data_5F5I # _model_server_result.job_id EDJ-WXGrds2IAIuO2pNt5Q _model_server_result.datetime_utc '2024-11-16 05:02:05' _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 5f5i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":504}' # _entry.id 5F5I # _exptl.entry_id 5F5I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 242.273 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-[[(phenylmethyl)amino]methyl]pyridine-4-carboxylic 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 90 _cell.angle_gamma 90 _cell.entry_id 5F5I _cell.length_a 101.03 _cell.length_b 149.58 _cell.length_c 57.92 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5F5I _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,K 1 1 B,G,H,I,J,L 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 F 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 metalc ? metalc1 A NE2 HIS 192 A HIS 188 1_555 C NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc2 A OE1 GLU 194 A GLU 190 1_555 C NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc3 A SG CYS 238 A CYS 234 1_555 D ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc4 A NE2 HIS 244 A HIS 240 1_555 D ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc5 A NE2 HIS 280 A HIS 276 1_555 C NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc6 A SG CYS 310 A CYS 306 1_555 D ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc7 A SG CYS 312 A CYS 308 1_555 D ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc8 C NI NI . A NI 501 1_555 F N1 5V1 . A 5V1 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc9 C NI NI . A NI 501 1_555 F N2 5V1 . A 5V1 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc10 C NI NI . A NI 501 1_555 K O HOH . A HOH 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc11 B NE2 HIS 192 B HIS 188 1_555 G NI NI . B NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc12 B OE1 GLU 194 B GLU 190 1_555 G NI NI . B NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc13 B SG CYS 238 B CYS 234 1_555 H ZN ZN . B ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc14 B NE2 HIS 244 B HIS 240 1_555 H ZN ZN . B ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc15 B NE2 HIS 280 B HIS 276 1_555 G NI NI . B NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc16 B SG CYS 310 B CYS 306 1_555 H ZN ZN . B ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc17 B SG CYS 312 B CYS 308 1_555 H ZN ZN . B ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc18 G NI NI . B NI 501 1_555 J N1 5V1 . B 5V1 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc19 G