A 1 501 501 HEM HEM . K 3 DEB A 1 502 502 DEB DEB . L 2 HEM B 1 501 501 HEM HEM . M 3 DEB B 1 502 502 DEB DEB . N 2 HEM C 1 501 501 HEM HEM . O 3 DEB C 1 502 502 DEB DEB . P 2 HEM D 1 501 501 HEM HEM . Q 3 DEB D 1 502 502 DEB DEB . R 2 HEM E 1 501 501 HEM HEM . S 3 DEB E 1 502 502 DEB DEB . T 2 HEM F 1 501 501 HEM HEM . U 3 DEB F 1 502 502 DEB DEB . V 2 HEM G 1 501 501 HEM HEM . W 3 DEB G 1 502 502 DEB DEB . X 2 HEM H 1 501 501 HEM HEM . Y 3 DEB H 1 502 502 DEB DEB . Z 2 HEM I 1 501 501 HEM HEM . AA 3 DEB I 1 502 502 DEB DEB . BA 4 HOH A 1 601 601 HOH HOH . BA 4 HOH A 2 602 602 HOH HOH . BA 4 HOH A 3 603 603 HOH HOH . BA 4 HOH A 4 604 604 HOH HOH . BA 4 HOH A 5 605 605 HOH HOH . BA 4 HOH A 6 606 606 HOH HOH . BA 4 HOH A 7 607 607 HOH HOH . BA 4 HOH A 8 608 608 HOH HOH . BA 4 HOH A 9 609 609 HOH HOH . BA 4 HOH A 10 610 610 HOH HOH . BA 4 HOH A 11 611 611 HOH HOH . BA 4 HOH A 12 612 612 HOH HOH . BA 4 HOH A 13 613 613 HOH HOH . BA 4 HOH A 14 614 614 HOH HOH . BA 4 HOH A 15 615 615 HOH HOH . BA 4 HOH A 16 616 616 HOH HOH . BA 4 HOH A 17 617 617 HOH HOH . BA 4 HOH A 18 618 618 HOH HOH . BA 4 HOH A 19 619 619 HOH HOH . BA 4 HOH A 20 620 620 HOH HOH . BA 4 HOH A 21 621 621 HOH HOH . BA 4 HOH A 22 622 622 HOH HOH . BA 4 HOH A 23 623 623 HOH HOH . BA 4 HOH A 24 624 624 HOH HOH . BA 4 HOH A 25 625 625 HOH HOH . BA 4 HOH A 26 626 626 HOH HOH . CA 4 HOH B 1 601 601 HOH HOH . CA 4 HOH B 2 602 602 HOH HOH . CA 4 HOH B 3 603 603 HOH HOH . CA 4 HOH B 4 604 604 HOH HOH . CA 4 HOH B 5 605 605 HOH HOH . CA 4 HOH B 6 606 606 HOH HOH . CA 4 HOH B 7 607 607 HOH HOH . DA 4 HOH C 1 601 601 HOH HOH . DA 4 HOH C 2 602 602 HOH HOH . DA 4 HOH C 3 603 603 HOH HOH . DA 4 HOH C 4 604 604 HOH HOH . DA 4 HOH C 5 605 605 HOH HOH . DA 4 HOH C 6 606 606 HOH HOH . DA 4 HOH C 7 607 607 HOH HOH . DA 4 HOH C 8 608 608 HOH HOH . DA 4 HOH C 9 609 609 HOH HOH . DA 4 HOH C 10 610 610 HOH HOH . DA 4 HOH C 11 611 611 HOH HOH . DA 4 HOH C 12 612 612 HOH HOH . DA 4 HOH C 13 613 613 HOH HOH . EA 4 HOH D 1 601 601 HOH HOH . EA 4 HOH D 2 602 602 HOH HOH . EA 4 HOH D 3 603 603 HOH HOH . EA 4 HOH D 4 604 604 HOH HOH . EA 4 HOH D 5 605 605 HOH HOH . EA 4 HOH D 6 606 606 HOH HOH . EA 4 HOH D 7 607 607 HOH HOH . EA 4 HOH D 8 608 608 HOH HOH . EA 4 HOH D 9 609 609 HOH HOH . EA 4 HOH D 10 610 610 HOH HOH . EA 4 HOH D 11 611 611 HOH HOH . EA 4 HOH D 12 612 612 HOH HOH . EA 4 HOH D 13 613 613 HOH HOH . EA 4 HOH D 14 614 614 HOH HOH . EA 4 HOH D 15 615 615 HOH HOH . EA 4 HOH D 16 616 616 HOH HOH . EA 4 HOH D 17 617 617 HOH HOH . EA 4 HOH D 18 618 618 HOH HOH . EA 4 HOH D 19 619 619 HOH HOH . EA 4 HOH D 20 620 620 HOH HOH . EA 4 HOH D 21 621 621 HOH HOH . EA 4 HOH D 22 622 622 HOH HOH . EA 4 HOH D 23 623 623 HOH HOH . EA 4 HOH D 24 624 624 HOH HOH . EA 4 HOH D 25 625 625 HOH HOH . EA 4 HOH D 26 626 626 HOH HOH . EA 4 HOH D 27 627 627 HOH HOH . EA 4 HOH D 28 628 628 HOH HOH . FA 4 HOH E 1 601 601 HOH HOH . FA 4 HOH E 2 602 602 HOH HOH . FA 4 HOH E 3 603 603 HOH HOH . FA 4 HOH E 4 604 604 HOH HOH . FA 4 HOH E 5 605 605 HOH HOH . FA 4 HOH E 6 606 606 HOH HOH . FA 4 HOH E 7 607 607 HOH HOH . GA 4 