data_4XBJ # _model_server_result.job_id xBVtwdPJXZ6HRuCmJaUeag _model_server_result.datetime_utc '2024-10-31 17:31:42' _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 4xbj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 4XBJ # _exptl.entry_id 4XBJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 356.206 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '{1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC ACID' _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 4XBJ _cell.length_a 147.978 _cell.length_b 147.978 _cell.length_c 163.578 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XBJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 168 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 6' # 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,H,I,J,P,Q 1 1 C,D,K,L,M,N,O,R,S 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 ? 2 E N N ? 2 I N N ? 2 K N N # _chem_comp.formula 'C10 H18 N2 O8 P2' _chem_comp.formula_weight 356.206 _chem_comp.id IN5 _chem_comp.mon_nstd_flag . _chem_comp.name '{1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC 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 C1 N1 IN5 doub 173 n y C1 C5 IN5 sing 174 n y C1 H1 IN5 sing 175 n n C2 C3 IN5 doub 176 n y C2 N1 IN5 sing 177 n y C2 C6 IN5 sing 178 n n C3 C4 IN5 sing 179 n y C3 O1 IN5 sing 180 n n O4 P1 IN5 doub 181 n n O5 P1 IN5 sing 182 n n O5 HO5 IN5 sing 183 n n C7 C5 IN5 sing 184 n n C7 O2 IN5 sing 185 n n C7 H71 IN5 sing 186 n n C7 H72 IN5 sing 187 n n C8 C4 IN5 sing 188 n n C8 N2 IN5 sing 189 n n C8 H81 IN5 sing 190 n n C8 H82 IN5 sing 191 n n C9 C10 IN5 sing 192 n n C9 N2 IN5 sing 193 n n C9 P2 IN5 sing 194 n n C9 H9 IN5 sing 195 n n C10 H101 IN5 sing 196 n n C10 H102 IN5 sing 197 n n C10 H103 IN5 sing 198 n n C4 C5 IN5 doub 199 n y O1 HO1 IN5 sing 200 n n C6 H61 IN5 sing 201 n n C6 H62 IN5 sing 202 n n C6 H63 IN5 sing 203 n n O2 P1 IN5 sing 204 n n N2 HN2 IN5 sing 205 n n P1 O3 IN5 sing 206 n n O3 HO3 IN5 sing 207 n n P2 O6 IN5 doub 208 n n P2 O7 IN5 sing 209 n n P2 O8 IN5 sing 210 n n O7 HO7 IN5 sing 211 n n O8 HO8 IN5 sing 212 n n # _atom_sites.entry_id 4XBJ _atom_sites.fract_transf_matrix[1][1] 0.006758 _atom_sites.fract_transf_matrix[1][2] 0.003902 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007803 _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] 