data_7Y0E # _model_server_result.job_id Vj7FBWq-tucl91qZlrP39w _model_server_result.datetime_utc '2024-11-06 20:52:07' _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 7y0e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":601}' # _entry.id 7Y0E # _exptl.entry_id 7Y0E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 179.176 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '4-carbamimidamidobenzoic acid' _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 100.08 _cell.angle_gamma 90 _cell.entry_id 7Y0E _cell.length_a 49.157 _cell.length_b 93.537 _cell.length_c 92.35 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Y0E _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # 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,L,M 1 1 C,D,H,I,J,K,N,O 2 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 ? 5 G N N ? 5 J 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 disulf ? disulf1 A SG CYS 12 A CYS 120 1_555 A SG CYS 31 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 25 A CYS 133 1_555 A SG CYS 40 A CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 64 A CYS 172 1_555 A SG CYS 123 A CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 77 A CYS 185 1_555 A SG CYS 133 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 A SG CYS 136 A CYS 244 1_555 B SG CYS 110 C CYS 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 B SG CYS 26 C CYS 281 1_555 B SG CYS 42 C CYS 297 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf7 B SG CYS 155 C CYS 410 1_555 B SG CYS 171 C CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 B SG CYS 182 C CYS 437 1_555 B SG CYS 210 C CYS 465 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 C SG CYS 5 B CYS 113 1_555 C SG CYS 18 B CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 C SG CYS 12 B CYS 120 1_555 C SG CYS 31 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 C SG CYS 25 B CYS 133 1_555 C SG CYS 40 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf12 C SG CYS 64 B CYS 172 1_555 C SG CYS 123 B CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf13 C SG CYS 77 B CYS 185 1_555 C SG CYS 133 B CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf14 C SG CYS 136 B CYS 244 1_555 D SG CYS 110 D CYS 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf15 D SG CYS 26 D CYS 281 1_555 D SG CYS 42 D CYS 297 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.166 ? disulf ? disulf16 D SG CYS 155 D CYS 410 1_555 D SG CYS 171 D CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf17 D SG CYS 182 D CYS 437 1_555 D SG CYS 210 D CYS 465 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 105 A ASN 213 1_555 E C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 B OG SER 186 C SER 441 1_555 G C6 GBS . C GBS 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? covale ? covale3 C ND2 ASN 105 B ASN 213 1_555 H C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale4 D OG SER 186 D SER 441 1_555 J C6 GBS . D GBS 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? metalc ? metalc1 A O ASN 23 A ASN 131 1_555 F CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc2 A OD1 ASP 26 A ASP 134 1_555 F CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc3 A O VAL 28 A VAL 136 1_555 F CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc4 A OD2 ASP 36 A ASP 144 1_555 F CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc5 A OE2 GLU 37 A GLU 145 1_555 F CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc6 C O ASN 23 B ASN 131 1_555 I CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc7 C OD1 ASP 26 B ASP 134 1_555 I CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc8 C O VAL 28 B VAL 136 1_555 I CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc9 C OD2 ASP 36 B ASP 144 1_555 I CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc10 C OE2 GLU 37 B GLU 145 1_555 I CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? # _chem_comp.formula 'C8 H9 N3 O2' _chem_comp.formula_weight 179.176 _chem_comp.id GBS _chem_comp.mon_nstd_flag . _chem_comp.name '4-carbamimidamidobenzoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Nafamostat, bound form' # 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 C6 O GBS doub 83 n n C6 C5 GBS sing 84 n n C5 C GBS doub 85 n y C5 C4 GBS sing 86 n y C C1 GBS sing 87 n y C4 C3 GBS doub 88 n y C1 C2 GBS doub 89 n y C3 C2 GBS sing 90 n y C2 N2 GBS sing 91 n n N2 C18 GBS sing 92 n n C18 N4 GBS doub 93 n n C18 N3 GBS sing 94 n n C6 O1 GBS sing 95 n n C3 H1 GBS sing 96 n n C4 H2 GBS sing 97 n n C1 H3 GBS sing 98 n n N4 H4 GBS sing 99 n n N2 H5 GBS sing 100 n n N3 H6 GBS sing 101 n n N3 H7 GBS sing 102 n n C H8 GBS sing 103 n n O1 H9 GBS sing 104 n n # _atom_sites.entry_id 7Y0E _atom_sites.fract_transf_matrix[1][1] 0.020343 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003616 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010691 _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] 0.010998 _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 3 NAG A 1 301 502 NAG NAG . F 4 CA A 1 302 1 CA CA . G 5 GBS C 1 601 501 GBS GBS . H 3 NAG B 1 301 502 NAG NAG . I 4 CA B 1 302 2 CA CA . J 5 GBS D 1 601 501 GBS GBS . K 6 GOL D 1 602 503 GOL GOL . L 7 HOH A 1 401 151 HOH HOH . L 7 HOH A 2 402 117 HOH HOH . L 7 HOH A 3 403 121 HOH HOH . L 7 HOH A 4 404 46 HOH HOH . L 7 HOH A 5 405 47 HOH HOH . L 7 HOH A 6 406 148 HOH HOH . L 7 HOH A 7 407 75 HOH HOH . L 7 HOH A 8 408 108 HOH HOH . L 7 HOH A 9 409 15 HOH HOH . L 7 HOH A 10 410 101 HOH HOH . L 7 HOH A 11 411 109 HOH HOH . L 7 HOH A 12 412 80 HOH HOH . L 7 HOH A 13 413 61 HOH HOH . L 7 HOH A 14 414 140 HOH HOH . L 7 HOH A 15 415 106 HOH HOH . L 7 HOH A 16 416 123 HOH HOH . L 7 HOH A 17 417 115 HOH HOH . L 7 HOH A 18 418 71 HOH HOH . L 7 HOH A 19 419 65 HOH HOH . L 7 HOH A 20 420 138 HOH HOH . L 7 HOH A 21 421 59 HOH HOH . L 7 HOH A 22 422 76 HOH HOH . L 7 HOH A 23 423 79 HOH HOH . L 7 HOH A 24 424 89 HOH HOH . L 7 HOH A 25 425 87 HOH HOH . L 7 HOH A 26 426 149 HOH HOH . L 7 HOH A 27 427 78 HOH HOH . M 7 HOH C 1 701 33 HOH HOH . M 7 HOH C 2 702 16 HOH HOH . M 7 HOH C 3 703 3 HOH HOH . M 7 HOH C 4 704 39 HOH HOH . M 7 HOH C 5 705 97 HOH HOH . M 7 HOH C 6 706 66 HOH HOH . M 7 HOH C 7 707 30 HOH HOH . M 7 HOH C 8 708 72 HOH HOH . M 7 HOH C 9 709 83 HOH HOH . M 7 HOH C 10 710 27 HOH HOH . M 7 HOH C 11 711 95 HOH HOH . M 7 HOH C 12 712 85 HOH HOH . M 7 HOH C 13 713 18 HOH HOH . M 7 HOH C 14 714 35 HOH HOH . M 7 HOH C 15 715 153 HOH HOH . M 7 HOH C 16 716 91 HOH HOH . M 7 HOH C 17 717 13 HOH HOH . M 7 HOH C 18 718 62 HOH HOH . M 7 HOH C 19 719 10 HOH HOH . M 7 HOH C 20 720 37 HOH HOH . M 7 HOH C 21 721 58 HOH HOH . M 7 HOH C 22 722 54 HOH HOH . M 7 HOH C 23 723 24 HOH HOH . M 7 HOH C 24 724 63 HOH HOH . M 7 HOH C 25 725 21 HOH HOH . M 7 HOH C 26 726 50 HOH HOH . M 7 HOH C 27 727 137 HOH HOH . M 7 HOH C 28 728 90 HOH HOH . M 7 HOH C 29 729 11 HOH HOH . M 7 HOH C 30 730 68 HOH HOH . M 7 HOH C 31 731 17 HOH HOH . M 7 HOH C 32 732 98 HOH HOH . M 7 HOH C 33 733 77 HOH HOH . M 7 HOH C 34 734 53 HOH HOH . M 7 HOH C 35 735 34 HOH HOH . M 7 HOH C 36 736 70 HOH HOH . M 7 HOH C 37 737 48 HOH HOH . M 7 HOH C 38 738 4 HOH HOH . M 7 HOH C 39 739 6 HOH HOH . M 7 HOH C 40 740 60 HOH HOH . M 7 HOH C 41 741 49 HOH HOH . M 7 HOH C 42 742 132 HOH HOH . M 7 HOH C 43 743 99 HOH HOH . M 7 HOH C 44 744 130 HOH HOH . M 7 HOH C 45 745 119 HOH HOH . M 7 HOH C 46 746 25 HOH HOH . M 7 HOH C 47 747 44 HOH HOH . M 7 HOH C 48 748 88 HOH HOH . M 7 HOH C 49 749 129 HOH HOH . M 7 HOH C 50 750 40 HOH HOH . M 7 HOH C 51 751 69 HOH HOH . M 7 HOH C 52 752 31 HOH HOH . M 7 HOH C 53 753 116 HOH HOH . M 7 HOH C 54 754 36 HOH HOH . M 7 HOH C 55 755 150 HOH HOH . M 7 HOH C 56 756 29 HOH HOH . M 7 HOH C 57 757 154 HOH HOH . M 7 HOH C 58 758 114 HOH HOH . M 7 HOH C 59 759 57 HOH HOH . M 7 HOH C 60 760 38 HOH HOH . M 7 HOH C 61 761 28 HOH HOH . M 7 HOH C 62 762 2 HOH HOH . M 7 HOH C 63 763 51 HOH HOH . M 7 HOH C 64 764 141 HOH HOH . M 7 HOH C 65 765 157 HOH HOH . M 7 HOH C 66 766 155 HOH HOH . M 7 HOH C 67 767 86 HOH HOH . M 7 HOH C 68 768 82 HOH HOH . M 7 HOH C 69 769 128 HOH HOH . M 7 HOH C 70 770 111 HOH HOH . M 7 HOH C 71 771 152 HOH HOH . M 7 HOH C 72 772 134 HOH HOH . N 7 HOH B 1 701 147 HOH HOH . N 7 HOH B 2 702 93 HOH HOH . N 7 HOH B 3 703 103 HOH HOH . N 7 HOH B 4 704 105 HOH HOH . N 7 HOH B 5 705 12 HOH HOH . N 7 HOH B 6 706 92 HOH HOH . N 7 HOH B 7 707 135 HOH HOH . O 7 HOH D 1 701 23 HOH HOH . O 7 HOH D 2 702 26 HOH HOH . O 7 HOH D 3 703 20 HOH HOH . O 7 HOH D 4 704 94 HOH HOH . O 7 HOH D 5 705 96 HOH HOH . O 7 HOH D 6 706 143 HOH HOH . O 7 HOH D 7 707 32 HOH HOH . O 7 HOH D 8 708 45 HOH HOH . O 7 HOH D 9 709 104 HOH HOH . O 7 HOH D 10 710 5 HOH HOH . O 7 HOH D 11 711 1 HOH HOH . O 7 HOH D 12 712 125 HOH HOH . O 7 HOH D 13 713 74 HOH HOH . O 7 HOH D 14 714 102 HOH HOH . O 7 HOH D 15 715 56 HOH HOH . O 7 HOH D 16 716 19 HOH HOH . O 7 HOH D 17 717 9 HOH HOH . O 7 HOH D 18 718 22 HOH HOH . O 7 HOH D 19 719 67 HOH HOH . O 7 HOH D 20 720 84 HOH HOH . O 7 HOH D 21 721 8 HOH HOH . O 7 HOH D 22 722 144 HOH HOH . O 7 HOH D 23 723 7 HOH HOH . O 7 HOH D 24 724 52 HOH HOH . O 7 HOH D 25 725 14 HOH HOH . O 7 HOH D 26 726 133 HOH HOH . O 7 HOH D 27 727 81 HOH HOH . O 7 HOH D 28 728 146 HOH HOH . O 7 HOH D 29 729 73 HOH HOH . O 7 HOH D 30 730 107 HOH HOH . O 7 HOH D 31 731 127 HOH HOH . O 7 HOH D 32 732 64 HOH HOH . O 7 HOH D 33 733 41 HOH HOH . O 7 HOH D 34 734 42 HOH HOH . O 7 HOH D 35 735 100 HOH HOH . O 7 HOH D 36 736 122 HOH HOH . O 7 HOH D 37 737 113 HOH HOH . O 7 HOH D 38 738 110 HOH HOH . O 7 HOH D 39 739 142 HOH HOH . O 7 HOH D 40 740 126 HOH HOH . O 7 HOH D 41 741 124 HOH HOH . O 7 HOH D 42 742 136 HOH HOH . O 7 HOH D 43 743 55 HOH HOH . O 7 HOH D 44 744 112 HOH HOH . O 7 HOH D 45 745 43 HOH HOH . O 7 HOH D 46 746 120 HOH HOH . O 7 HOH D 47 747 139 HOH HOH . O 7 HOH D 48 748 131 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 C2 GBS . . . J 5 -24.252 17.552 -16.11 1 46.36 ? C2 GBS 601 D 1 HETATM 2 C C3 GBS . . . J 5 -23.187 18.341 -15.679 1 43.79 ? C3 GBS 601 D 1 HETATM 3 C C4 GBS . . . J 5 -21.908 18.101 -16.14 1 42.88 ? C4 GBS 601 D 1 HETATM 4 C C6 GBS . . . J 5 -20.271 16.755 -17.56 1 43.6 ? C6 GBS 601 D 1 HETATM 5 C C1 GBS . . . J 5 -24.009 16.523 -17.009 1 46.6 ? C1 GBS 601 D 1 HETATM 6 N N4 GBS . . . J 5 -27.745 17.155 -15.136 1 45.46 ? N4 GBS 601 D 1 HETATM 7 C C5 GBS . . . J 5 -21.669 17.083 -17.048 1 41.13 ? C5 GBS 601 D 1 HETATM 8 C C18 GBS . . . J 5 -26.478 16.827 -15.284 1 46.13 ? C18 GBS 601 D 1 HETATM 9 O O GBS . . . J 5 -19.264 17.073 -16.875 1 45.48 ? O GBS 601 D 1 HETATM 10 N N2 GBS . . . J 5 -25.578 17.774 -15.659 1 50.21 ? N2 GBS 601 D 1 HETATM 11 N N3 GBS . . . J 5 -26.081 15.594 -15.063 1 48.83 ? N3 GBS 601 D 1 HETATM 12 C C GBS . . . J 5 -22.73 16.295 -17.459 1 46.31 ? C GBS 601 D 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 12 #