data_6RV6 # _model_server_result.job_id Po7j4TcI8cutGEMuW2vnHA _model_server_result.datetime_utc '2024-10-13 16:28:17' _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 6rv6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":511}' # _entry.id 6RV6 # _exptl.entry_id 6RV6 _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 12 _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 6RV6 _cell.length_a 219.79 _cell.length_b 219.79 _cell.length_c 47.44 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RV6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41' # _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,H,I,J,K,L,M,N,O,P,Q,R _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 ? 5 G N N ? 5 H N N ? 5 I N N ? 5 J N N ? 5 K N N ? 5 L N N ? 5 M N N ? 5 N N N ? 5 O N N ? 5 P N N ? 5 Q N N ? 5 R N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 BGC FUC C1 O1 . O3 HO3 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 1 FUC NAG C1 O1 . O6 HO6 . 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 3 n C FUC 1 C 1 FUC A 1023 FUC 3 n C BGC 2 C 2 BGC A 1024 BGC 3 n D FUC 1 D 1 FUC A 1027 FUC 3 n D BGC 2 D 2 BGC A 1028 BGC 3 n E FUC 1 E 1 FUC B 1036 FUC 3 n E BGC 2 E 2 BGC B 1037 BGC 4 n F NAG 1 F 1 NAG B 1043 NAG 4 n F NAG 2 F 2 NAG B 1044 NAG 4 n F FUC 3 F 3 FUC B 1042 FUC # 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 5 A CYS 32 1_555 A SG CYS 29 A CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 16 A CYS 43 1_555 A SG CYS 45 A CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 30 A CYS 57 1_555 A SG CYS 48 A CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 A SG CYS 62 A CYS 89 1_555 A SG CYS 100 A CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 66 A CYS 93 1_555 A SG CYS 106 A CYS 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf6 A SG CYS 77 A CYS 104 1_555 A SG CYS 84 A CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 A SG CYS 105 A CYS 132 1_555 A SG CYS 143 A CYS 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf8 A SG CYS 121 A CYS 148 1_555 A SG CYS 157 A CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf9 A SG CYS 125 A CYS 152 1_555 A SG CYS 163 A CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 A SG CYS 136 A CYS 163 1_555 A SG CYS 147 A CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 B SG CYS 15 B CYS 269 1_555 B SG CYS 52 B CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf12 B SG CYS 19 B CYS 273 1_555 B SG CYS 58 B CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf13 B SG CYS 30 B CYS 284 1_555 B SG CYS 42 B CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf14 B SG CYS 73 B CYS 327 1_555 B SG CYS 116 B CYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf15 B SG CYS 83 B CYS 337 1_555 B SG CYS 122 B CYS 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf16 B SG CYS 96 B CYS 350 1_555 B SG CYS 106 B CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf17 B SG CYS 137 B CYS 391 1_555 B SG CYS 201 B CYS 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf18 B SG CYS 141 B CYS 395 1_555 B SG CYS 207 B CYS 461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf19 B SG CYS 153 B CYS 407 1_555 B SG CYS 185 B CYS 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A CD1 TRP 56 A TRP 83 1_555 G C1 MAN . A MAN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.519 ? covale ? covale2 A CD1 TRP 59 A TRP 86 1_555 H C1 MAN . A MAN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.53 ? covale ? covale3 A OG1 THR 65 A THR 92 1_555 D C1 FUC . D FUC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 A CD1 TRP 112 A TRP 139 1_555 I C1 MAN . A MAN 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.522 ? covale ? covale5 A CD1 TRP 115 A TRP 142 1_555 J C1 MAN . A MAN 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.519 ? covale ? covale6 A CD1 TRP 118 A TRP 