0.006113 _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 2 IN5 A 1 401 401 IN5 IN5 . F 3 SO4 A 1 402 2 SO4 SO4 . G 3 SO4 A 1 403 3 SO4 SO4 . H 3 SO4 A 1 404 6 SO4 SO4 . I 2 IN5 B 1 401 401 IN5 IN5 . J 3 SO4 B 1 402 1 SO4 SO4 . K 2 IN5 C 1 401 401 IN5 IN5 . L 3 SO4 C 1 402 4 SO4 SO4 . M 3 SO4 C 1 403 5 SO4 SO4 . N 3 SO4 C 1 404 7 SO4 SO4 . O 3 SO4 D 1 401 8 SO4 SO4 . P 4 HOH A 1 501 14 HOH HOH . P 4 HOH A 2 502 165 HOH HOH . P 4 HOH A 3 503 120 HOH HOH . P 4 HOH A 4 504 231 HOH HOH . P 4 HOH A 5 505 236 HOH HOH . P 4 HOH A 6 506 155 HOH HOH . P 4 HOH A 7 507 25 HOH HOH . P 4 HOH A 8 508 81 HOH HOH . P 4 HOH A 9 509 30 HOH HOH . P 4 HOH A 10 510 100 HOH HOH . P 4 HOH A 11 511 23 HOH HOH . P 4 HOH A 12 512 7 HOH HOH . P 4 HOH A 13 513 93 HOH HOH . P 4 HOH A 14 514 2 HOH HOH . P 4 HOH A 15 515 5 HOH HOH . P 4 HOH A 16 516 6 HOH HOH . P 4 HOH A 17 517 10 HOH HOH . P 4 HOH A 18 518 11 HOH HOH . P 4 HOH A 19 519 12 HOH HOH . P 4 HOH A 20 520 19 HOH HOH . P 4 HOH A 21 521 20 HOH HOH . P 4 HOH A 22 522 26 HOH HOH . P 4 HOH A 23 523 33 HOH HOH . P 4 HOH A 24 524 36 HOH HOH . P 4 HOH A 25 525 37 HOH HOH . P 4 HOH A 26 526 39 HOH HOH . P 4 HOH A 27 527 40 HOH HOH . P 4 HOH A 28 528 41 HOH HOH . P 4 HOH A 29 529 43 HOH HOH . P 4 HOH A 30 530 44 HOH HOH . P 4 HOH A 31 531 46 HOH HOH . P 4 HOH A 32 532 48 HOH HOH . P 4 HOH A 33 533 49 HOH HOH . P 4 HOH A 34 534 51 HOH HOH . P 4 HOH A 35 535 52 HOH HOH . P 4 HOH A 36 536 54 HOH HOH . P 4 HOH A 37 537 55 HOH HOH . P 4 HOH A 38 538 57 HOH HOH . P 4 HOH A 39 539 60 HOH HOH . P 4 HOH A 40 540 63 HOH HOH . P 4 HOH A 41 541 64 HOH HOH . P 4 HOH A 42 542 65 HOH HOH . P 4 HOH A 43 543 67 HOH HOH . P 4 HOH A 44 544 68 HOH HOH . P 4 HOH A 45 545 75 HOH HOH . P 4 HOH A 46 546 76 HOH HOH . P 4 HOH A 47 547 78 HOH HOH . P 4 HOH A 48 548 80 HOH HOH . P 4 HOH A 49 549 86 HOH HOH . P 4 HOH A 50 550 92 HOH HOH . P 4 HOH A 51 551 94 HOH HOH . P 4 HOH A 52 552 98 HOH HOH . P 4 HOH A 53 553 101 HOH HOH . P 4 HOH A 54 554 102 HOH HOH . P 4 HOH A 55 555 105 HOH HOH . P 4 HOH A 56 556 108 HOH HOH . P 4 HOH A 57 557 109 HOH HOH . P 4 HOH A 58 558 111 HOH HOH . P 4 HOH A 59 559 112 HOH HOH . P 4 HOH A 60 560 113 HOH HOH . P 4 HOH A 61 561 114 HOH HOH . P 4 HOH A 62 562 122 HOH HOH . P 4 HOH A 63 563 123 HOH HOH . P 4 HOH A 64 564 126 