data_3VN4 # _model_server_result.job_id -t8BpP1E2lRfCk51RLVHTA _model_server_result.datetime_utc '2025-02-05 17:59:24' _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 3vn4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":702}' # _entry.id 3VN4 # _exptl.entry_id 3VN4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 180.156 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description alpha-D-mannopyranose _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 111.56 _cell.angle_gamma 90 _cell.entry_id 3VN4 _cell.length_a 153.378 _cell.length_b 53.243 _cell.length_c 76.615 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VN4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 PISA dimeric 2 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,C,D,E,F 1 1 A,B,C,D,E,F 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 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_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 BGC FUC C1 O1 . O3 HO3 . 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 B NAG 1 B 1 NAG A 901 NAG 2 n B NAG 2 B 2 NAG A 902 NAG 3 n C FUC 1 C 1 FUC A 903 FUC 3 n C BGC 2 C 2 BGC A 904 BGC # 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 27 A CYS 311 1_555 A SG CYS 53 A CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 38 A CYS 322 1_555 A SG CYS 63 A CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 48 A CYS 332 1_555 A SG CYS 82 A CYS 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 76 A CYS 360 1_555 A SG CYS 87 A CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 112 A CYS 396 1_555 A SG CYS 149 A CYS 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 A SG CYS 116 A CYS 400 1_555 A SG CYS 154 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf7 A SG CYS 127 A CYS 411 1_555 A SG CYS 139 A CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 A SG CYS 166 A CYS 450 1_555 A SG CYS 203 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf9 A SG CYS 199 A CYS 483 1_555 A SG CYS 238 A CYS 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 A SG CYS 224 A CYS 508 1_555 A SG CYS 243 A CYS 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 A SG CYS 248 A CYS 532 1_555 A SG CYS 264 A CYS 548 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? disulf ? disulf12 A SG CYS 261 A CYS 545 1_555 A SG CYS 271 A CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? covale ? covale1 A CD1 TRP 103 A TRP 387 1_555 E C1 MAN . A MAN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.48 ? covale ? covale2 A OG SER 115 A SER 399 1_555 C C1 FUC . C FUC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 A ND2 ASN 268 A ASN 552 1_555 D C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 A ND2 ASN 330 A ASN 614 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 C O3 FUC . C FUC 1 1_555 C C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? # _chem_comp.formula 'C6 H12 O6' _chem_comp.formula_weight 180.156 _chem_comp.id MAN _chem_comp.mon_nstd_flag . _chem_comp.name alpha-D-mannopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms alpha-D-mannose;D-mannose;mannose # 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 MAN sing 265 n n C1 O1 MAN sing 266 n n C1 O5 MAN sing 267 n n C1 H1 MAN sing 268 n n C2 C3 MAN sing 269 n n C2 O2 MAN sing 270 n n C2 H2 MAN sing 271 