NI NI . B NI 501 1_555 J N2 5V1 . B 5V1 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc20 G NI NI . B NI 501 1_555 L O HOH . B HOH 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? # _chem_comp.formula 'C14 H14 N2 O2' _chem_comp.formula_weight 242.273 _chem_comp.id 5V1 _chem_comp.mon_nstd_flag . _chem_comp.name '2-[[(phenylmethyl)amino]methyl]pyridine-4-carboxylic acid' _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 O1 C1 5V1 doub 1 n n C1 O2 5V1 sing 2 n n C1 C2 5V1 sing 3 n n C10 C9 5V1 doub 4 n y C10 C11 5V1 sing 5 n y C3 C2 5V1 doub 6 n y C3 C4 5V1 sing 7 n y C2 C14 5V1 sing 8 n y C9 C8 5V1 sing 9 n y C11 C12 5V1 doub 10 n y C4 N1 5V1 doub 11 n y C14 C5 5V1 doub 12 n y C8 C7 5V1 sing 13 n n C8 C13 5V1 doub 14 n y C12 C13 5V1 sing 15 n y C7 N2 5V1 sing 16 n n N1 C5 5V1 sing 17 n y C5 C6 5V1 sing 18 n n C6 N2 5V1 sing 19 n n C4 H1 5V1 sing 20 n n C6 H2 5V1 sing 21 n n C6 H3 5V1 sing 22 n n C7 H4 5V1 sing 23 n n C7 H5 5V1 sing 24 n n C10 H6 5V1 sing 25 n n C13 H7 5V1 sing 26 n n C3 H8 5V1 sing 27 n n N2 H9 5V1 sing 28 n n C9 H11 5V1 sing 29 n n C11 H12 5V1 sing 30 n n C12 H13 5V1 sing 31 n n C14 H14 5V1 sing 32 n n O2 H15 5V1 sing 33 n n # _atom_sites.entry_id 5F5I _atom_sites.fract_transf_matrix[1][1] 0.009898 _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] 0.006685 _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] 0.017265 _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 C 2 NI A 1 501 501 NI NI . D 3 ZN A 1 502 502 ZN ZN . E 4 SO4 A 1 503 1 SO4 SO4 . F 5 5V1 A 1 504 1 5V1 LIG . G 2 NI B 1 501 501 NI NI . H 3 ZN B 1 502 502 ZN ZN . I 4 SO4 B 1 503 2 SO4 SO4 . J 5 5V1 B 1 504 2 5V1 LIG . K 6 HOH A 1 601 28 HOH HOH . K 6 HOH A 2 602 84 HOH HOH . K 6 HOH A 3 603 215 HOH HOH . K 6 HOH A 4 604 46 HOH HOH . K 6 HOH A 5 605 97 HOH HOH . K 6 HOH A 6 606 43 HOH HOH . K 6 HOH A 7 607 163 HOH HOH . K 6 HOH A 8 608 11 HOH HOH . K 6 HOH A 9 609 160 HOH HOH . K 6 HOH A 10 610 272 HOH HOH . K 6 HOH A 11 611 7 HOH HOH . K 6 HOH A 12 612 13 HOH HOH . K 6 HOH A 13 613 16 HOH HOH . K 6 HOH A 14 614 55 HOH HOH . K 6 HOH A 15 615 252 HOH HOH . K 6 HOH A 16 616 63 HOH HOH . K 6 HOH A 17 617 204 HOH HOH . K 6 HOH A 18 618 47 HOH HOH . K 6 HOH A 19 619 5 HOH HOH . K 6 HOH A 20 620 87 HOH HOH . K 6 HOH A 21 621 44 HOH HOH . K 6 HOH A 22 622 30 HOH HOH . K 6 HOH A 23 623 140 HOH HOH . K 6 HOH A 24 624 112 HOH HOH . K 6 HOH A 25 625 40 HOH HOH . K 6 HOH A 26 626 83 HOH HOH . K 6 HOH A 27 627 151 HOH HOH . K 6 HOH A 28 628 1 HOH HOH . K 6 HOH A 29 629 138 HOH HOH . K 6 HOH A 30 630 4 HOH HOH . K 6 HOH A 31 631 