HOH HOH . P 4 HOH A 65 565 127 HOH HOH . P 4 HOH A 66 566 129 HOH HOH . P 4 HOH A 67 567 132 HOH HOH . P 4 HOH A 68 568 135 HOH HOH . P 4 HOH A 69 569 136 HOH HOH . P 4 HOH A 70 570 141 HOH HOH . P 4 HOH A 71 571 142 HOH HOH . P 4 HOH A 72 572 144 HOH HOH . P 4 HOH A 73 573 145 HOH HOH . P 4 HOH A 74 574 146 HOH HOH . P 4 HOH A 75 575 147 HOH HOH . P 4 HOH A 76 576 150 HOH HOH . P 4 HOH A 77 577 151 HOH HOH . P 4 HOH A 78 578 153 HOH HOH . P 4 HOH A 79 579 154 HOH HOH . P 4 HOH A 80 580 156 HOH HOH . P 4 HOH A 81 581 161 HOH HOH . P 4 HOH A 82 582 166 HOH HOH . P 4 HOH A 83 583 171 HOH HOH . P 4 HOH A 84 584 172 HOH HOH . P 4 HOH A 85 585 173 HOH HOH . P 4 HOH A 86 586 174 HOH HOH . P 4 HOH A 87 587 176 HOH HOH . P 4 HOH A 88 588 178 HOH HOH . P 4 HOH A 89 589 179 HOH HOH . P 4 HOH A 90 590 180 HOH HOH . P 4 HOH A 91 591 181 HOH HOH . P 4 HOH A 92 592 187 HOH HOH . P 4 HOH A 93 593 197 HOH HOH . P 4 HOH A 94 594 203 HOH HOH . P 4 HOH A 95 595 204 HOH HOH . P 4 HOH A 96 596 208 HOH HOH . P 4 HOH A 97 597 213 HOH HOH . P 4 HOH A 98 598 214 HOH HOH . P 4 HOH A 99 599 217 HOH HOH . P 4 HOH A 100 600 218 HOH HOH . P 4 HOH A 101 601 219 HOH HOH . P 4 HOH A 102 602 220 HOH HOH . P 4 HOH A 103 603 221 HOH HOH . P 4 HOH A 104 604 222 HOH HOH . P 4 HOH A 105 605 226 HOH HOH . P 4 HOH A 106 606 228 HOH HOH . P 4 HOH A 107 607 229 HOH HOH . P 4 HOH A 108 608 230 HOH HOH . P 4 HOH A 109 609 232 HOH HOH . Q 4 HOH B 1 501 157 HOH HOH . Q 4 HOH B 2 502 13 HOH HOH . Q 4 HOH B 3 503 163 HOH HOH . Q 4 HOH B 4 504 58 HOH HOH . Q 4 HOH B 5 505 134 HOH HOH . Q 4 HOH B 6 506 199 HOH HOH . Q 4 HOH B 7 507 18 HOH HOH . Q 4 HOH B 8 508 45 HOH HOH . Q 4 HOH B 9 509 188 HOH HOH . Q 4 HOH B 10 510 131 HOH HOH . Q 4 HOH B 11 511 42 HOH HOH . Q 4 HOH B 12 512 168 HOH HOH . Q 4 HOH B 13 513 74 HOH HOH . Q 4 HOH B 14 514 16 HOH HOH . Q 4 HOH B 15 515 72 HOH HOH . Q 4 HOH B 16 516 1 HOH HOH . Q 4 HOH B 17 517 3 HOH HOH . Q 4 HOH B 18 518 8 HOH HOH . Q 4 HOH B 19 519 9 HOH HOH . Q 4 HOH B 20 520 15 HOH HOH . Q 4 HOH B 21 521 17 HOH HOH . Q 4 HOH B 22 522 21 HOH HOH . Q 4 HOH B 23 523 22 HOH HOH . Q 4 HOH B 24 524 24 HOH HOH . Q 4 HOH B 25 525 27 HOH HOH . Q 4 HOH B 26 526 28 HOH HOH . Q 4 HOH B 27 527 29 HOH HOH . Q 4 HOH B 28 528 32 HOH HOH . Q 4 HOH B 29 529 34 HOH HOH . Q 4 HOH B 30 530 35 HOH HOH . Q 4 HOH