data_3PAK # _model_server_result.job_id pAMclEGT43Lk3xWTT-E8lw _model_server_result.datetime_utc '2024-11-24 08:08:11' _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 3pak # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":500}' # _entry.id 3PAK # _exptl.entry_id 3PAK _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 90 _cell.angle_gamma 120 _cell.entry_id 3PAK _cell.length_a 97.796 _cell.length_b 97.796 _cell.length_c 45.088 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PAK _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # 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_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 97.796 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 48.898 84.69382 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 55 A CYS 135 1_555 A SG CYS 146 A CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 A SG CYS 124 A CYS 204 1_555 A SG CYS 138 A CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 A OE1 GLU 91 A GLU 171 1_555 C NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc2 A OE1 GLU 115 A GLU 195 1_555 B CA CA . A CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc3 A OE1 GLU 122 A GLU 202 1_555 B CA CA . A CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc4 A O GLU 122 A GLU 202 1_555 C NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc5 A OD1 ASN 134 A ASN 214 1_555 B CA CA . A CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc6 A OD1 ASP 135 A ASP 215 1_555 B CA CA . A CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc7 A O ASP 135 A ASP 215 1_555 B CA CA . A CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc8 B CA CA . A CA 300 1_555 E O4 MAN . A MAN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc9 B CA CA . A CA 300 1_555 E O3 MAN . A MAN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc10 B CA CA . A CA 300 1_555 F O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? # _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 218 n n C1 O1 MAN sing 219 n n C1 O5 MAN sing 220 n n C1 H1 MAN sing 221 n n C2 C3 MAN sing 222 n n C2 O2 MAN sing 223 n n C2 H2 MAN sing 224 n n C3 C4 MAN sing 225 n n C3 O3 MAN sing 226 n n C3 H3 MAN sing 227 n n C4 C5 MAN sing 228 n n C4 O4 MAN sing 229 n n C4 H4 MAN sing 230 n n C5 C6 MAN sing 231 n n C5 O5 MAN sing 232 n n C5 H5 MAN sing 233 n n C6 O6 MAN sing 234 n n C6 H61 MAN sing 235 n n C6 H62 MAN sing 236 n n O1 HO1 MAN sing 237 n n O2 HO2 MAN sing 238 n n O3 HO3 MAN sing 239 n n O4 HO4 MAN sing 240 n n O6 HO6 MAN sing 241 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 3PAK _atom_sites.fract_transf_matrix[1][1] 0.010225 _atom_sites.fract_transf_matrix[1][2] 0.005904 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011807 _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] 0.022179 _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 1 300 300 CA CA . C 3 NA A 1 301 301 NA NA . D 4 SO4 A 1 302 302 SO4 SO4 . E 5 MAN A 1 500 500 MAN MAN . F 6 HOH A 1 501 501 HOH HOH . F 6 HOH A 2 502 502 HOH HOH . F 6 HOH A 3 503 503 HOH HOH . F 6 HOH A 4 504 504 HOH HOH . F 6 HOH A 5 505 505 HOH HOH . F 6 HOH A 6 506 506 HOH HOH . F 6 