data_6DZF # _model_server_result.job_id r0blime1_V3QAmXNmZtVbQ _model_server_result.datetime_utc '2024-11-26 21:58:21' _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 6dzf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":304}' # _entry.id 6DZF # _exptl.entry_id 6DZF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.13 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description alpha-D-xylopyranose _entity.pdbx_number_of_molecules 1 _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 6DZF _cell.length_a 54.122 _cell.length_b 56.841 _cell.length_c 65.478 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DZF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 7 A CYS 22 1_555 A SG CYS 137 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 41 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 109 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 A SG CYS 116 A CYS 136 1_555 A SG CYS 183 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf6 A SG CYS 173 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc1 A OE1 GLU 52 A GLU 70 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc2 A O ASN 54 A ASN 72 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc3 A O VAL 57 A VAL 75 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc4 A OE2 GLU 62 A GLU 80 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc5 B CA CA . A CA 301 1_555 F O HOH . A HOH 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc6 B CA CA . A CA 301 1_555 F O HOH . A HOH 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? # _chem_comp.formula 'C5 H10 O5' _chem_comp.formula_weight 150.13 _chem_comp.id XYS _chem_comp.mon_nstd_flag . _chem_comp.name alpha-D-xylopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms alpha-D-xylose;D-xylose;xylose;XYLOPYRANOSE # 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 XYS sing 397 n n C1 O1 XYS sing 398 n n C1 O5 XYS sing 399 n n C1 H1 XYS sing 400 n n C2 C3 XYS sing 401 n n C2 O2 XYS sing 402 n n C2 H2 XYS sing 403 n n C3 C4 XYS sing 404 n n C3 O3 XYS sing 405 n n C3 H3 XYS sing 406 n n C4 C5 XYS sing 407 n n C4 O4 XYS sing 408 n n C4 H4 XYS sing 409 n n C5 O5 XYS sing 410 n n C5 H51 XYS sing 411 n n C5 H52 XYS sing 412 n n O1 HO1 XYS sing 413 n n O2 HO2 XYS sing 414 n n O3 HO3 XYS sing 415 n n O4 HO4 XYS sing 416 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 XYS DXylpa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 XYS a-D-xylopyranose 'COMMON NAME' GMML 1 XYS a-D-Xylp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 XYS Xyl 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 6DZF _atom_sites.fract_transf_matrix[1][1] 0.018477 _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] 0.017593 _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] 0.015272 _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 B 2 CA A 1 301 301 CA CA . C 3 BEN A 1 302 302 BEN BEN . D 4 SO4 A 1 303 303 SO4 SO4 . E 5 XYS A 1 304 304 XYS XYS . F 6 HOH A 1 401 401 HOH HOH . F 6 HOH A 2 402 402 HOH HOH . F 6 HOH A 3 403 403 HOH HOH . F 6 HOH A 4 404 404 HOH HOH . F 6 HOH A 5 405 405 HOH HOH . F 6 HOH A 6 406 406 HOH HOH . F 6 HOH A 7 407 407 HOH HOH . F 6 HOH A 8 408 409 HOH HOH . F 6 HOH A 9 409 412 HOH HOH . F 6 HOH A 10 410 414 HOH HOH . F 6 HOH A 11 411 411 HOH HOH . F 6 HOH A 12 412 408 HOH HOH . F 6 HOH A 13 413 410 HOH HOH . F 6 HOH A 14 414 413 HOH HOH . F 6 HOH A 15 415 415 HOH HOH . F 6 HOH A 16 416 416 HOH HOH . F 6 HOH A 17 417 