B 31 531 38 HOH HOH . Q 4 HOH B 32 532 47 HOH HOH . Q 4 HOH B 33 533 50 HOH HOH . Q 4 HOH B 34 534 53 HOH HOH . Q 4 HOH B 35 535 56 HOH HOH . Q 4 HOH B 36 536 59 HOH HOH . Q 4 HOH B 37 537 61 HOH HOH . Q 4 HOH B 38 538 62 HOH HOH . Q 4 HOH B 39 539 66 HOH HOH . Q 4 HOH B 40 540 69 HOH HOH . Q 4 HOH B 41 541 70 HOH HOH . Q 4 HOH B 42 542 71 HOH HOH . Q 4 HOH B 43 543 73 HOH HOH . Q 4 HOH B 44 544 77 HOH HOH . Q 4 HOH B 45 545 79 HOH HOH . Q 4 HOH B 46 546 82 HOH HOH . Q 4 HOH B 47 547 83 HOH HOH . Q 4 HOH B 48 548 84 HOH HOH . Q 4 HOH B 49 549 85 HOH HOH . Q 4 HOH B 50 550 87 HOH HOH . Q 4 HOH B 51 551 88 HOH HOH . Q 4 HOH B 52 552 89 HOH HOH . Q 4 HOH B 53 553 90 HOH HOH . Q 4 HOH B 54 554 91 HOH HOH . Q 4 HOH B 55 555 95 HOH HOH . Q 4 HOH B 56 556 96 HOH HOH . Q 4 HOH B 57 557 97 HOH HOH . Q 4 HOH B 58 558 99 HOH HOH . Q 4 HOH B 59 559 103 HOH HOH . Q 4 HOH B 60 560 104 HOH HOH . Q 4 HOH B 61 561 106 HOH HOH . Q 4 HOH B 62 562 107 HOH HOH . Q 4 HOH B 63 563 110 HOH HOH . Q 4 HOH B 64 564 115 HOH HOH . Q 4 HOH B 65 565 116 HOH HOH . Q 4 HOH B 66 566 117 HOH HOH . Q 4 HOH B 67 567 118 HOH HOH . Q 4 HOH B 68 568 119 HOH HOH . Q 4 HOH B 69 569 121 HOH HOH . Q 4 HOH B 70 570 124 HOH HOH . Q 4 HOH B 71 571 125 HOH HOH . Q 4 HOH B 72 572 128 HOH HOH . Q 4 HOH B 73 573 130 HOH HOH . Q 4 HOH B 74 574 137 HOH HOH . Q 4 HOH B 75 575 138 HOH HOH . Q 4 HOH B 76 576 140 HOH HOH . Q 4 HOH B 77 577 143 HOH HOH . Q 4 HOH B 78 578 148 HOH HOH . Q 4 HOH B 79 579 149 HOH HOH . Q 4 HOH B 80 580 152 HOH HOH . Q 4 HOH B 81 581 159 HOH HOH . Q 4 HOH B 82 582 160 HOH HOH . Q 4 HOH B 83 583 162 HOH HOH . Q 4 HOH B 84 584 167 HOH HOH . Q 4 HOH B 85 585 169 HOH HOH . Q 4 HOH B 86 586 170 HOH HOH . Q 4 HOH B 87 587 183 HOH HOH . Q 4 HOH B 88 588 184 HOH HOH . Q 4 HOH B 89 589 186 HOH HOH . Q 4 HOH B 90 590 189 HOH HOH . Q 4 HOH B 91 591 190 HOH HOH . Q 4 HOH B 92 592 192 HOH HOH . Q 4 HOH B 93 593 193 HOH HOH . Q 4 HOH B 94 594 195 HOH HOH . Q 4 HOH B 95 595 200 HOH HOH . Q 4 HOH B 96 596 207 HOH HOH . Q 4 HOH B 97 597 209 HOH HOH . Q 4 HOH B 98 598 210 HOH HOH . Q 4 HOH B 99 599 212 HOH HOH . Q 4 HOH B 100 600 215 HOH HOH . Q 4 HOH B 101 601 224 HOH HOH . Q 4 HOH B 102 602 225 HOH HOH . Q 4 HOH B 103 603 227 HOH HOH . Q 4 HOH B 104 604 233 HOH HOH . Q 4 HOH B 105 605 235 HOH HOH . R 4 HOH C 1 501 185 