212 HOH HOH . K 6 HOH A 32 632 49 HOH HOH . K 6 HOH A 33 633 18 HOH HOH . K 6 HOH A 34 634 98 HOH HOH . K 6 HOH A 35 635 6 HOH HOH . K 6 HOH A 36 636 187 HOH HOH . K 6 HOH A 37 637 23 HOH HOH . K 6 HOH A 38 638 38 HOH HOH . K 6 HOH A 39 639 62 HOH HOH . K 6 HOH A 40 640 258 HOH HOH . K 6 HOH A 41 641 8 HOH HOH . K 6 HOH A 42 642 21 HOH HOH . K 6 HOH A 43 643 206 HOH HOH . K 6 HOH A 44 644 232 HOH HOH . K 6 HOH A 45 645 17 HOH HOH . K 6 HOH A 46 646 76 HOH HOH . K 6 HOH A 47 647 19 HOH HOH . K 6 HOH A 48 648 168 HOH HOH . K 6 HOH A 49 649 80 HOH HOH . K 6 HOH A 50 650 41 HOH HOH . K 6 HOH A 51 651 153 HOH HOH . K 6 HOH A 52 652 12 HOH HOH . K 6 HOH A 53 653 127 HOH HOH . K 6 HOH A 54 654 67 HOH HOH . K 6 HOH A 55 655 137 HOH HOH . K 6 HOH A 56 656 85 HOH HOH . K 6 HOH A 57 657 24 HOH HOH . K 6 HOH A 58 658 56 HOH HOH . K 6 HOH A 59 659 105 HOH HOH . K 6 HOH A 60 660 102 HOH HOH . K 6 HOH A 61 661 146 HOH HOH . K 6 HOH A 62 662 245 HOH HOH . K 6 HOH A 63 663 222 HOH HOH . K 6 HOH A 64 664 123 HOH HOH . K 6 HOH A 65 665 32 HOH HOH . K 6 HOH A 66 666 270 HOH HOH . K 6 HOH A 67 667 167 HOH HOH . K 6 HOH A 68 668 162 HOH HOH . K 6 HOH A 69 669 157 HOH HOH . K 6 HOH A 70 670 99 HOH HOH . K 6 HOH A 71 671 150 HOH HOH . K 6 HOH A 72 672 144 HOH HOH . K 6 HOH A 73 673 42 HOH HOH . K 6 HOH A 74 674 96 HOH HOH . K 6 HOH A 75 675 145 HOH HOH . K 6 HOH A 76 676 260 HOH HOH . K 6 HOH A 77 677 229 HOH HOH . K 6 HOH A 78 678 101 HOH HOH . K 6 HOH A 79 679 203 HOH HOH . K 6 HOH A 80 680 10 HOH HOH . K 6 HOH A 81 681 142 HOH HOH . K 6 HOH A 82 682 266 HOH HOH . K 6 HOH A 83 683 20 HOH HOH . L 6 HOH B 1 601 15 HOH HOH . L 6 HOH B 2 602 170 HOH HOH . L 6 HOH B 3 603 29 HOH HOH . L 6 HOH B 4 604 233 HOH HOH . L 6 HOH B 5 605 149 HOH HOH . L 6 HOH B 6 606 159 HOH HOH . L 6 HOH B 7 607 224 HOH HOH . L 6 HOH B 8 608 3 HOH HOH . L 6 HOH B 9 609 136 HOH HOH . L 6 HOH B 10 610 75 HOH HOH . L 6 HOH B 11 611 36 HOH HOH . L 6 HOH B 12 612 120 HOH HOH . L 6 HOH B 13 613 131 HOH HOH . L 6 HOH B 14 614 164 HOH HOH . L 6 HOH B 15 615 118 HOH HOH . L 6 HOH B 16 616 119 HOH HOH . L 6 HOH B 17 617 205 HOH HOH . L 6 HOH B 18 618 9 HOH HOH . L 6 HOH B 19 619 33 HOH HOH . L 6 HOH B 20 620 141 HOH HOH . L 6 HOH B 21 621 66 HOH HOH . L 6 HOH B 22 622 27 HOH HOH . L 6 HOH B 23 623 225 HOH HOH . L 6 HOH B 24 624 53 HOH HOH . L 6 HOH B 25 625 50 HOH HOH . L 6 HOH B 26 626 71 HOH HOH . L 6 HOH B 27 627 14 HOH HOH . L 6 HOH B 28 628 271 HOH HOH . L 6 HOH B 29 629 171 HOH HOH . L 6 HOH B 30 630 22 HOH HOH . L 6 HOH B 31 631 82 HOH HOH . L 6 HOH B 32 632 2 HOH HOH . L 6 HOH B 33 633 269 HOH HOH . L 6 HOH B 34 634 267 HOH HOH . L 6 HOH B 35 635 109 HOH HOH . L 6 HOH B 36 636 79 HOH HOH . L 6 HOH B 37 637 209 HOH HOH . L 6 HOH B 38 638 139 HOH HOH . L 6 HOH B 39 639 156 HOH HOH . L 6 HOH B 40 640 48 HOH HOH . L 6 HOH B 41 641 70 HOH HOH . L 6 HOH B 42 642 35 HOH HOH . L 6 HOH B 43 643 126 HOH HOH . L 6 HOH B 44 644 175 HOH HOH . L 6 HOH B 45 645 34 HOH HOH . L 6 HOH B 46 646 25 HOH HOH . L 6 HOH B 47 647 218 HOH HOH . L 6 HOH B 48 648 77 HOH HOH . L 6 HOH B 49 649 223 HOH HOH . L 6 HOH B 50 650 237 HOH HOH . L 6 HOH B 51 651 241 HOH HOH . L 6 HOH B 52 652 234 HOH HOH . L 6 HOH B 53 653 57 HOH HOH . L 6 HOH B 54 654 196 HOH HOH . L 6 HOH B 55 655 134 HOH HOH . L 6 HOH B 56 656 59 HOH HOH . L 6 HOH B 57 657 147 HOH HOH . L 6 HOH B 58 658 220 HOH HOH . L 6 HOH B 59 659 200 HOH HOH . L 6 HOH B 60 660 268 HOH HOH . L 6 HOH B 61 661 255 HOH HOH . L 6 HOH B 62 662 148 HOH HOH . L 6 HOH B 63 663 235 HOH HOH . L 6 HOH B 64 664 65 HOH HOH . L 6 HOH B 65 665 135 HOH HOH . L 6 HOH B 66 666 236 HOH HOH . L 6 HOH B 67 667 78 HOH HOH . L 6 HOH B 68 668 106 HOH HOH . L 6 HOH B 69 669 111 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 5V1 . . . J 5 -41.074 -55.246 3.186 1 47.12 ? N1 5V1 504 B 1 HETATM 2 C C4 5V1 . . . J 5 -41.268 -54.245 2.306 1 47.25 ? C4 5V1 504 B 1 HETATM 3 C C5 5V1 . . . J 5 -42.015 -56.211 3.283 1 50.57 ? C5 5V1 504 B 1 HETATM 4 C C6 5V1 . . . J 5 -41.745 -57.318 4.272 1 49.7 ? C6 5V1 504 B 1 HETATM 5 C C7 5V1 . . . J 5 -39.784 -58.268 3.195 1 51.55 ? C7 5V1 504 B 1 HETATM 6 C C8 5V1 . . . J 5 -39.942 -59.766 3.223 1 52.14 ? C8 5V1 504 B 1 HETATM 7 C C10 5V1 . . . J 5 -39.109 -61.948 3.82 1 54.34 ? C10 5V1 504 B 1 HETATM 8 C C13 5V1 . . . J 5 -41.077 -60.373 2.699 1 52.4 ? C13 5V1 504 B 1 HETATM 9 O O1 5V1 . . . J 5 -44.514 -55.086 -0.475 1 48.04 ? O1 5V1 504 B 1 HETATM 10 C C1 5V1 . . . J 5 -44.574 -55.109 0.747 1 48.57 ? C1 5V1 504 B 1 HETATM 11 C C2 5V1 . . . J 5 -43.354 -55.154 1.597 1 49.11 ? C2 5V1 504 B 1 HETATM 12 C C3 5V1 . . . J 5 -42.386 -54.162 1.501 1 47.88 ? C3 5V1 504 B 1 HETATM 13 N N2 5V1 . . . J 5 -40.331 -57.637 4.407 1 50.68 ? N2 5V1 504 B 1 HETATM 14 C C9 5V1 . . . J 5 -38.96 -60.573 3.785 1 52.53 ? C9 5V1 504 B 1 HETATM 15 C C11 5V1 . . . J 5 -40.239 -62.536 3.292 1 54.67 ? C11 5V1 504 B 1 HETATM 16 C C12 5V1 . . . J 5 -41.223 -61.748 2.732 1 54.1 ? C12 5V1 504 B 1 HETATM 17 C C14 5V1 . . . J 5 -43.163 -56.194 2.5 1 50.53 ? C14 5V1 504 B 1 HETATM 18 O O2 5V1 . . . J 5 -45.699 -55.096 1.421 1 47.33 ? O2 5V1 504 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 18 #