145 1_555 K C1 MAN . A MAN 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.523 ? covale ? covale7 A OG1 THR 124 A THR 151 1_555 C C1 FUC . C FUC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale8 B CD1 TRP 6 B TRP 260 1_555 Q C1 MAN . B MAN 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.523 ? covale ? covale9 B CD1 TRP 9 B TRP 263 1_555 R C1 MAN . B MAN 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.517 ? covale ? covale10 B OG1 THR 18 B THR 272 1_555 E C1 FUC . E FUC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 B CD1 TRP 67 B TRP 321 1_555 L C1 MAN . B MAN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.521 ? covale ? covale12 B CD1 TRP 70 B TRP 324 1_555 M C1 MAN . B MAN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.52 ? covale ? covale13 B CD1 TRP 128 B TRP 382 1_555 N C1 MAN . B MAN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.53 ? covale ? covale14 B CD1 TRP 131 B TRP 385 1_555 P C1 MAN . B MAN 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.52 ? covale ? covale15 B CD1 TRP 134 B TRP 388 1_555 O C1 MAN . B MAN 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.521 ? covale ? covale16 B ND2 ASN 174 B ASN 428 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale17 C O3 FUC . C FUC 1 1_555 C C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale18 D O3 FUC . D FUC 1 1_555 D C1 BGC . D BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale19 E O3 FUC . E FUC 1 1_555 E C1 BGC . E BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale20 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale21 F O6 NAG . F NAG 1 1_555 F C1 FUC . F FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? # _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 263 n n C1 O1 MAN sing 264 n n C1 O5 MAN sing 265 n n C1 H1 MAN sing 266 n n C2 C3 MAN sing 267 n n C2 O2 MAN sing 268 n n C2 H2 MAN sing 269 n n C3 C4 MAN sing 270 n n C3 O3 MAN sing 271 n n C3 H3 MAN sing 272 n n C4 C5 MAN sing 273 n n C4 O4 MAN sing 274 n n C4 H4 MAN sing 275 n n C5 C6 MAN sing 276 n n C5 O5 MAN sing 277 n n C5 H5 MAN sing 278 n n C6 O6 MAN sing 279 n n C6 H61 MAN sing 280 n n C6 H62 MAN sing 281 n n O1 HO1 MAN sing 282 n n O2 HO2 MAN sing 283 n n O3 HO3 MAN sing 284 n n O4 HO4 MAN sing 285 n n O6 HO6 MAN sing 286 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 6RV6 _atom_sites.fract_transf_matrix[1][1] 0.00455 _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] 0.00455 _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] 0.021079 _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 G 5 MAN A 1 203 1025 MAN MAN . H 5 MAN A 1 204 1026 MAN MAN . I 5 MAN A 1 207 1029 MAN MAN . J 5 MAN A 1 208 1030 MAN MAN . K 5 MAN A 1 209 1031 MAN MAN . L 5 MAN B 1 503 1038 MAN MAN . M 5 MAN B 1 504 1039 MAN MAN . N 5 MAN B 1 505 1040 MAN MAN . O 5 MAN B 1 509 1046 MAN MAN . P 5 MAN B 1 510 1048 MAN MAN . Q 5 MAN B 1 511 1096 MAN MAN . R 5 MAN B 1 512 1097 MAN MAN . # 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 . . . Q 5 56.197 7.683 41.35 1 210.64 ? C1 MAN 511 B 1 HETATM 2 C C2 MAN . . . Q 5 56.391 9.208 41.53 1 210.8 ? C2 MAN 511 B 1 HETATM 3 C C3 MAN . . . Q 5 57.821 9.655 41.209 1 214.69 ? C3 MAN 511 B 1 HETATM 4 C C4 MAN . . . Q 5 58.324 9.084 39.866 1 211.15 ? C4 MAN 511 B 1 HETATM 5 C C5 MAN . . . Q 5 58.089 7.544 39.752 1 207.23 ? C5 MAN 511 B 1 HETATM 6 C C6 MAN . . . Q 5 59.067 6.673 40.548 1 204.74 ? C6 MAN 511 B 1 HETATM 7 O O2 MAN . . . Q 5 56.181 9.608 42.877 1 207.83 ? O2 MAN 511 B 1 HETATM 8 O O3 MAN . . . Q 5 58.733 9.405 42.284 1 221.39 ? O3 MAN 511 B 1 HETATM 9 O O4 MAN . . . Q 5 57.638 9.747 38.816 1 210.56 ? O4 MAN 511 B 1 HETATM 10 O O5 MAN . . . Q 5 56.728 7.163 40.143 1 208.17 ? O5 MAN 511 B 1 HETATM 11 O O6 MAN . . . Q 5 58.8 5.298 40.244 1 200.15 ? O6 MAN 511 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 11 #