data_6S08 # _model_server_result.job_id sgo16XXHzNDkC2JG41pHRg _model_server_result.datetime_utc '2024-12-16 15:29:31' _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 6s08 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 6S08 # _exptl.entry_id 6S08 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 180.156 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description alpha-D-mannopyranose _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 99.56 _cell.angle_gamma 90 _cell.entry_id 6S08 _cell.length_a 111.995 _cell.length_b 114.86 _cell.length_c 39.822 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6S08 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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 ? 4 D N N ? 4 E N N ? 4 F N N ? 4 G N N ? 4 H N N ? 4 I N N ? 4 K N N ? 4 M N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 BGC _pdbx_entity_branch_link.comp_id_2 FUC _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 O3 _pdbx_entity_branch_link.leaving_atom_id_2 HO3 _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 3 n C FUC 1 C 1 FUC A 503 FUC 3 n C BGC 2 C 2 BGC A 504 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 16 A CYS 269 1_555 A SG CYS 53 A CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? disulf ? disulf2 A SG CYS 20 A CYS 273 1_555 A SG CYS 59 A CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? disulf ? disulf3 A SG CYS 31 A CYS 284 1_555 A SG CYS 43 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? disulf ? disulf4 A SG CYS 74 A CYS 327 1_555 A SG CYS 117 A CYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? disulf ? disulf5 A SG CYS 84 A CYS 337 1_555 A SG CYS 123 A CYS 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf6 A SG CYS 97 A CYS 350 1_555 A SG CYS 107 A CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? disulf ? disulf7 A SG CYS 138 A CYS 391 1_555 A SG CYS 202 A CYS 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf8 A SG CYS 142 A CYS 395 1_555 A SG CYS 208 A CYS 461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf9 A SG CYS 154 A CYS 407 1_555 A SG CYS 186 A CYS 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? disulf ? disulf10 B SG CYS 7 B CYS 32 1_555 B SG CYS 31 B CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? disulf ? disulf11 B SG CYS 18 B CYS 43 1_555 B SG CYS 47 B CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf12 B SG CYS 32 B CYS 57 1_555 B SG CYS 50 B CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? disulf ? disulf13 B SG CYS 64 B CYS 89 1_555 B SG CYS 102 B CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf14 B SG CYS 68 B CYS 93 1_555 B SG CYS 107 B CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf15 B SG CYS 79 B CYS 104 1_555 B SG CYS 86 B CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? covale ? covale1 A CD1 TRP 7 A TRP 260 1_555 H C1 MAN . A MAN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.509 ? covale ? covale2 A CD1 TRP 10 A TRP 263 1_555 I C1 MAN . A MAN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.511 ? covale ? covale3 A OG1 THR 19 A THR 272 1_555 C C1 FUC . C FUC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale4 A CD1 