data_4P9H # _model_server_result.job_id CN_nMEwvDbcLK_rSy0pWNw _model_server_result.datetime_utc '2024-11-27 14:38:12' _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 4p9h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":603}' # _entry.id 4P9H # _exptl.entry_id 4P9H _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 120.152 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description BENZAMIDINE _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 4P9H _cell.length_a 66.529 _cell.length_b 132.492 _cell.length_c 142.769 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4P9H _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 ? 11 L N N ? 11 M N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 oligosaccharide 7 oligosaccharide 8 oligosaccharide 9 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 6 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 6 5 4 MAN MAN C1 O1 . O2 HO2 . sing 6 ? 6 6 5 MAN MAN C1 O1 . O2 HO2 . sing 7 ? 6 7 3 MAN BMA C1 O1 . O6 HO6 . sing 8 ? 6 8 7 MAN MAN C1 O1 . O6 HO6 . sing 9 ? 6 9 8 MAN MAN C1 O1 . O2 HO2 . sing 10 ? 6 10 7 MAN MAN C1 O1 . O3 HO3 . sing 11 ? 7 2 1 NAG NAG C1 O1 . O4 HO4 . sing 12 ? 7 3 2 BMA NAG C1 O1 . O4 HO4 . sing 13 ? 7 4 3 MAN BMA C1 O1 . O3 HO3 . sing 14 ? 8 2 1 NAG NAG C1 O1 . O4 HO4 . sing 15 ? 8 3 2 BMA NAG C1 O1 . O4 HO4 . sing 16 ? 8 4 3 MAN BMA C1 O1 . O3 HO3 . sing 17 ? 8 5 3 MAN BMA C1 O1 . O6 HO6 . sing 18 ? 9 2 1 NAG NAG C1 O1 . O4 HO4 . sing 19 ? 9 3 2 BMA NAG C1 O1 . O4 HO4 . sing 20 ? 9 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 5 n E NAG 1 A 1 NAG C 1001 NAG 5 n E NAG 2 A 2 NAG C 1002 NAG 6 n F NAG 1 B 1 NAG G 604 NAG 6 n F NAG 2 B 2 NAG G 605 NAG 6 n F BMA 3 B 3 BMA G 606 BMA 6 n F MAN 4 B 4 MAN G 607 MAN 6 n F MAN 5 B 5 MAN G 608 MAN 6 n F MAN 6 B 6 MAN G 609 MAN 6 n F MAN 7 B 7 MAN G 610 MAN 6 n F MAN 8 B 8 MAN G 611 MAN 6 n F MAN 9 B 9 MAN G 613 MAN 6 n F MAN 10 B 10 MAN G 612 MAN 7 n G NAG 1 D 1 NAG G 615 NAG 7 n G NAG 2 D 2 NAG G 616 NAG 7 n G BMA 3 D 3 BMA G 617 BMA 7 n G MAN 4 D 4 MAN G 618 MAN 8 n H NAG 1 E 1 NAG G 619 NAG 8 n H NAG 2 E 2 NAG G 620 NAG 8 n H BMA 3 E 3 BMA G 621 BMA 8 n H MAN 4 E 4 MAN G 622 MAN 8 n H MAN 5 E 5 MAN G 623 MAN 5 n I NAG 1 F 1 NAG G 624 NAG 5 n I NAG 2 F 2 NAG G 625 NAG 9 n J NAG 1 I 1 NAG G 627 NAG 9 n J NAG 2 I 2 NAG G 628 NAG 9 n J BMA 3 I 3 BMA G 629 BMA 9 n J MAN 4 I 4 MAN G 630 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 16 C CYS 16 1_555 A SG CYS 84 C CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 130 C CYS 130 1_555 A SG CYS 159 C CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 B SG CYS 11 G CYS 54 1_555 B SG CYS 31 G CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf4 B SG CYS 22 G CYS 65 1_555 B SG CYS 72 G CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 B SG CYS 76 G CYS 119 1_555 B SG CYS 89 G CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf6 B SG CYS 102 G CYS 218 1_555 B SG CYS 131 G CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf7 B SG CYS 112 G CYS 228 1_555 B SG CYS 123 G CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf8 B SG CYS 180 G CYS 296 1_555 B SG CYS 199 G CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 B SG CYS 245 G CYS 378 1_555 B SG CYS 306 G CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 B SG CYS 252 G CYS 385 1_555 B SG CYS 279 G CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf11 B SG CYS 262 G CYS 395 1_555 B SG CYS 271 G CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf12 C SG CYS 22 H CYS 22 1_555 C SG CYS 99 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 C SG CYS 159 H CYS 140 1_555 C SG CYS 215 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf14 D SG CYS 23 L CYS 23 1_555 D SG CYS 89 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf15 D SG CYS 135 L CYS 134 1_555 D SG CYS 195 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 73 C ASN 73 1_555 E C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 B CB CYS 22 G CYS 65 1_555 B SG CYS 72 G CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? covale ? covale3 B ND2 ASN 118 G ASN 234 1_555 F C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale4 B ND2 ASN 125 G ASN 241 1_555 N C1 NAG . G NAG 614 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale5 B ND2 ASN 146 G ASN 262 1_555 G C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale6 B ND2 ASN 160 G ASN 276 1_555 H C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale7 B ND2 ASN 179 G ASN 295 1_555 I C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale8 B ND2 ASN 223 G ASN 355 1_555 O C1 NAG . G NAG 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale9 B ND2 ASN 253 G ASN 386 1_555 J C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale10 C ND2 ASN 88 H ASN 82 1_555 P C1 NAG . H NAG 1001 1_555 B ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale11 E O4 NAG . A NAG 1 1_555 E C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale12 F O4 NAG . B NAG 1 1_555 F C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale13 F O4 NAG . B NAG 2 1_555 F C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale14 F O3 BMA . B BMA 3 1_555 F C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale15 F O6 BMA . B BMA 3 1_555 F C1 MAN . B MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale16 F O2 MAN . B MAN 4 1_555 F C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale17 F O2 MAN . B MAN 5 1_555 F C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale18 F O6 MAN . B MAN 7 1_555 F C1 MAN . B MAN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale19 F O3 MAN . B MAN 7 1_555 F C1 MAN . B MAN 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale20 F O2 MAN . B MAN 8 1_555 F C1 MAN . B MAN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale21 G O4 NAG . D NAG 1 1_555 G C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale22 G O4 NAG . D NAG 2 1_555 G C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale23 G O3 BMA . D BMA 3 1_555 G C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale24 H O4 NAG . E NAG 1 1_555 H C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale25 H O4 NAG . E NAG 2 1_555 H C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale26 H O3 BMA . E BMA 3 1_555 H C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale27 H O6 BMA . E BMA 3 1_555 H C1 MAN . E MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale28 I O4 NAG . F NAG 1 1_555 I C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale29 J O4 NAG . I NAG 1 1_555 J C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale30 J O4 NAG . I NAG 2 1_555 J C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale31 J O6 BMA . I BMA 3 1_555 J C1 MAN . I MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _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 4P9H _atom_sites.fract_transf_matrix[1][1] 0.015031 _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] 0.007548 _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] 0.007004 _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 10 EPE G 1 601 601 EPE EPE . L 11 BEN G 1 602 602 BEN BAM . M 11 BEN G 1 603 603 BEN BAM . N 12 NAG G 1 614 614 NAG NAG . O 12 NAG G 1 626 626 NAG NAG . P 12 NAG H 1 1001 1001 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 . . . M 11 57.217 -17.215 77.449 0.83 43.44 ? C1 BEN 603 G 1 HETATM 2 C C2 BEN . . . M 11 56.471 -17.078 78.598 0.83 46.21 ? C2 BEN 603 G 1 HETATM 3 C C3 BEN . . . M 11 56.934 -17.645 79.781 0.83 52.75 ? C3 BEN 603 G 1 HETATM 4 C C4 BEN . . . M 11 58.129 -18.339 79.817 0.83 43.41 ? C4 BEN 603 G 1 HETATM 5 C C5 BEN . . . M 11 58.882 -18.464 78.664 0.83 40.06 ? C5 BEN 603 G 1 HETATM 6 C C6 BEN . . . M 11 58.416 -17.895 77.488 0.83 47.91 ? C6 BEN 603 G 1 HETATM 7 C C BEN . . . M 11 56.75 -16.596 76.157 0.83 49.72 ? C BEN 603 G 1 HETATM 8 N N1 BEN . . . M 11 57.62 -16.204 75.238 0.83 42.97 ? N1 BEN 603 G 1 HETATM 9 N N2 BEN . . . M 11 55.359 -16.436 75.931 0.83 55.58 ? N2 BEN 603 G 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 9 #