n n C3 C4 MAN sing 272 n n C3 O3 MAN sing 273 n n C3 H3 MAN sing 274 n n C4 C5 MAN sing 275 n n C4 O4 MAN sing 276 n n C4 H4 MAN sing 277 n n C5 C6 MAN sing 278 n n C5 O5 MAN sing 279 n n C5 H5 MAN sing 280 n n C6 O6 MAN sing 281 n n C6 H61 MAN sing 282 n n C6 H62 MAN sing 283 n n O1 HO1 MAN sing 284 n n O2 HO2 MAN sing 285 n n O3 HO3 MAN sing 286 n n O4 HO4 MAN sing 287 n n O6 HO6 MAN sing 288 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 MAN DManpa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 MAN a-D-mannopyranose 'COMMON NAME' GMML 1 MAN a-D-Manp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 MAN Man 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3VN4 _atom_sites.fract_transf_matrix[1][1] 0.00652 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002576 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018782 _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] 0.014034 _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 D 4 NAG A 1 701 900 NAG NAG . E 5 MAN A 1 702 905 MAN BMA . F 6 HOH A 1 1001 1 HOH HOH . F 6 HOH A 2 1002 26 HOH HOH . F 6 HOH A 3 1003 18 HOH HOH . F 6 HOH A 4 1004 25 HOH HOH . F 6 HOH A 5 1005 37 HOH HOH . F 6 HOH A 6 1006 40 HOH HOH . F 6 HOH A 7 1007 6 HOH HOH . F 6 HOH A 8 1008 20 HOH HOH . F 6 HOH A 9 1009 2 HOH HOH . F 6 HOH A 10 1010 16 HOH HOH . F 6 HOH A 11 1011 36 HOH HOH . F 6 HOH A 12 1012 13 HOH HOH . F 6 HOH A 13 1013 19 HOH HOH . F 6 HOH A 14 1014 14 HOH HOH . F 6 HOH A 15 1015 5 HOH HOH . F 6 HOH A 16 1016 34 HOH HOH . F 6 HOH A 17 1017 23 HOH HOH . F 6 HOH A 18 1018 42 HOH HOH . F 6 HOH A 19 1019 3 HOH HOH . F 6 HOH A 20 1020 28 HOH HOH . F 6 HOH A 21 1021 33 HOH HOH . F 6 HOH A 22 1022 45 HOH HOH . F 6 HOH A 23 1023 29 HOH HOH . F 6 HOH A 24 1024 4 HOH HOH . F 6 HOH A 25 1025 35 HOH HOH . F 6 HOH A 26 1026 8 HOH HOH . F 6 HOH A 27 1027 24 HOH HOH . F 6 HOH A 28 1028 17 HOH HOH . F 6 HOH A 29 1029 44 HOH HOH . F 6 HOH A 30 1030 7 HOH HOH . F 6 HOH A 31 1031 43 HOH HOH . F 6 HOH A 32 1032 22 HOH HOH . F 6 HOH A 33 1033 9 HOH HOH . F 6 HOH A 34 1034 12 HOH HOH . F 6 HOH A 35 1035 38 HOH HOH . F 6 HOH A 36 1036 15 HOH HOH . F 6 HOH A 37 1037 39 HOH HOH . F 6 HOH A 38 1038 31 HOH HOH . F 6 HOH A 39 1039 10 HOH HOH . F 6 HOH A 40 1040 30 HOH HOH . F 6 HOH A 41 1041 21 HOH HOH . F 6 HOH A 42 1042 41 HOH HOH . F 6 HOH A 43 1043 11 HOH HOH . F 6 HOH A 44 1044 32 HOH HOH . F 6 HOH A 45 1045 27 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 MAN . . . E 5 4.833 21.749 -24.63 1 72.14 ? C1 MAN 702 A 1 HETATM 2 C C2 MAN . . . E 5 3.993 20.875 -25.577 1 73.67 ? C2 MAN 702 A 1 HETATM 3 C C3 MAN . . . E 5 4.895 20.073 -26.517 1 74.15 ? C3 MAN 702 A 1 HETATM 4 C C4 MAN . . . E 5 6.143 19.615 -25.771 1 74.4 ? C4 MAN 702 A 1 HETATM 5 C C5 MAN . . . E 5 6.941 20.828 -25.289 1 74.57 ? C5 MAN 702 A 1 HETATM 6 C C6 MAN . . . E 5 8.158 21.094 -26.171 1 75.06 ? C6 MAN 702 A 1 HETATM 7 O O2 MAN . . . E 5 3.091 21.69 -26.335 1 73.57 ? O2 MAN 702 A 1 HETATM 8 O O3 MAN . . . E 5 5.281 20.878 -27.642 1 74.45 ? O3 MAN 702 A 1 HETATM 9 O O4 MAN . . . E 5 5.768 18.817 -24.639 1 74.35 ? O4 MAN 702 A 1 HETATM 10 O O5 MAN . . . E 5 6.099 21.99 -25.275 1 74.32 ? O5 MAN 702 A 1 HETATM 11 O O6 MAN . . . E 5 9.124 21.849 -25.428 1 75.47 ? O6 MAN 702 A 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 11 #