HOH F 1 601 601 HOH HOH . GA 4 HOH F 2 602 602 HOH HOH . GA 4 HOH F 3 603 603 HOH HOH . GA 4 HOH F 4 604 604 HOH HOH . GA 4 HOH F 5 605 605 HOH HOH . GA 4 HOH F 6 606 606 HOH HOH . GA 4 HOH F 7 607 607 HOH HOH . GA 4 HOH F 8 608 608 HOH HOH . GA 4 HOH F 9 609 609 HOH HOH . GA 4 HOH F 10 610 610 HOH HOH . GA 4 HOH F 11 611 611 HOH HOH . GA 4 HOH F 12 612 612 HOH HOH . GA 4 HOH F 13 613 613 HOH HOH . GA 4 HOH F 14 614 614 HOH HOH . GA 4 HOH F 15 615 615 HOH HOH . HA 4 HOH G 1 601 601 HOH HOH . HA 4 HOH G 2 602 602 HOH HOH . HA 4 HOH G 3 603 603 HOH HOH . HA 4 HOH G 4 604 604 HOH HOH . HA 4 HOH G 5 605 605 HOH HOH . IA 4 HOH H 1 601 601 HOH HOH . IA 4 HOH H 2 602 602 HOH HOH . IA 4 HOH H 3 603 603 HOH HOH . IA 4 HOH H 4 604 604 HOH HOH . IA 4 HOH H 5 605 605 HOH HOH . IA 4 HOH H 6 606 606 HOH HOH . IA 4 HOH H 7 607 607 HOH HOH . IA 4 HOH H 8 608 608 HOH HOH . IA 4 HOH H 9 609 609 HOH HOH . IA 4 HOH H 10 610 610 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 DEB . . . M 3 -38.454 -6.997 37.423 1 56.65 ? C1 DEB 502 B 1 HETATM 2 C C2 DEB . . . M 3 -39.339 -7.897 36.605 1 54.32 ? C2 DEB 502 B 1 HETATM 3 C C3 DEB . . . M 3 -40.211 -8.789 37.502 1 52.36 ? C3 DEB 502 B 1 HETATM 4 C C4 DEB . . . M 3 -40.174 -10.263 37.108 1 52.1 ? C4 DEB 502 B 1 HETATM 5 C C5 DEB . . . M 3 -40.892 -11.129 38.153 1 52.77 ? C5 DEB 502 B 1 HETATM 6 C C6 DEB . . . M 3 -40.133 -11.45 39.453 1 52.8 ? C6 DEB 502 B 1 HETATM 7 C C7 DEB . . . M 3 -38.68 -11.885 39.291 1 53.06 ? C7 DEB 502 B 1 HETATM 8 C C8 DEB . . . M 3 -37.942 -11.98 40.628 1 54.33 ? C8 DEB 502 B 1 HETATM 9 C C9 DEB . . . M 3 -37.422 -10.629 41.047 1 55.77 ? C9 DEB 502 B 1 HETATM 10 C C10 DEB . . . M 3 -36.284 -9.987 40.283 1 55.35 ? C10 DEB 502 B 1 HETATM 11 C C11 DEB . . . M 3 -36.603 -8.532 39.904 1 55.23 ? C11 DEB 502 B 1 HETATM 12 C C12 DEB . . . M 3 -35.604 -7.909 38.913 1 54.89 ? C12 DEB 502 B 1 HETATM 13 C C13 DEB . . . M 3 -36.203 -6.636 38.313 1 53.4 ? C13 DEB 502 B 1 HETATM 14 C C14 DEB . . . M 3 -35.116 -5.667 37.878 1 53.53 ? C14 DEB 502 B 1 HETATM 15 C C15 DEB . . . M 3 -35.736 -4.399 37.335 1 55.36 ? C15 DEB 502 B 1 HETATM 16 O O16 DEB . . . M 3 -37.015 -6.952 37.181 1 53.97 ? O16 DEB 502 B 1 HETATM 17 O O17 DEB . . . M 3 -38.945 -6.286 38.286 1 62.07 ? O17 DEB 502 B 1 HETATM 18 C C18 DEB . . . M 3 -40.163 -7.002 35.677 1 54.44 ? C18 DEB 502 B 1 HETATM 19 O O19 DEB . . . M 3 -41.568 -8.346 37.439 1 51.72 ? O19 DEB 502 B 1 HETATM 20 C C20 DEB . . . M 3 -40.799 -10.492 35.731 1 52.74 ? C20 DEB 502 B 1 HETATM 21 O O21 DEB . . . M 3 -41.296 -12.365 37.55 1 52.13 ? O21 DEB 502 B 1 HETATM 22 C C22 DEB . . . M 3 -40.914 -12.543 40.18 1 52.35 ? C22 DEB 502 B 1 HETATM 23 C C23 DEB . . . M 3 -36.802 -12.997 40.552 1 55.07 ? C23 DEB 502 B 1 HETATM 24 O O24 DEB . . . M 3 -37.931 -10.082 42.019 1 57.87 ? O24 DEB 502 B 1 HETATM 25 C C25 DEB . . . M 3 -34.99 -10.113 41.085 1 55.26 ? C25 DEB 502 B 1 HETATM 26 O O26 DEB . . . M 3 -36.639 -7.697 41.075 1 53.92 ? O26 DEB 502 B 1 HETATM 27 C C27 DEB . . . M 3 -35.117 -8.86 37.814 1 54.59 ? C27 DEB 502 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #