data_2VLC # _model_server_result.job_id rkrOPTsaKHVqhmY6t5d2hQ _model_server_result.datetime_utc '2025-02-27 13:10:27' _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 2vlc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":602}' # _entry.id 2VLC # _exptl.entry_id 2VLC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.13 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description beta-D-xylopyranose _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 2VLC _cell.length_a 52.388 _cell.length_b 126.329 _cell.length_c 161.451 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VLC _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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,I,J,M 1 1 B,F,G,H,K,L,N 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 ? 4 J N N ? 4 K N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NAG 1 C 1 NAG A 1549 AS5 2 n C NAG 2 C 2 NAG A 1549 AS5 2 n D NAG 1 D 1 NAG A 1550 AS5 2 n D NAG 2 D 2 NAG A 1550 AS5 2 n E NAG 1 E 1 NAG A 1551 AS5 2 n E NAG 2 E 2 NAG A 1551 AS5 2 n F NAG 1 F 1 NAG B 1550 AS5 2 n F NAG 2 F 2 NAG B 1550 AS5 2 n G NAG 1 G 1 NAG B 1551 AS5 2 n G NAG 2 G 2 NAG B 1551 AS5 2 n H NAG 1 H 1 NAG B 1552 AS5 2 n H NAG 2 H 2 NAG B 1552 AS5 # 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 273 A CYS 251 1_555 A SG CYS 311 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 327 A CYS 305 1_555 A SG CYS 346 A CYS 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 A SG CYS 370 A CYS 348 1_555 A SG CYS 387 A CYS 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf4 A SG CYS 458 A CYS 436 1_555 A SG CYS 471 A CYS 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 A SG CYS 497 A CYS 475 1_555 A SG CYS 515 A CYS 493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 B SG CYS 273 B CYS 251 1_555 B SG CYS 311 B CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf7 B SG CYS 327 B CYS 305 1_555 B SG CYS 346 B CYS 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf8 B SG CYS 370 B CYS 348 1_555 B SG CYS 387 B CYS 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf9 B SG CYS 458 B CYS 436 1_555 B SG CYS 471 B CYS 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf10 B SG CYS 497 B CYS 475 1_555 B SG CYS 515 B CYS 493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? covale ? covale1 A ND2 ASN 402 A ASN 380 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 5.736 ? covale ? covale2 A ND2 ASN 442 A ASN 420 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 4.243 ? covale ? covale3 B ND2 ASN 402 B ASN 380 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 8.307 ? covale ? covale4 B ND2 ASN 442 B ASN 420 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 4.084 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale9 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale10 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _chem_comp.formula 'C5 H10 O5' _chem_comp.formula_weight 150.13 _chem_comp.id XYP _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-xylopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms beta-D-xylose;D-xylose;xylose # 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 XYP sing 430 n n O1 HO1 XYP sing 431 n n C1 C2 XYP sing 432 n n C1 O5 XYP sing 433 n n C1 H1 XYP sing 434 n n C2 C3 XYP sing 435 n n C2 O2 XYP sing 436 n n C2 H2 XYP sing 437 n n C3 C4 XYP sing 438 n n C3 O3 XYP sing 439 n n C3 H3 XYP sing 440 n n C4 C5 XYP sing 441 n n C4 O4 XYP sing 442 n n C4 H4 XYP sing 443 n n C5 O5 XYP sing 444 n n C5 H51 XYP sing 445 n n C5 H52 XYP sing 446 n n O2 HO2 XYP sing 447 n n O3 HO3 XYP sing 448 n n O4 HO4 XYP sing 449 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 XYP DXylpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 XYP b-D-xylopyranose 'COMMON NAME' GMML 1 XYP b-D-Xylp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 XYP Xyl 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 2VLC _atom_sites.fract_transf_matrix[1][1] 0.019088 _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] 0.007916 _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] 0.006194 _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 I 3 BMA A 1 601 1552 BMA BMA . J 4 XYP A 1 602 1553 XYP XYP . K 4 XYP B 1 601 1553 XYP XYS . L 3 BMA B 1 602 1549 BMA BMA . M 5 HOH A 1 701 2040 HOH HOH . M 5 HOH A 2 702 2043 HOH HOH . M 5 HOH A 3 703 2045 HOH HOH . M 5 HOH A 4 704 2001 HOH HOH . M 5 HOH A 5 705 2026 HOH HOH . M 5 HOH A 6 706 2047 HOH HOH . M 5 HOH A 7 707 2020 HOH HOH . M 5 HOH A 8 708 2054 HOH HOH . M 5 HOH A 9 709 2046 HOH HOH . M 5 HOH A 10 710 2017 HOH HOH . M 5 HOH A 11 711 2002 HOH HOH . M 5 HOH A 12 712 2033 HOH HOH . M 5 HOH A 13 713 2032 HOH HOH . M 5 HOH A 14 714 2059 HOH HOH . M 5 HOH A 15 715 2024 HOH HOH . M 5 HOH A 16 716 2022 HOH HOH . M 5 HOH A 17 717 2006 HOH HOH . M 5 HOH A 18 718 2009 HOH HOH . M 5 HOH A 19 719 2066 HOH HOH . M 5 HOH A 20 720 2048 HOH HOH . M 5 HOH A 21 721 2025 HOH HOH . M 5 HOH A 22 722 2031 HOH HOH . M 5 HOH A 23 723 2055 HOH HOH . M 5 HOH A 24 724 2060 HOH HOH . M 5 HOH A 25 725 2011 HOH HOH . M 5 HOH A 26 726 2037 HOH HOH . M 5 HOH A 27 727 2061 HOH HOH . M 5 HOH A 28 728 2028 HOH HOH . M 5 HOH A 29 729 2062 HOH HOH . M 5 HOH A 30 730 2008 HOH HOH . M 5 HOH A 31 731 2035 HOH HOH . M 5 HOH A 32 732 2012 HOH HOH . M 5 HOH A 33 733 2021 HOH HOH . M 5 HOH A 34 734 2057 HOH HOH . M 5 HOH A 35 735 2049 HOH HOH . M 5 HOH A 36 736 2044 HOH HOH . M 5 HOH A 37 737 2063 HOH HOH . M 5 HOH A 38 738 2030 HOH HOH . M 5 HOH A 39 739 2052 HOH HOH . M 5 HOH A 40 740 2013 HOH HOH . M 5 HOH A 41 741 2056 HOH HOH . M 5 HOH A 42 742 2041 HOH HOH . M 5 HOH A 43 743 2051 HOH HOH . M 5 HOH A 44 744 2016 HOH HOH . M 5 HOH A 45 745 2019 HOH HOH . M 5 HOH A 46 746 2036 HOH HOH . M 5 HOH A 47 747 2027 HOH HOH . M 5 HOH A 48 748 2065 HOH HOH . M 5 HOH A 49 749 2064 HOH HOH . M 5 HOH A 50 750 2003 HOH HOH . M 5 HOH A 51 751 2018 HOH HOH . M 5 HOH A 52 752 2029 HOH HOH . M 5 HOH A 53 753 2050 HOH HOH . M 5 HOH A 54 754 2050 HOH HOH . M 