HOH HOH . R 4 HOH C 2 502 31 HOH HOH . R 4 HOH C 3 503 133 HOH HOH . R 4 HOH C 4 504 164 HOH HOH . R 4 HOH C 5 505 175 HOH HOH . R 4 HOH C 6 506 177 HOH HOH . R 4 HOH C 7 507 191 HOH HOH . R 4 HOH C 8 508 194 HOH HOH . R 4 HOH C 9 509 198 HOH HOH . R 4 HOH C 10 510 202 HOH HOH . R 4 HOH C 11 511 205 HOH HOH . R 4 HOH C 12 512 211 HOH HOH . R 4 HOH C 13 513 216 HOH HOH . R 4 HOH C 14 514 223 HOH HOH . S 4 HOH D 1 501 4 HOH HOH . S 4 HOH D 2 502 139 HOH HOH . S 4 HOH D 3 503 158 HOH HOH . S 4 HOH D 4 504 182 HOH HOH . S 4 HOH D 5 505 196 HOH HOH . S 4 HOH D 6 506 201 HOH HOH . S 4 HOH D 7 507 206 HOH HOH . S 4 HOH D 8 508 234 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 C1 IN5 . . . E 2 50.682 2.96 6.942 1 12.05 ? C1 IN5 401 A 1 HETATM 2 C C2 IN5 . . . E 2 50.434 0.572 7.1 1 13.56 ? C2 IN5 401 A 1 HETATM 3 C C3 IN5 . . . E 2 50.042 0.521 5.757 1 14.59 ? C3 IN5 401 A 1 HETATM 4 O O4 IN5 . . . E 2 46.721 5.429 3.878 1 11.96 ? O4 IN5 401 A 1 HETATM 5 O O5 IN5 . . . E 2 48.578 6.791 4.897 1 10.09 ? O5 IN5 401 A 1 HETATM 6 C C7 IN5 . . . E 2 50.199 4.221 4.846 1 13 ? C7 IN5 401 A 1 HETATM 7 C C8 IN5 . . . E 2 49.565 1.652 3.513 1 15.38 ? C8 IN5 401 A 1 HETATM 8 C C9 IN5 . . . E 2 47.715 1.275 1.867 1 18.66 ? C9 IN5 401 A 1 HETATM 9 C C10 IN5 . . . E 2 48.544 2.061 0.858 1 18.01 ? C10 IN5 401 A 1 HETATM 10 N N1 IN5 . . . E 2 50.754 1.791 7.708 1 13.01 ? N1 IN5 401 A 1 HETATM 11 C C4 IN5 . . . E 2 49.902 1.702 5.015 1 15.32 ? C4 IN5 401 A 1 HETATM 12 C C5 IN5 . . . E 2 50.275 2.916 5.604 1 12.78 ? C5 IN5 401 A 1 HETATM 13 O O1 IN5 . . . E 2 49.711 -0.701 5.254 1 16.8 ? O1 IN5 401 A 1 HETATM 14 C C6 IN5 . . . E 2 50.495 -0.665 7.956 1 13.74 ? C6 IN5 401 A 1 HETATM 15 O O2 IN5 . . . E 2 48.818 4.359 4.518 1 12.28 ? O2 IN5 401 A 1 HETATM 16 N N2 IN5 . . . E 2 48.149 1.454 3.271 1 18.82 ? N2 IN5 401 A 1 HETATM 17 P P1 IN5 . . . E 2 48.203 5.715 3.907 1 10.7 ? P1 IN5 401 A 1 HETATM 18 O O3 IN5 . . . E 2 48.81 5.902 2.536 1 9.59 ? O3 IN5 401 A 1 HETATM 19 P P2 IN5 . . . E 2 47.705 -0.514 1.437 1 21.28 ? P2 IN5 401 A 1 HETATM 20 O O6 IN5 . . . E 2 47.002 -1.267 2.514 1 22.83 ? O6 IN5 401 A 1 HETATM 21 O O7 IN5 . . . E 2 46.975 -0.711 0.095 1 19.33 ? O7 IN5 401 A 1 HETATM 22 O O8 IN5 . . . E 2 49.152 -1.028 1.317 1 21.18 ? O8 IN5 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #