data_3DUV # _model_server_result.job_id Sireu7DvuYjeJyWBqGwp5A _model_server_result.datetime_utc '2024-11-27 00:08:48' _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 3duv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":263}' # _entry.id 3DUV # _exptl.entry_id 3DUV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 238.192 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '3-deoxy-alpha-D-manno-oct-2-ulopyranosonic 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 3DUV _cell.length_a 48.418 _cell.length_b 82.609 _cell.length_c 115.712 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DUV _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 2 C N N ? 2 E 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 covale ? covale1 A C MSE 1 A MSE 1 1_555 A N SER 2 A SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C PRO 28 A PRO 28 1_555 A N MSE 29 A MSE 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C MSE 29 A MSE 29 1_555 A N ILE 30 A ILE 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 A C CYS 66 A CYS 66 1_555 A N MSE 67 A MSE 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C MSE 67 A MSE 67 1_555 A N THR 68 A THR 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 A C ASN 122 A ASN 122 1_555 A N MSE 123 A MSE 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 A C MSE 123 A MSE 123 1_555 A N ALA 124 A ALA 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale8 A C PHE 167 A PHE 167 1_555 A N MSE 168 A MSE 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale9 A C MSE 168 A MSE 168 1_555 A N ASN 169 A ASN 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale10 B C MSE 1 B MSE 1 1_555 B N SER 2 B SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale11 B C PRO 28 B PRO 28 1_555 B N MSE 29 B MSE 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale12 B C MSE 29 B MSE 29 1_555 B N ILE 30 B ILE 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale13 B C CYS 66 B CYS 66 1_555 B N MSE 67 B MSE 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale14 B C MSE 67 B MSE 67 1_555 B N THR 68 B THR 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale15 B C ASN 122 B ASN 122 1_555 B N MSE 123 B MSE 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale16 B C MSE 123 B MSE 123 1_555 B N ALA 124 B ALA 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale17 B C PHE 167 B PHE 167 1_555 B N MSE 168 B MSE 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale18 B C MSE 168 B MSE 168 1_555 B N ASN 169 B ASN 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? # _chem_comp.formula 'C8 H14 O8' _chem_comp.formula_weight 238.192 _chem_comp.id KDO _chem_comp.mon_nstd_flag . _chem_comp.name '3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid' _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms '3-deoxy-d-manno-oct-2-ulopyranosonic acid;2-keto-3-deoxy-D-mannooctanoic acid;3-deoxy-alpha-D-manno-oct-2-ulosonic acid;3-deoxy-D-manno-oct-2-ulosonic acid;3-deoxy-manno-oct-2-ulosonic acid' # 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 O1A KDO doub 173 n n C1 O1B KDO sing 174 n n C1 C2 KDO sing 175 n n O1B HO1B KDO sing 176 n n C2 O2 KDO sing 177 n n C2 C3 KDO sing 178 n n C2 O6 KDO sing 179 n n O2 HO2 KDO sing 180 n n C3 C4 KDO sing 181 n n C3 H31 KDO sing 182 n n C3 H32 KDO sing 183 n n C4 O4 KDO sing 184 n n C4 C5 KDO sing 185 n n C4 H4 KDO sing 186 n n O4 HO4 KDO sing 187 n n C5 O5 KDO sing 188 n n C5 C6 KDO sing 189 n n C5 H5 KDO sing 190 n n O5 HO5 KDO sing 191 n n C6 O6 KDO sing 192 n n C6 C7 KDO