data_9NTJ # _model_server_result.job_id xSZsJEbEoSHNxDx4ykb4OQ _model_server_result.datetime_utc '2025-07-17 21:52:49' _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 9ntj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":609}' # _entry.id 9NTJ # _exptl.entry_id 9NTJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 268.269 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCOFORMYCIN" _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 90 _cell.entry_id 9NTJ _cell.length_a 67.349 _cell.length_b 109.609 _cell.length_c 171.555 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9NTJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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,J,K,L,M,N,O,P,Q,R,S,T,U,V _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 K N N ? 6 T 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 . 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 728 NAG 2 n C NAG 2 C 2 NAG A 729 NAG 2 n C BMA 3 C 3 BMA A 730 BMA 2 n C MAN 4 C 4 MAN A 731 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 142 A CYS 142 1_555 A SG CYS 164 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 B SG CYS 142 B CYS 142 1_555 B SG CYS 164 B CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 81 A ASN 81 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 132 A ASN 132 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 189 A ASN 189 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 A ND2 ASN 384 A ASN 384 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 B ND2 ASN 81 B ASN 81 1_555 M C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 B ND2 ASN 132 B ASN 132 1_555 L C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 B ND2 ASN 189 B ASN 189 1_555 N C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 B ND2 ASN 384 B ASN 384 1_555 O C1 NAG . B NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale10 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale11 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? metalc ? metalc1 A NE2 HIS 117 A HIS 117 1_555 J ZN ZN . A ZN 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc2 A NE2 HIS 119 A HIS 119 1_555 J ZN ZN . A ZN 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc3 A NE2 HIS 362 A HIS 362 1_555 J ZN ZN . A ZN 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc4 A OD1 ASP 447 A ASP 447 1_555 J ZN ZN . A ZN 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc5 J ZN ZN . A ZN 607 1_555 K O8 DCF . A DCF 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc6 B NE2 HIS 117 B HIS 117 1_555 S ZN ZN . B ZN 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc7 B NE2 HIS 119 B HIS 119 1_555 S ZN ZN . B ZN 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc8 B NE2 HIS 362 B HIS 362 1_555 S ZN ZN . B ZN 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc9 B OD1 ASP 447 B ASP 447 1_555 S ZN ZN . B ZN 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc10 S ZN ZN . B ZN 