TRP 68 A TRP 321 1_555 E C1 MAN . A MAN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.51 ? covale ? covale5 A CD1 TRP 71 A TRP 324 1_555 D C1 MAN . A MAN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.514 ? covale ? covale6 A CD1 TRP 129 A TRP 382 1_555 F C1 MAN . A MAN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.512 ? covale ? covale7 A CD1 TRP 132 A TRP 385 1_555 G C1 MAN . A MAN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.503 ? covale ? covale8 A CD1 TRP 135 A TRP 388 1_555 K C1 MAN . A MAN 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.513 ? covale ? covale9 B CD1 TRP 58 B TRP 83 1_555 M C1 MAN . B MAN 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.518 ? covale ? covale10 B OG1 THR 67 B THR 92 1_555 N C1 FUC . B FUC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale11 C O3 FUC . C FUC 1 1_555 C C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? metalc ? metalc1 A O ILE 82 A ILE 335 1_555 L NA NA . A NA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? metalc ? metalc2 A O GLN 85 A GLN 338 1_555 L NA NA . A NA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? metalc ? metalc3 A O ILE 87 A ILE 340 1_555 L NA NA . A NA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.784 ? # _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 6S08 _atom_sites.fract_transf_matrix[1][1] 0.008929 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001504 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008706 _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] 0.025465 _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 MAN A 1 501 506 MAN MAN . E 4 MAN A 1 502 505 MAN MAN . F 4 MAN A 1 503 507 MAN MAN . G 4 MAN A 1 504 508 MAN MAN . H 4 MAN A 1 505 500 MAN MAN . I 4 MAN A 1 506 501 MAN MAN . J 5 PGE A 1 507 511 PGE PGE . K 4 MAN A 1 508 509 MAN MAN . L 6 NA A 1 509 200 NA NA . M 4 MAN B 1 200 200 MAN MAN . N 7 FUC B 1 201 201 FUC FUC . O 8 HOH A 1 601 84 HOH HOH . O 8 HOH A 2 602 82 HOH HOH . O 8 HOH A 3 603 50 HOH HOH . O 8 HOH A 4 604 64 HOH HOH . O 8 HOH A 5 605 121 HOH HOH . O 8 HOH A 6 606 2 HOH HOH . O 8 HOH A 7 607 9 HOH HOH . O 8 HOH A 8 608 33 HOH HOH . O 8 HOH A 9 609 98 HOH HOH . O 8 HOH A 10 610 59 HOH HOH . O 8 HOH A 11 611 85 HOH HOH . O 8 HOH A 12 612 3 HOH HOH . O 8 HOH A 13 613 27 HOH HOH . O 8 HOH A 14 614 32 HOH HOH . O 8 HOH A 15 615 70 HOH HOH . O 8 HOH A 16 616 75 HOH HOH . O 8 HOH A 17 617 111 HOH HOH . O 8 HOH A 18 618 7 HOH HOH . O 8 HOH A 19 619 80 HOH HOH . O 8 HOH A 20 620 38 HOH HOH . O 8 HOH A 21 621 31 HOH HOH . O 8 HOH A 22 622 42 HOH HOH . O 8 HOH A 23 623 37 HOH HOH . O 8 HOH A 24 624 108 HOH HOH . O 8 HOH A 25 625 61 HOH HOH . O 8 HOH A 26 626 89 HOH HOH . O 8 HOH A 27 627 25 HOH HOH . O 8 HOH A 28 628 40 HOH HOH . O 8 HOH A 29 629 45 HOH HOH . O 8 HOH A 30 630 28 HOH HOH . O 8 HOH A 31 631 14 HOH HOH . O 8 HOH A 32 632 106 HOH HOH . O 8 HOH A 33 633 10 HOH HOH . O 8 HOH A 34 634 3 HOH HOH . O 8 HOH A 35 635 51 HOH HOH . O 8 HOH A 36 636 19 HOH HOH . O 8 HOH A 37 637 47 HOH HOH . O 8 HOH A 38 638 21 HOH HOH . O 8 HOH A 39 639 1 HOH HOH . O 8 HOH A 40 640 24 HOH HOH . O 8 HOH A 41 641 88 HOH HOH . O 8 HOH A 42 642 20 HOH HOH . O 