HOH A 7 507 507 HOH HOH . F 6 HOH A 8 508 508 HOH HOH . F 6 HOH A 9 509 509 HOH HOH . F 6 HOH A 10 510 510 HOH HOH . F 6 HOH A 11 511 511 HOH HOH . F 6 HOH A 12 512 512 HOH HOH . F 6 HOH A 13 513 513 HOH HOH . F 6 HOH A 14 514 514 HOH HOH . F 6 HOH A 15 515 515 HOH HOH . F 6 HOH A 16 516 516 HOH HOH . F 6 HOH A 17 517 517 HOH HOH . F 6 HOH A 18 518 518 HOH HOH . F 6 HOH A 19 519 519 HOH HOH . F 6 HOH A 20 520 520 HOH HOH . F 6 HOH A 21 521 521 HOH HOH . F 6 HOH A 22 522 522 HOH HOH . F 6 HOH A 23 523 523 HOH HOH . F 6 HOH A 24 524 524 HOH HOH . F 6 HOH A 25 525 525 HOH HOH . F 6 HOH A 26 526 526 HOH HOH . F 6 HOH A 27 527 527 HOH HOH . F 6 HOH A 28 528 528 HOH HOH . F 6 HOH A 29 529 529 HOH HOH . F 6 HOH A 30 530 530 HOH HOH . F 6 HOH A 31 531 531 HOH HOH . F 6 HOH A 32 532 532 HOH HOH . F 6 HOH A 33 533 533 HOH HOH . F 6 HOH A 34 534 534 HOH HOH . F 6 HOH A 35 535 535 HOH HOH . F 6 HOH A 36 536 536 HOH HOH . F 6 HOH A 37 537 537 HOH HOH . F 6 HOH A 38 538 538 HOH HOH . F 6 HOH A 39 539 539 HOH HOH . F 6 HOH A 40 540 540 HOH HOH . F 6 HOH A 41 541 541 HOH HOH . F 6 HOH A 42 542 542 HOH HOH . F 6 HOH A 43 543 543 HOH HOH . F 6 HOH A 44 544 544 HOH HOH . F 6 HOH A 45 545 545 HOH HOH . F 6 HOH A 46 546 546 HOH HOH . F 6 HOH A 47 547 547 HOH HOH . F 6 HOH A 48 548 548 HOH HOH . F 6 HOH A 49 549 549 HOH HOH . F 6 HOH A 50 550 550 HOH HOH . F 6 HOH A 51 551 551 HOH HOH . F 6 HOH A 52 552 552 HOH HOH . F 6 HOH A 53 553 553 HOH HOH . F 6 HOH A 54 554 554 HOH HOH . F 6 HOH A 55 555 555 HOH HOH . F 6 HOH A 56 556 556 HOH HOH . F 6 HOH A 57 557 557 HOH HOH . F 6 HOH A 58 558 558 HOH HOH . F 6 HOH A 59 559 559 HOH HOH . F 6 HOH A 60 560 560 HOH HOH . F 6 HOH A 61 561 561 HOH HOH . F 6 HOH A 62 562 562 HOH HOH . F 6 HOH A 63 563 563 HOH HOH . F 6 HOH A 64 564 564 HOH HOH . F 6 HOH A 65 565 565 HOH HOH . F 6 HOH A 66 566 566 HOH HOH . F 6 HOH A 67 567 567 HOH HOH . F 6 HOH A 68 568 568 HOH HOH . F 6 HOH A 69 569 569 HOH HOH . F 6 HOH A 70 570 570 HOH HOH . F 6 HOH A 71 571 571 HOH HOH . F 6 HOH A 72 572 572 HOH HOH . F 6 HOH A 73 573 573 HOH HOH . F 6 HOH A 74 574 574 HOH HOH . F 6 HOH A 75 575 575 HOH HOH . F 6 HOH A 76 576 576 HOH HOH . F 6 HOH A 77 577 577 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 82.059 37.244 52.352 1 56.03 ? C1 MAN 500 A 1 HETATM 2 C C2 MAN . . . E 5 83.008 37.749 51.256 1 55.47 ? C2 MAN 500 A 1 HETATM 3 C C3 MAN . . . E 5 82.653 37.054 49.935 1 53.36 ? C3 MAN 500 A 1 HETATM 4 C C4 MAN . . . E 5 82.727 35.533 50.115 1 53.64 ? C4 MAN 500 A 1 HETATM 5 C C5 MAN . . . E 5 81.843 35.082 51.289 1 55.02 ? C5 MAN 500 A 1 HETATM 6 C C6 MAN . . . E 5 82.029 33.601 51.577 1 57.1 ? C6 MAN 500 A 1 HETATM 7 O O1 MAN . . . E 5 80.742 37.522 52.004 1 58.47 ? O1 MAN 500 A 1 HETATM 8 O O2 MAN . . . E 5 84.354 37.444 51.616 1 55.99 ? O2 MAN 500 A 1 HETATM 9 O O3 MAN . . . E 5 83.563 37.465 48.927 1 49.54 ? O3 MAN 500 A 1 HETATM 10 O O4 MAN . . . E 5 82.303 34.888 48.927 1 49.26 ? O4 MAN 500 A 1 HETATM 11 O O5 MAN . . . E 5 82.194 35.811 52.498 1 57.26 ? O5 MAN 500 A 1 HETATM 12 O O6 MAN . . . E 5 81.194 33.158 52.639 1 59.37 ? O6 MAN 500 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 12 #