5 HOH A 55 755 2067 HOH HOH . M 5 HOH A 56 756 2034 HOH HOH . M 5 HOH A 57 757 2014 HOH HOH . M 5 HOH A 58 758 2023 HOH HOH . M 5 HOH A 59 759 2005 HOH HOH . M 5 HOH A 60 760 2042 HOH HOH . M 5 HOH A 61 761 2053 HOH HOH . M 5 HOH A 62 762 2039 HOH HOH . M 5 HOH A 63 763 2058 HOH HOH . M 5 HOH A 64 764 2010 HOH HOH . M 5 HOH A 65 765 2038 HOH HOH . M 5 HOH A 66 766 2015 HOH HOH . M 5 HOH A 67 767 2004 HOH HOH . M 5 HOH A 68 768 2007 HOH HOH . M 5 HOH A 69 769 2068 HOH HOH . M 5 HOH A 70 770 2052 HOH HOH . N 5 HOH B 1 701 2011 HOH HOH . N 5 HOH B 2 702 2008 HOH HOH . N 5 HOH B 3 703 2007 HOH HOH . N 5 HOH B 4 704 2038 HOH HOH . N 5 HOH B 5 705 2021 HOH HOH . N 5 HOH B 6 706 2035 HOH HOH . N 5 HOH B 7 707 2045 HOH HOH . N 5 HOH B 8 708 2048 HOH HOH . N 5 HOH B 9 709 2042 HOH HOH . N 5 HOH B 10 710 2031 HOH HOH . N 5 HOH B 11 711 2025 HOH HOH . N 5 HOH B 12 712 2003 HOH HOH . N 5 HOH B 13 713 2032 HOH HOH . N 5 HOH B 14 714 2028 HOH HOH . N 5 HOH B 15 715 2029 HOH HOH . N 5 HOH B 16 716 2002 HOH HOH . N 5 HOH B 17 717 2022 HOH HOH . N 5 HOH B 18 718 2012 HOH HOH . N 5 HOH B 19 719 2034 HOH HOH . N 5 HOH B 20 720 2017 HOH HOH . N 5 HOH B 21 721 2049 HOH HOH . N 5 HOH B 22 722 2036 HOH HOH . N 5 HOH B 23 723 2044 HOH HOH . N 5 HOH B 24 724 2018 HOH HOH . N 5 HOH B 25 725 2047 HOH HOH . N 5 HOH B 26 726 2005 HOH HOH . N 5 HOH B 27 727 2015 HOH HOH . N 5 HOH B 28 728 2039 HOH HOH . N 5 HOH B 29 729 2037 HOH HOH . N 5 HOH B 30 730 2020 HOH HOH . N 5 HOH B 31 731 2041 HOH HOH . N 5 HOH B 32 732 2009 HOH HOH . N 5 HOH B 33 733 2030 HOH HOH . N 5 HOH B 34 734 2046 HOH HOH . N 5 HOH B 35 735 2014 HOH HOH . N 5 HOH B 36 736 2040 HOH HOH . N 5 HOH B 37 737 2027 HOH HOH . N 5 HOH B 38 738 2006 HOH HOH . N 5 HOH B 39 739 2010 HOH HOH . N 5 HOH B 40 740 2033 HOH HOH . N 5 HOH B 41 741 2023 HOH HOH . N 5 HOH B 42 742 2043 HOH HOH . N 5 HOH B 43 743 2051 HOH HOH . N 5 HOH B 44 744 2001 HOH HOH . N 5 HOH B 45 745 2013 HOH HOH . N 5 HOH B 46 746 2019 HOH HOH . N 5 HOH B 47 747 2026 HOH HOH . N 5 HOH B 48 748 2024 HOH HOH . N 5 HOH B 49 749 2004 HOH HOH . N 5 HOH B 50 750 2016 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 O O1 XYP . . . J 4 -3.246 2.669 41.134 0.25 6.69 ? O1 XYP 602 A 1 HETATM 2 C C1 XYP . . . J 4 -4.198 3.605 41.635 0.25 3.55 ? C1 XYP 602 A 1 HETATM 3 C C2 XYP . . . J 4 -5.401 3.73 40.708 0.25 4.35 ? C2 XYP 602 A 1 HETATM 4 C C3 XYP . . . J 4 -6.648 3.281 41.459 0.25 3.23 ? C3 XYP 602 A 1 HETATM 5 C C4 XYP . . . J 4 -6.34 1.915 42.046 0.25 2.56 ? C4 XYP 602 A 1 HETATM 6 C C5 XYP . . . J 4 -5.309 2.136 43.151 0.25 2.06 ? C5 XYP 602 A 1 HETATM 7 O O2 XYP . . . J 4 -5.582 5.074 40.333 0.25 3.48 ? O2 XYP 602 A 1 HETATM 8 O O3 XYP . . . J 4 -7.774 3.255 40.61 0.25 3.56 ? O3 XYP 602 A 1 HETATM 9 O O4 XYP . . . J 4 -7.507 1.271 42.513 0.25 2 ? O4 XYP 602 A 1 HETATM 10 O O5 XYP . . . J 4 -4.552 3.321 42.928 0.25 2 ? O5 XYP 602 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 1185 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 10 #