608 1_555 T O8 DCF . B DCF 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.849 ? # _chem_comp.formula 'C11 H16 N4 O4' _chem_comp.formula_weight 268.269 _chem_comp.id DCF _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYCOFORMYCIN" _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 N1 C2 DCF doub 107 n y N1 C9 DCF sing 108 n y C2 N3 DCF sing 109 n y C2 H2 DCF sing 110 n n N3 C10 DCF sing 111 n y N3 C1S DCF sing 112 n n C9 C10 DCF doub 113 n y C9 C8 DCF sing 114 n n C10 N4 DCF sing 115 n n N4 C5 DCF doub 116 n n C5 N6 DCF sing 117 n n C5 H5 DCF sing 118 n n N6 C7 DCF sing 119 n n N6 HN6 DCF sing 120 n n C7 C8 DCF sing 121 n n C7 H71 DCF sing 122 n n C7 H72 DCF sing 123 n n C8 O8 DCF sing 124 n n C8 H8 DCF sing 125 n n O8 HO8 DCF sing 126 n n C2S C3S DCF sing 127 n n C2S C1S DCF sing 128 n n C2S H2S1 DCF sing 129 n n C2S H2S2 DCF sing 130 n n C3S O3S DCF sing 131 n n C3S C4S DCF sing 132 n n C3S H3S DCF sing 133 n n O3S HO3 DCF sing 134 n n O5S C5S DCF sing 135 n n O5S HO5 DCF sing 136 n n C5S C4S DCF sing 137 n n C5S H5S1 DCF sing 138 n n C5S H5S2 DCF sing 139 n n C4S O4S DCF sing 140 n n C4S H4S DCF sing 141 n n O4S C1S DCF sing 142 n n C1S H1S DCF sing 143 n n # _atom_sites.entry_id 9NTJ _atom_sites.fract_transf_matrix[1][1] 0.014848 _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] 0.009123 _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] 0.005829 _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 D 3 NAG A 1 601 725 NAG NAG . E 3 NAG A 1 602 726 NAG NAG . F 3 NAG A 1 603 727 NAG NAG . G 4 EDO A 1 604 825 EDO EDO . H 4 EDO A 1 605 925 EDO EDO . I 4 EDO A 1 606 1025 EDO EDO . J 5 ZN A 1 607 2 ZN ZN . K 6 DCF A 1 608 1 DCF DCF . L 3 NAG B 1 601 725 NAG NAG . M 3 NAG B 1 602 726 NAG NAG . N 3 NAG B 1 603 727 NAG NAG . O 3 NAG B 1 604 728 NAG NAG . P 4 EDO B 1 605 825 EDO EDO . Q 4 EDO B 1 606 925 EDO EDO . R 4 EDO B 1 607 1025 EDO EDO . S 5 ZN B 1 608 1 ZN ZN . T 6 DCF B 1 609 2 DCF DCF . U 7 HOH A 1 701 175 HOH HOH . U 7 HOH A 2 702 158 HOH HOH . U 7 HOH A 3 703 141 HOH HOH . U 7 HOH A 4 704 176 HOH HOH . U 7 HOH A 5 705 17 HOH HOH . U 7 HOH A 6 706 144 HOH HOH . U 7 HOH A 7 707 182 HOH HOH . U 7 HOH A 8 708 152 HOH HOH . U 7 HOH A 9 709 69 HOH HOH . U 7 HOH A 10 710 55 HOH HOH . U 7 HOH A 11 711 68 HOH HOH . U 7 HOH A 12 712 31 HOH HOH . U 7 HOH A 13 713 51 HOH HOH . U 7 HOH A 14 714 74 HOH HOH . U 7 HOH A 15 715 46 HOH HOH . U 7 HOH A 16 716 61 HOH HOH . U 7 HOH A 17 717 3 HOH HOH . U 7 HOH A 18 718 54 HOH HOH . U 7 HOH A 19 719 156 HOH HOH . U 7 HOH A 20 720 131 HOH HOH . U 7 HOH A 21 721 155 HOH HOH . U 7 HOH A 22 722 164 HOH HOH . U 7 HOH A 23 723 40 HOH HOH . U 7 HOH A 24 724 181 HOH HOH . U 7 HOH A 25 725 159 HOH HOH . U 7 HOH A 26 726 5 HOH HOH . U 7 HOH A 27 727 168 HOH HOH . U 7 HOH A 28 728 95 HOH HOH . U 7 HOH A 29 729 96 HOH HOH . U 7 HOH A 30 730 171 HOH HOH . U 7 HOH A 31 731 44 HOH HOH . U 7 HOH A 32 732 128 HOH HOH . U 7 HOH A 33 733 177 HOH HOH . U 7 HOH A 34 734 178 HOH HOH . U 7 HOH A 35 735 12 HOH HOH . U 7 HOH A 36 736 120 HOH HOH . U 7 HOH A 37 737 183 HOH HOH . U 7 HOH A 38 738 83 HOH HOH . U 7 HOH A 39 739 170 HOH HOH . U 7 HOH A 40 740 92 HOH HOH . V 7 HOH B 1 701 107 HOH HOH . V 7 HOH B 2 702 150 HOH HOH . V 7 HOH B 3 703 103 HOH HOH . V 7 HOH B 4 704 99 HOH HOH . V 7 HOH B 5 705 173 HOH HOH . V 7 HOH B 6 706 72 HOH HOH . V 7 HOH B 7 707 41 HOH HOH . V 7 HOH B 8 708 109 HOH HOH . V 7 HOH B 9 709 35 HOH HOH . V 7 HOH B 10 710 66 HOH HOH . V 7 HOH B 11 711 122 HOH HOH . V 7 HOH B 12 712 43 HOH HOH . V 7 HOH B 13 713 76 HOH HOH . V 7 HOH B 14 714 174 HOH HOH . V 7 HOH B 15 715 172 HOH HOH . V 7 HOH B 16 716 102 HOH HOH . V 7 HOH B 17 717 13 HOH HOH . V 7 HOH B 18 718 39 HOH HOH . V 7 HOH B 19 719 134 HOH HOH . V 7 HOH B 20 720 165 HOH HOH . V 7 HOH B 21 721 86 HOH HOH . V 7 HOH B 22 722 48 HOH HOH . V 7 HOH B 23 723 71 HOH HOH . V 7 HOH B 24 724 130 HOH HOH . V 7 HOH B 25 725 104 HOH HOH . V 7 HOH B 26 726 114 HOH HOH . V 7 HOH B 27 727 146 HOH HOH . V 7 HOH B 28 728 33 HOH HOH . V 7 HOH B 29 729 115 HOH HOH . V 7 HOH B 30 730 180 HOH HOH . V 7 HOH B 31 731 124 HOH HOH . V 7 HOH B 32 732 137 HOH HOH . V 7 HOH B 33 733 6 HOH HOH . V 7 HOH B 34 734 94 HOH HOH . V 7 HOH B 35 735 87 HOH HOH . V 7 HOH B 36 736 138 HOH HOH . V 7 HOH B 37 737 179 HOH HOH . V 7 HOH B 38 738 45 HOH HOH . V 7 HOH B 39 739 161 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 N N1 DCF . . . T 6 40.946 -10.267 -61.017 1 17.71 ? N1 DCF 609 B 1 HETATM 2 C C2 DCF . . . T 6 40.856 -11.328 -61.781 1 16.99 ? C2 DCF 609 B 1 HETATM 3 N N3 DCF . . . T 6 40.839 -12.499 -61.07 1 17.05 ? N3 DCF 609 B 1 HETATM 4 C C9 DCF . . . T 6 40.99 -10.769 -59.73 1 18.36 ? C9 DCF 609 B 1 HETATM 5 C C10 DCF . . . T 6 40.925 -12.142 -59.743 1 19.79 ? C10 DCF 609 B 1 HETATM 6 N N4 DCF . . . T 6 40.937 -13.108 -58.77 1 22.74 ? N4 DCF 609 B 1 HETATM 7 C C5 DCF . . . T 6 41.343 -12.8 -57.596 1 23.73 ? C5 DCF 609 B 1 HETATM 8 N N6 DCF . . . T 6 41.342 -11.675 -56.878 1 22 ? N6 DCF 609 B 1 HETATM 9 C C7 DCF . . . T 6 40.608 -10.473 -57.247 1 24.19 ? C7 DCF 609 B 1 HETATM 10 C C8 DCF . . . T 6 41.103 -9.854 -58.546 1 20.43 ? C8 DCF 609 B 1 HETATM 11 O O8 DCF . . . T 6 42.439 -9.401 -58.347 1 24.28 ? O8 DCF 609 B 1 HETATM 12 C C2S DCF . . . T 6 39.349 -14.397 -61.791 1 24.04 ? C2S DCF 609 B 1 HETATM 13 C C3S DCF . . . T 6 39.118 -14.316 -63.295 1 22.07 ? C3S DCF 609 B 1 HETATM 14 O O3S DCF . . . T 6 38.271 -15.376 -63.742 1 18.9 ? O3S DCF 609 B 1 HETATM 15 O O5S DCF . . . T 6 42.117 -13.948 -65.598 1 23.41 ? O5S DCF 609 B 1 HETATM 16 C C5S DCF . . . T 6 40.756 -13.849 -65.201 1 20.06 ? C5S DCF 609 B 1 HETATM 17 C C4S DCF . . . T 6 40.524 -14.492 -63.853 1 19.09 ? C4S DCF 609 B 1 HETATM 18 O O4S DCF . . . T 6 41.394 -13.88 -62.88 1 18.34 ? O4S DCF 609 B 1 HETATM 19 C C1S DCF . . . T 6 40.769 -13.872 -61.603 1 20.78 ? C1S DCF 609 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 19 #