sing 193 n n C6 H6 KDO sing 194 n n C7 O7 KDO sing 195 n n C7 C8 KDO sing 196 n n C7 H7 KDO sing 197 n n O7 HO7 KDO sing 198 n n C8 O8 KDO sing 199 n n C8 H81 KDO sing 200 n n C8 H82 KDO sing 201 n n O8 HO8 KDO sing 202 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version KDO DKdopa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 KDO a-D-Kdop 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 KDO Kdo 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3DUV _atom_sites.fract_transf_matrix[1][1] 0.020653 _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] 0.012105 _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] 0.008642 _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 KDO A 1 263 260 KDO KDO . D 3 P4C A 1 270 270 P4C P4C . E 2 KDO B 1 263 261 KDO KDO . F 4 HOH A 1 300 300 HOH HOH . F 4 HOH A 2 301 301 HOH HOH . F 4 HOH A 3 302 302 HOH HOH . F 4 HOH A 4 303 303 HOH HOH . F 4 HOH A 5 304 304 HOH HOH . F 4 HOH A 6 305 305 HOH HOH . F 4 HOH A 7 306 306 HOH HOH . F 4 HOH A 8 309 309 HOH HOH . F 4 HOH A 9 310 310 HOH HOH . F 4 HOH A 10 311 311 HOH HOH . F 4 HOH A 11 312 312 HOH HOH . F 4 HOH A 12 313 313 HOH HOH . F 4 HOH A 13 315 315 HOH HOH . F 4 HOH A 14 317 317 HOH HOH . F 4 HOH A 15 318 318 HOH HOH . F 4 HOH A 16 319 319 HOH HOH . F 4 HOH A 17 321 321 HOH HOH . F 4 HOH A 18 322 322 HOH HOH . F 4 HOH A 19 330 330 HOH HOH . F 4 HOH A 20 364 364 HOH HOH . F 4 HOH A 21 366 366 HOH HOH . F 4 HOH A 22 374 374 HOH HOH . F 4 HOH A 23 382 382 HOH HOH . F 4 HOH A 24 386 386 HOH HOH . F 4 HOH A 25 388 388 HOH HOH . F 4 HOH A 26 389 389 HOH HOH . F 4 HOH A 27 391 391 HOH HOH . F 4 HOH A 28 392 392 HOH HOH . F 4 HOH A 29 395 395 HOH HOH . F 4 HOH A 30 401 401 HOH HOH . F 4 HOH A 31 403 403 HOH HOH . F 4 HOH A 32 407 407 HOH HOH . F 4 HOH A 33 411 411 HOH HOH . F 4 HOH A 34 414 414 HOH HOH . F 4 HOH A 35 429 429 HOH HOH . F 4 HOH A 36 454 454 HOH HOH . F 4 HOH A 37 465 465 HOH HOH . F 4 HOH A 38 466 466 HOH HOH . F 4 HOH A 39 488 488 HOH HOH . F 4 HOH A 40 493 493 HOH HOH . F 4 HOH A 41 494 494 HOH HOH . F 4 HOH A 42 496 496 HOH HOH . F 4 HOH A 43 503 503 HOH HOH . F 4 HOH A 44 507 507 HOH HOH . F 4 HOH A 45 508 508 HOH HOH . F 4 HOH A 46 509 509 HOH HOH . F 4 HOH A 47 512 512 HOH HOH . F 4 HOH A 48 517 517 HOH HOH . F 4 HOH A 49 518 518 HOH HOH . F 4 HOH A 50 519 519 HOH HOH . F 4 HOH A 51 522 522 HOH HOH . F 4 HOH A 52 530 530 HOH HOH . F 4 HOH A 53 531 531 HOH HOH . F 4 HOH A 54 536 536 HOH HOH . F 4 HOH A 55 545 545 HOH HOH . F 4 HOH A 56 549 549 HOH HOH . F 4 HOH A 57 560 560 HOH HOH . F 4 HOH A 58 563 563 HOH HOH . F 4 HOH A 59 564 564 HOH HOH . F 4 HOH A 60 580 580 HOH HOH . F 4 HOH A 61 594 594 HOH HOH . F 4 HOH A 62 602 602 HOH HOH . F 4 HOH A 63 670 670 HOH HOH . F 4 HOH A 64 680 680 HOH HOH . F 4 HOH A 65 709 709 HOH HOH . F 4 HOH A 66 753 753 HOH HOH . F 4 HOH A 67 760 760 HOH HOH . F 4 HOH A 68 795 795 HOH HOH . F 4 HOH A 69 800 800 HOH HOH . F 4 HOH A 70 812 812 HOH HOH . F 4 HOH A 71 839 839 HOH HOH . F 4 HOH A 72 843 843 HOH HOH . F 4 HOH A 73 874 874 HOH HOH . F 4 HOH A 74 910 910 HOH HOH . G 4 HOH B 1 323 323 HOH HOH . G 4 HOH B 2 324 324 HOH HOH . G 4 HOH B 3 326 326 HOH HOH . G 4 HOH B 4 328 328 HOH HOH . G 4 HOH B 5 332 332 HOH HOH . G 4 HOH B 6 333 333 HOH HOH . G 4 HOH B 7 334 334 HOH HOH . G 4 HOH B 8 335 335 HOH HOH . G 4 HOH B 9 336 336 HOH HOH . G 4 HOH B 10 338 338 HOH HOH . G 4 HOH B 11 339 339 HOH HOH . G 4 HOH B 12 341 341 HOH HOH . G 4 HOH B 13 342 342 HOH HOH . G 4 HOH B 14 343 343 HOH HOH . G 4 HOH B 15 347 347 HOH HOH . G 4 HOH B 16 351 351 HOH HOH . G 4 HOH B 17 352 352 HOH HOH . G 4 HOH B 18 357 357 HOH HOH . G 4 HOH B 19 358 358 HOH HOH . G 4 HOH B 20 360 360 HOH HOH . G 4 HOH B 21 362 362 HOH HOH . G 4 HOH B 22 385 385 HOH HOH . G 4 HOH B 23 397 397 HOH HOH . G 4 HOH B 24 406 406 HOH HOH . G 4 HOH B 25 408 408 HOH HOH . G 4 HOH B 26 409 409 HOH HOH . G 4 HOH B 27 417 417 HOH HOH . G 4 HOH B 28 418 418 HOH HOH . G 4 HOH B 29 419 419 HOH HOH . G 4 HOH B 30 423 423 HOH HOH . G 4 HOH B 31 426 426 HOH HOH . G 4 HOH B 32 430 430 HOH HOH . G 4 HOH B 33 434 434 HOH HOH . G 4 HOH B 34 435 435 HOH HOH . G 4 HOH B 35 436 436 HOH HOH . G 4 HOH B 36 438 438 HOH HOH . G 4 HOH B 37 439 439 HOH HOH . G 4 HOH B 38 440 440 HOH HOH . G 4 HOH B 39 444 444 HOH HOH . G 4 HOH B 40 450 450 HOH HOH . G 4 HOH B 41 451 451 HOH HOH . G 4 HOH B 42 475 475 HOH HOH . G 4 HOH B 43 481 481 HOH HOH . G 4 HOH B 44 486 486 HOH HOH . G 4 HOH B 45 490 490 HOH HOH . G 4 HOH B 46 495 495 HOH HOH . G 4 HOH B 47 497 497 HOH HOH . G 4 HOH B 48 498 498 HOH HOH . G 4 HOH B 49 499 499 HOH HOH . G 4 HOH B 50 500 500 HOH HOH . G 4 HOH B 51 501 501 HOH HOH . G 4 HOH B 52 502 502 HOH HOH . G 4 HOH B 53 504 504 HOH HOH . G 4 HOH B 54 505 505 HOH HOH . G 4 HOH B 55 506 506 HOH HOH . G 4 HOH B 56 510 510 HOH HOH . G 4 HOH B 57 511 511 HOH HOH . G 4 HOH B 58 514 514 HOH HOH . G 4 HOH B 59 515 515 HOH HOH . G 4 HOH B 60 523 523 HOH HOH . G 4 HOH B 61 524 524 HOH HOH . G 4 HOH B 62 532 532 HOH HOH . G 4 HOH B 63 535 535 HOH HOH . G 4 HOH B 64 540 540 HOH HOH . G 4 HOH B 65 569 569 HOH HOH . G 4 HOH B 66 577 577 HOH HOH . G 4 HOH B 67 584 584 HOH HOH . G 4 HOH B 68 588 588 HOH HOH . G 4 HOH B 69 610 610 HOH HOH . G 4 HOH B 70 613 613 HOH HOH . G 4 HOH B 71 677 677 HOH HOH . G 4 HOH B 72 699 699 HOH HOH . G 4 HOH B 73 711 711 HOH HOH . G 4 HOH B 74 747 747 HOH HOH . G 4 HOH B 75 750 750 HOH HOH . G 4 HOH B 76 756 756 HOH HOH . G 4 HOH B 77 758 758 HOH HOH . G 4 HOH B 78 784 784 HOH HOH . G 4 HOH B 79 785 785 HOH HOH . G 4 HOH B 80 787 787 HOH HOH . G 4 HOH B 81 791 791 HOH HOH . G 4 HOH B 82 799 799 HOH HOH . G 4 HOH B 83 825 825 HOH HOH . G 4 HOH B 84 836 836 HOH HOH . G 4 HOH B 85 842 842 HOH HOH . G 4 HOH B 86 847 847 HOH HOH . G 4 HOH B 87 849 849 HOH HOH . G 4 HOH B 88 870 870 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 KDO . . . E 2 14.735 66.728 94.06 1 29.28 ? C1 KDO 263 B 1 HETATM 2 O O1A KDO . . . E 2 14.063 66.127 93.194 1 33.03 ? O1A KDO 263 B 1 HETATM 3 O O1B KDO . . . E 2 15.974 66.655 94.21 1 37.06 ? O1B KDO 263 B 1 HETATM 4 C C2 KDO . . . E 2 13.967 67.629 95.029 1 25.14 ? C2 KDO 263 B 1 HETATM 5 O O2 KDO . . . E 2 13.13 66.816 95.859 1 24.31 ? O2 KDO 263 B 1 HETATM 6 C C3 KDO . . . E 2 14.951 68.425 95.89 1 21.4 ? C3 KDO 263 B 1 HETATM 7 C C4 KDO . . . E 2 14.162 69.31 96.857 1 19.66 ? C4 KDO 263 B 1 HETATM 8 O O4 KDO . . . E 2 15.063 70.15 97.582 1 18.94 ? O4 KDO 263 B 1 HETATM 9 C C5 KDO . . . E 2 13.165 70.178 96.088 1 19.54 ? C5 KDO 263 B 1 HETATM 10 O O5 KDO . . . E 2 13.88 71.13 95.295 1 18.59 ? O5 KDO 263 B 1 HETATM 11 C C6 KDO . . . E 2 12.316 69.292 95.174 1 18.32 ? C6 KDO 263 B 1 HETATM 12 O O6 KDO . . . E 2 13.157 68.544 94.284 1 22.29 ? O6 KDO 263 B 1 HETATM 13 C C7 KDO . . . E 2 11.322 70.144 94.382 1 20.27 ? C7 KDO 263 B 1 HETATM 14 O O7 KDO . . . E 2 10.344 70.677 95.28 1 20.64 ? O7 KDO 263 B 1 HETATM 15 C C8 KDO . . . E 2 10.624 69.31 93.304 1 19.84 ? C8 KDO 263 B 1 HETATM 16 O O8 KDO . . . E 2 9.981 68.177 93.892 1 15.93 ? O8 KDO 263 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 16 #