data_1YCF # _model_server_result.job_id g_q-Qc8f2LYBMXaIhR0iPg _model_server_result.datetime_utc '2024-10-14 08:24:05' _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 1ycf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 1YCF # _exptl.entry_id 1YCF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 31.999 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'OXYGEN MOLECULE' _entity.pdbx_number_of_molecules 4 _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 1YCF _cell.length_a 159.67 _cell.length_b 159.67 _cell.length_c 276.798 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YCF _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 PISA dimeric 2 software_defined_assembly 4 PISA dimeric 2 software_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,K,L,M,T,U 1 1 C,D,N,O,P,Q,R,S,V,W 2 1 A,B,E,F,G,H,I,J,K,L,M,T,U 3 1 C,D,N,O,P,Q,R,S,V,W 3 2 A,E,F,G,H,I,T 4 1 C,N,O,P,V 4 2 B,J,K,L,M,U 5 1 D,Q,R,S,W 5 2 # 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' 5_653 -x+3/2,y+1/2,-z-5/4 -1 0 0 0 1 0 0 0 -1 239.505 79.835 -345.9975 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 H N N ? 4 L N N ? 4 O N N ? 4 R 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 covale ? covale1 Q O FEO . D FEO 530 1_555 R O1 OXY . D OXY 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc1 A OG SER 1 A SER 2 1_555 E ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.797 ? metalc ? metalc2 A N SER 1 A SER 2 1_555 E ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc3 A NE2 HIS 80 A HIS 81 1_555 G FE1 FEO . A FEO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc4 A OE2 GLU 82 A GLU 83 1_555 G FE1 FEO . A FEO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc5 A OD2 ASP 84 A ASP 85 1_555 G FE2 FEO . A FEO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc6 A NE2 HIS 85 A HIS 86 1_555 G FE2 FEO . A FEO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc7 A NE2 HIS 147 A HIS 148 1_555 G FE1 FEO . A FEO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc8 A OD2 ASP 166 A ASP 167 1_555 G FE1 FEO . A FEO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc9 A OD1 ASP 166 A ASP 167 1_555 G FE2 FEO . A FEO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc10 A NE2 HIS 227 A HIS 228 1_555 G FE2 FEO . A FEO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc11 A NE2 HIS 270 A HIS 271 1_555 F ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc12 A OD2 ASP 274 A ASP 275 1_555 F ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc13 G FE1 FEO . A FEO 500 1_555 H O1 OXY . A OXY 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.989 ? metalc ? metalc14 G FE2 FEO . A FEO 500 1_555 H O1 OXY . A OXY 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.917 ? metalc ? metalc15 E ZN ZN . A ZN 502 1_555 C NE2 HIS 270 C HIS 271 5_653 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc16 E ZN ZN . A ZN 502 1_555 C OD2 ASP 274 C ASP 275 5_653 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc17 F ZN ZN . A ZN 503 1_555 C N SER 1 C SER 2 5_653 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc18 F ZN ZN . A ZN 503 1_555 C OE2 GLU 59 C GLU 60 5_653 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc19 B NE2 HIS 80 B HIS 81 1_555 K FE1 FEO . B FEO 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc20 B OE2 GLU 82 B GLU 83 1_555 K FE1 FEO . B FEO 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? metalc ? metalc21 B OD2 ASP 84 B ASP 85 1_555 K FE2 FEO . B FEO 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc22 B NE2 HIS 85 B HIS 86 1_555 K FE2 FEO . B FEO 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc23 B NE2 HIS 147 B HIS 148 1_555 K FE1 FEO . B FEO 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc24 B OD1 ASP 166 B ASP 167 1_555 K FE2 FEO . B FEO 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc25 B OD2 ASP 166 B ASP 167 1_555 K FE1 FEO . B FEO 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc26 B NE2 HIS 227 B HIS 228 1_555 K FE2 FEO . B FEO 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc27 K FE2 FEO . B FEO 510 1_555 L O1 OXY . B OXY 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc28 C NE2 HIS 80 C HIS 81 1_555 N FE1 FEO . C FEO 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc29 C OE1 GLU 82 C GLU 83 1_555 N FE1 FEO . C FEO 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc30 C OD2 ASP 84 C ASP 85 1_555 N FE2 FEO . C FEO 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc31 C NE2 HIS 85 C HIS 86 1_555 N FE2 FEO . C FEO 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc32 C NE2 HIS 147 C HIS 148 1_555 N FE1 FEO . C FEO 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc33 C OD2 ASP 166 C ASP 167 1_555 N FE1 FEO . C FEO 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc34 C OD1 ASP 166 C ASP 167 1_555 N FE2 FEO . C FEO 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc35 C NE2 HIS 227 C HIS 228 1_555 N FE2 FEO . C FEO 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc36 N FE1 FEO . C FEO 520 1_555 O O1 OXY . C OXY 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.057 ? metalc ? metalc37 D NE2 HIS 80 D HIS 81 1_555 Q FE1 FEO . D FEO 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc38 D OE2 GLU 82 D GLU 83 1_555 Q FE1 FEO . D FEO 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? metalc ? metalc39 D OD2 ASP 84 D ASP 85 1_555 Q FE2 FEO . D FEO 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc40 D NE2 HIS 85 D HIS 86 1_555 Q FE2 FEO . D FEO 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc41 D NE2 HIS 147 D HIS 148 1_555 Q FE1 FEO . D FEO 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc42 D OD2 ASP 166 D ASP 167 1_555 Q FE1 FEO . D FEO 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc43 D OD2 ASP 166 D ASP 167 1_555 Q FE2 FEO . D FEO 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.013 ? metalc ? metalc44 D OD1 ASP 166 D ASP 167 1_555 Q FE2 FEO . D FEO 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc45 D NE2 HIS 227 D HIS 228 1_555 Q FE2 FEO . D FEO 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc46 Q FE1 FEO . D FEO 530 1_555 R O1 OXY . D OXY 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.906 ? metalc ? metalc47 Q FE2 FEO . D FEO 530 1_555 R O1 OXY . D OXY 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc48 Q FE2 FEO . D FEO 530 1_555 R O2 OXY . D OXY 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.134 ? # _chem_comp.formula O2 _chem_comp.formula_weight 31.999 _chem_comp.id OXY _chem_comp.mon_nstd_flag . _chem_comp.name 'OXYGEN MOLECULE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _chem_comp_bond.atom_id_1 O1 _chem_comp_bond.atom_id_2 O2 _chem_comp_bond.comp_id OXY _chem_comp_bond.value_order doub _chem_comp_bond.pdbx_ordinal 293 _chem_comp_bond.pdbx_stereo_config n _chem_comp_bond.pdbx_aromatic_flag n # _atom_sites.entry_id 1YCF _atom_sites.fract_transf_matrix[1][1] 0.006263 _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] 0.006263 _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] 0.003613 _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 ZN A 1 502 502 ZN ZN2 . F 2 ZN A 1 503 503 ZN ZN2 . G 3 FEO A 1 500 500 FEO FEO . H 4 OXY A 1 501 400 OXY OXY . I 5 FMN A 1 701 701 FMN FMN . J 2 ZN B 1 512 502 ZN ZN2 . K 3 FEO B 1 510 500 FEO FEO . L 4 OXY B 1 511 400 OXY OXY . M 5 FMN B 1 702 701 FMN FMN . N 3 FEO C 1 520 500 FEO FEO . O 4 OXY C 1 521 400 OXY OXY . P 5 FMN C 1 703 701 FMN FMN . Q 3 FEO D 1 530 500 FEO FEO . R 4 OXY D 1 531 400 OXY OXY . S 5 FMN D 1 704 701 FMN FMN . T 6 HOH A 1 601 601 HOH HOH . T 6 HOH A 2 602 602 HOH HOH . T 6 HOH A 3 603 603 HOH HOH . T 6 HOH A 4 604 604 HOH HOH . T 6 HOH A 5 605 605 HOH HOH . T 6 HOH A 6 606 616 HOH HOH . T 6 HOH A 7 607 617 HOH HOH . T 6 HOH A 8 608 618 HOH HOH . T 6 HOH A 9 609 619 HOH HOH . T 6 HOH A 10 610 610 HOH HOH . T 6 HOH A 11 611 611 HOH HOH . T 6 HOH A 12 612 612 HOH HOH . T 6 HOH A 13 623 606 HOH HOH . T 6 HOH A 14 654 635 HOH HOH . T 6 HOH A 15 671 614 HOH HOH . U 6 HOH B 1 620 603 HOH HOH . U 6 HOH B 2 621 604 HOH HOH . U 6 HOH B 3 622 605 HOH HOH . U 6 HOH B 4 624 607 HOH HOH . U 6 HOH B 5 625 608 HOH HOH . U 6 HOH B 6 626 609 HOH HOH . U 6 HOH B 7 627 610 HOH HOH . U 6 HOH B 8 628 611 HOH HOH . U 6 HOH B 9 629 612 HOH HOH . U 6 HOH B 10 630 613 HOH HOH . U 6 HOH B 11 631 614 HOH HOH . U 6 HOH B 12 632 615 HOH HOH . U 6 HOH B 13 633 616 HOH HOH . U 6 HOH B 14 634 617 HOH HOH . V 6 HOH C 1 640 600 HOH HOH . V 6 HOH C 2 641 622 HOH HOH . V 6 HOH C 3 642 623 HOH HOH . V 6 HOH C 4 643 624 HOH HOH . V 6 HOH C 5 644 625 HOH HOH . V 6 HOH C 6 645 626 HOH HOH . V 6 HOH C 7 646 627 HOH HOH . V 6 HOH C 8 647 628 HOH HOH . V 6 HOH C 9 648 629 HOH HOH . V 6 HOH C 10 650 631 HOH HOH . V 6 HOH C 11 651 632 HOH HOH . V 6 HOH C 12 652 633 HOH HOH . V 6 HOH C 13 653 634 HOH HOH . V 6 HOH C 14 655 636 HOH HOH . V 6 HOH C 15 656 637 HOH HOH . V 6 HOH C 16 657 638 HOH HOH . W 6 HOH D 1 649 630 HOH HOH . W 6 HOH D 2 660 603 HOH HOH . W 6 HOH D 3 661 604 HOH HOH . W 6 HOH D 4 662 605 HOH HOH . W 6 HOH D 5 663 606 HOH HOH . W 6 HOH D 6 664 607 HOH HOH . W 6 HOH D 7 665 608 HOH HOH . W 6 HOH D 8 666 609 HOH HOH . W 6 HOH D 9 667 610 HOH HOH . W 6 HOH D 10 668 611 HOH HOH . W 6 HOH D 11 669 612 HOH HOH . W 6 HOH D 12 670 613 HOH HOH . W 6 HOH D 13 672 615 HOH HOH . W 6 HOH D 14 673 616 HOH HOH . W 6 HOH D 15 674 617 HOH HOH . W 6 HOH D 16 675 618 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 O1 OXY . . . H 4 107.553 41.986 -154.606 1 51.43 ? O1 OXY 501 A 1 HETATM 2 O O2 OXY . . . H 4 107.318 42.968 -153.796 1 56.87 ? O2 OXY 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 2 #