8 HOH A 43 643 35 HOH HOH . O 8 HOH A 44 644 96 HOH HOH . O 8 HOH A 45 645 95 HOH HOH . O 8 HOH A 46 646 17 HOH HOH . O 8 HOH A 47 647 71 HOH HOH . O 8 HOH A 48 648 99 HOH HOH . O 8 HOH A 49 649 15 HOH HOH . O 8 HOH A 50 650 5 HOH HOH . O 8 HOH A 51 651 81 HOH HOH . O 8 HOH A 52 652 123 HOH HOH . O 8 HOH A 53 653 30 HOH HOH . O 8 HOH A 54 654 112 HOH HOH . O 8 HOH A 55 655 110 HOH HOH . O 8 HOH A 56 656 53 HOH HOH . O 8 HOH A 57 657 6 HOH HOH . O 8 HOH A 58 658 66 HOH HOH . O 8 HOH A 59 659 79 HOH HOH . O 8 HOH A 60 660 107 HOH HOH . O 8 HOH A 61 661 54 HOH HOH . O 8 HOH A 62 662 101 HOH HOH . O 8 HOH A 63 663 97 HOH HOH . O 8 HOH A 64 664 83 HOH HOH . O 8 HOH A 65 665 115 HOH HOH . O 8 HOH A 66 666 56 HOH HOH . O 8 HOH A 67 667 100 HOH HOH . O 8 HOH A 68 668 12 HOH HOH . O 8 HOH A 69 669 87 HOH HOH . O 8 HOH A 70 670 92 HOH HOH . O 8 HOH A 71 671 102 HOH HOH . O 8 HOH A 72 672 22 HOH HOH . O 8 HOH A 73 673 116 HOH HOH . O 8 HOH A 74 674 93 HOH HOH . O 8 HOH A 75 675 11 HOH HOH . O 8 HOH A 76 676 52 HOH HOH . O 8 HOH A 77 677 44 HOH HOH . O 8 HOH A 78 678 41 HOH HOH . O 8 HOH A 79 679 36 HOH HOH . O 8 HOH A 80 680 90 HOH HOH . O 8 HOH A 81 681 124 HOH HOH . O 8 HOH A 82 682 77 HOH HOH . P 8 HOH B 1 301 46 HOH HOH . P 8 HOH B 2 302 78 HOH HOH . P 8 HOH B 3 303 60 HOH HOH . P 8 HOH B 4 304 119 HOH HOH . P 8 HOH B 5 305 2 HOH HOH . P 8 HOH B 6 306 13 HOH HOH . P 8 HOH B 7 307 43 HOH HOH . P 8 HOH B 8 308 34 HOH HOH . P 8 HOH B 9 309 91 HOH HOH . P 8 HOH B 10 310 18 HOH HOH . P 8 HOH B 11 311 76 HOH HOH . P 8 HOH B 12 312 105 HOH HOH . P 8 HOH B 13 313 29 HOH HOH . P 8 HOH B 14 314 104 HOH HOH . P 8 HOH B 15 315 1 HOH HOH . P 8 HOH B 16 316 74 HOH HOH . P 8 HOH B 17 317 68 HOH HOH . P 8 HOH B 18 318 49 HOH HOH . P 8 HOH B 19 319 23 HOH HOH . P 8 HOH B 20 320 114 HOH HOH . P 8 HOH B 21 321 57 HOH HOH . P 8 HOH B 22 322 94 HOH HOH . P 8 HOH B 23 323 8 HOH HOH . P 8 HOH B 24 324 16 HOH HOH . P 8 HOH B 25 325 86 HOH HOH . P 8 HOH B 26 326 4 HOH HOH . P 8 HOH B 27 327 55 HOH HOH . P 8 HOH B 28 328 67 HOH HOH . P 8 HOH B 29 329 58 HOH HOH . P 8 HOH B 30 330 63 HOH HOH . P 8 HOH B 31 331 122 HOH HOH . P 8 HOH B 32 332 120 HOH HOH . P 8 HOH B 33 333 117 HOH HOH . P 8 HOH B 34 334 118 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 . . . D 4 -38.183 -12.162 3.446 1 20.14 ? C1 MAN 501 A 1 HETATM 2 C C2 MAN . . . D 4 -37.619 -10.798 3.054 1 21.06 ? C2 MAN 501 A 1 HETATM 3 C C3 MAN . . . D 4 -38.659 -9.706 3.278 1 22.46 ? C3 MAN 501 A 1 HETATM 4 C C4 MAN . . . D 4 -39.188 -9.747 4.715 1 23.22 ? C4 MAN 501 A 1 HETATM 5 C C5 MAN . . . D 4 -39.714 -11.122 5.101 1 22.2 ? C5 MAN 501 A 1 HETATM 6 C C6 MAN . . . D 4 -41.033 -11.474 4.467 1 22.17 ? C6 MAN 501 A 1 HETATM 7 O O2 MAN . . . D 4 -37.247 -10.803 1.667 1 21.03 ? O2 MAN 501 A 1 HETATM 8 O O3 MAN . . . D 4 -39.727 -9.873 2.325 1 22.42 ? O3 MAN 501 A 1 HETATM 9 O O4 MAN . . . D 4 -38.142 -9.448 5.649 1 23.76 ? O4 MAN 501 A 1 HETATM 10 O O5 MAN . . . D 4 -38.738 -12.116 4.772 1 21.03 ? O5 MAN 501 A 1 HETATM 11 O O6 MAN . . . D 4 -41.481 -12.641 5.154 1 22.06 ? O6 MAN 501 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 780 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 11 #