417 HOH HOH . F 6 HOH A 18 418 418 HOH HOH . F 6 HOH A 19 419 419 HOH HOH . F 6 HOH A 20 420 420 HOH HOH . F 6 HOH A 21 421 421 HOH HOH . F 6 HOH A 22 422 422 HOH HOH . F 6 HOH A 23 423 423 HOH HOH . F 6 HOH A 24 424 424 HOH HOH . F 6 HOH A 25 425 426 HOH HOH . F 6 HOH A 26 426 427 HOH HOH . F 6 HOH A 27 427 428 HOH HOH . F 6 HOH A 28 428 425 HOH HOH . F 6 HOH A 29 429 429 HOH HOH . F 6 HOH A 30 430 430 HOH HOH . F 6 HOH A 31 431 431 HOH HOH . F 6 HOH A 32 432 432 HOH HOH . F 6 HOH A 33 433 435 HOH HOH . F 6 HOH A 34 434 433 HOH HOH . F 6 HOH A 35 435 434 HOH HOH . F 6 HOH A 36 436 436 HOH HOH . F 6 HOH A 37 437 437 HOH HOH . F 6 HOH A 38 438 438 HOH HOH . F 6 HOH A 39 439 439 HOH HOH . F 6 HOH A 40 440 442 HOH HOH . F 6 HOH A 41 441 443 HOH HOH . F 6 HOH A 42 442 440 HOH HOH . F 6 HOH A 43 443 441 HOH HOH . F 6 HOH A 44 444 444 HOH HOH . F 6 HOH A 45 445 445 HOH HOH . F 6 HOH A 46 446 446 HOH HOH . F 6 HOH A 47 447 447 HOH HOH . F 6 HOH A 48 448 448 HOH HOH . F 6 HOH A 49 449 452 HOH HOH . F 6 HOH A 50 450 449 HOH HOH . F 6 HOH A 51 451 451 HOH HOH . F 6 HOH A 52 452 455 HOH HOH . F 6 HOH A 53 453 450 HOH HOH . F 6 HOH A 54 454 453 HOH HOH . F 6 HOH A 55 455 454 HOH HOH . F 6 HOH A 56 456 457 HOH HOH . F 6 HOH A 57 457 456 HOH HOH . F 6 HOH A 58 458 459 HOH HOH . F 6 HOH A 59 459 458 HOH HOH . F 6 HOH A 60 460 460 HOH HOH . F 6 HOH A 61 461 461 HOH HOH . F 6 HOH A 62 462 462 HOH HOH . F 6 HOH A 63 463 464 HOH HOH . F 6 HOH A 64 464 463 HOH HOH . F 6 HOH A 65 465 465 HOH HOH . F 6 HOH A 66 466 466 HOH HOH . F 6 HOH A 67 467 467 HOH HOH . F 6 HOH A 68 468 468 HOH HOH . F 6 HOH A 69 469 469 HOH HOH . F 6 HOH A 70 470 471 HOH HOH . F 6 HOH A 71 471 470 HOH HOH . F 6 HOH A 72 472 472 HOH HOH . F 6 HOH A 73 473 473 HOH HOH . F 6 HOH A 74 474 474 HOH HOH . F 6 HOH A 75 475 475 HOH HOH . F 6 HOH A 76 476 476 HOH HOH . F 6 HOH A 77 477 477 HOH HOH . F 6 HOH A 78 478 478 HOH HOH . F 6 HOH A 79 479 479 HOH HOH . F 6 HOH A 80 480 480 HOH HOH . F 6 HOH A 81 481 481 HOH HOH . F 6 HOH A 82 482 482 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 XYS . . . E 5 8.491 -5.808 -21.791 1 25.35 ? C1 XYS 304 A 1 HETATM 2 C C2 XYS . . . E 5 7.858 -7.149 -21.589 1 58.75 ? C2 XYS 304 A 1 HETATM 3 C C3 XYS . . . E 5 6.478 -7.143 -22.228 1 46.82 ? C3 XYS 304 A 1 HETATM 4 C C4 XYS . . . E 5 5.645 -5.986 -21.693 1 69.75 ? C4 XYS 304 A 1 HETATM 5 C C5 XYS . . . E 5 6.441 -4.688 -21.565 1 51.38 ? C5 XYS 304 A 1 HETATM 6 O O1 XYS . . . E 5 8.524 -5.499 -23.165 1 32.71 ? O1 XYS 304 A 1 HETATM 7 O O2 XYS . . . E 5 8.664 -8.134 -22.199 1 42.98 ? O2 XYS 304 A 1 HETATM 8 O O3 XYS . . . E 5 5.819 -8.356 -21.944 1 47.31 ? O3 XYS 304 A 1 HETATM 9 O O4 XYS . . . E 5 4.527 -5.782 -22.532 1 70.81 ? O4 XYS 304 A 1 HETATM 10 O O5 XYS . . . E 5 7.783 -4.854 -21.146 1 26.46 ? O5 XYS 304 A 1 HETATM 11 H H2 XYS . . . E 5 7.788 -7.347 -20.52 1 70.5 ? H2 XYS 304 A 1 HETATM 12 H H3 XYS . . . E 5 6.599 -7.04 -23.306 1 56.18 ? H3 XYS 304 A 1 HETATM 13 H H4 XYS . . . E 5 5.304 -6.244 -20.69 1 83.7 ? H4 XYS 304 A 1 HETATM 14 H H51 XYS . . . E 5 6.42 -4.153 -22.514 1 61.66 ? H51 XYS 304 A 1 HETATM 15 H H52 XYS . . . E 5 5.978 -4.051 -20.811 1 61.66 ? H52 XYS 304 A 1 HETATM 16 H HO2 XYS . . . E 5 9.445 -7.708 -22.609 1 51.57 ? HO2 XYS 304 A 1 HETATM 17 H HO3 XYS . . . E 5 6.403 -8.925 -21.399 1 56.77 ? HO3 XYS 304 A 1 HETATM 18 H HO4 XYS . . . E 5 4.546 -6.432 -23.265 1 84.97 ? HO4 XYS 304 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 18 #