data_4COF # _model_server_result.job_id POhc829Yr4jawEEhFkPuRg _model_server_result.datetime_utc '2024-11-21 14:38:07' _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 4cof # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":500}' # _entry.id 4COF # _exptl.entry_id 4COF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 120.152 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description BENZAMIDINE _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 107.43 _cell.angle_gamma 90 _cell.entry_id 4COF _cell.length_a 174.1 _cell.length_b 108.9 _cell.length_c 207.44 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4COF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 K N N ? 3 O N N ? 3 R N N ? 3 U N N ? 3 X 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 # 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 F NAG 1 F 1 NAG A 3000 NAG 2 n F NAG 2 F 2 NAG A 3001 NAG 2 n F BMA 3 F 3 BMA A 3002 BMA 2 n G NAG 1 G 1 NAG B 3000 NAG 2 n G NAG 2 G 2 NAG B 3001 NAG 2 n G BMA 3 G 3 BMA B 3002 BMA 2 n H NAG 1 H 1 NAG C 3000 NAG 2 n H NAG 2 H 2 NAG C 3001 NAG 2 n H BMA 3 H 3 BMA C 3002 BMA 2 n I NAG 1 I 1 NAG D 3000 NAG 2 n I NAG 2 I 2 NAG D 3001 NAG 2 n I BMA 3 I 3 BMA D 3002 BMA 2 n J NAG 1 J 1 NAG E 3000 NAG 2 n J NAG 2 J 2 NAG E 3001 NAG 2 n J BMA 3 J 3 BMA E 3002 BMA # 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 139 A CYS 136 1_555 A SG CYS 153 A CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 B SG CYS 139 B CYS 136 1_555 B SG CYS 153 B CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? disulf ? disulf3 C SG CYS 139 C CYS 136 1_555 C SG CYS 153 C CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf4 D SG CYS 139 D CYS 136 1_555 D SG CYS 153 D CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf5 E SG CYS 139 E CYS 136 1_555 E SG CYS 153 E CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? covale ? covale1 A ND2 ASN 11 A ASN 8 1_555 L C1 NAG . A NAG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 A ND2 ASN 83 A ASN 80 1_555 N C1 NAG . A NAG 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale3 A ND2 ASN 152 A ASN 149 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale4 B ND2 ASN 83 B ASN 80 1_555 Q C1 NAG . B NAG 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale5 B ND2 ASN 152 B ASN 149 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale6 C ND2 ASN 83 C ASN 80 1_555 T C1 NAG . C NAG 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale7 C ND2 ASN 152 C ASN 149 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale8 D ND2 ASN 83 D ASN 80 1_555 W C1 NAG . D NAG 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale9 D ND2 ASN 152 D ASN 149 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale10 E ND2 ASN 83 E ASN 80 1_555 Z C1 NAG . E NAG 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale11 E ND2 ASN 152 E ASN 149 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale12 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale13 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale14 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale15 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale16 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale17 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale18 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale19 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale20 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale21 J O4 NAG . J NAG 2 1_555 J C1 BMA . J BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? # _chem_comp.formula 'C7 H8 N2' _chem_comp.formula_weight 120.152 _chem_comp.id BEN _chem_comp.mon_nstd_flag . _chem_comp.name BENZAMIDINE _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 BEN doub 70 n y C1 C6 BEN sing 71 n y C1 C BEN sing 72 n n C2 C3 BEN sing 73 n y C2 H2 BEN sing 74 n n C3 C4 BEN doub 75 n y C3 H3 BEN sing 76 n n C4 C5 BEN sing 77 n y C4 H4 BEN sing 78 n n C5 C6 BEN doub 79 n y C5 H5 BEN sing 80 n n C6 H6 BEN sing 81 n n C N1 BEN doub 82 e n C N2 BEN sing 83 n n N1 HN1 BEN sing 84 n n N2 HN21 BEN sing 85 n n N2 HN22 BEN sing 86 n n # _atom_sites.entry_id 4COF _atom_sites.fract_transf_matrix[1][1] 0.005744 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001803 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009183 _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] 0.005053 _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 K 3 BEN A 1 500 500 BEN BEN . L 4 NAG A 1 1000 1000 NAG NAG . M 5 CL A 1 1448 1448 CL CL . N 4 NAG A 1 2000 2000 NAG NAG . O 3 BEN B 1 500 500 BEN BEN . P 5 CL B 1 1448 1448 CL CL . Q 4 NAG B 1 2000 2000 NAG NAG . R 3 BEN C 1 500 500 BEN BEN . S 5 CL C 1 1448 1448 CL CL . T 4 NAG C 1 2000 2000 NAG NAG . U 3 BEN D 1 500 500 BEN BEN . V 5 CL D 1 1449 1449 CL CL . W 4 NAG D 1 2000 2000 NAG NAG . X 3 BEN E 1 500 500 BEN BEN . Y 5 CL E 1 1448 1448 CL CL . Z 4 NAG E 1 2000 2000 NAG NAG . # 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 BEN . . . U 3 0.417 24.918 120.584 1 117.61 ? C1 BEN 500 D 1 HETATM 2 C C2 BEN . . . U 3 0.221 25.235 121.986 1 118.06 ? C2 BEN 500 D 1 HETATM 3 C C3 BEN . . . U 3 1.277 25.712 122.787 1 118.02 ? C3 BEN 500 D 1 HETATM 4 C C4 BEN . . . U 3 2.545 25.903 122.207 1 118.19 ? C4 BEN 500 D 1 HETATM 5 C C5 BEN . . . U 3 2.769 25.582 120.841 1 118.16 ? C5 BEN 500 D 1 HETATM 6 C C6 BEN . . . U 3 1.721 25.095 120.014 1 118.09 ? C6 BEN 500 D 1 HETATM 7 C C BEN . . . U 3 -0.698 24.396 119.763 1 117.43 ? C BEN 500 D 1 HETATM 8 N N1 BEN . . . U 3 -0.432 24.094 118.528 1 117.23 ? N1 BEN 500 D 1 HETATM 9 N N2 BEN . . . U 3 -1.972 24.224 120.308 1 117.52 ? N2 BEN 500 D 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 9 #