data_9D77 # _model_server_result.job_id 3pBVMlV2LBH8gx9TrEWnuw _model_server_result.datetime_utc '2024-10-11 08:31:50' _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 9d77 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":505}' # _entry.id 9D77 # _exptl.entry_id 9D77 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _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 120 _cell.entry_id 9D77 _cell.length_a 189.26 _cell.length_b 189.26 _cell.length_c 45.88 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9D77 _symmetry.cell_setting ? _symmetry.Int_Tables_number 168 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 6' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 4_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 189.26 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 H N N ? 7 I N 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 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 2 6 1 FUC NAG C1 O1 . O6 HO6 . sing 6 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 7 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 8 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 9 ? 3 5 3 MAN BMA 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 2 n B NAG 1 B 1 NAG A 459 NAG 2 n B NAG 2 B 2 NAG A 460 NAG 2 n B BMA 3 B 3 BMA A 461 BMA 2 n B MAN 4 B 4 MAN A 463 MAN 2 n B MAN 5 B 5 MAN A 462 MAN 2 n B FUC 6 B 6 FUC A 464 FUC 3 n C NAG 1 C 1 NAG A 465 NAG 3 n C NAG 2 C 2 NAG A 466 NAG 3 n C BMA 3 C 3 BMA A 467 BMA 3 n C MAN 4 C 4 MAN A 469 MAN 3 n C MAN 5 C 5 MAN A 468 MAN 3 n D NAG 1 D 1 NAG A 470 NAG 3 n D NAG 2 D 2 NAG A 471 NAG 3 n D BMA 3 D 3 BMA A 472 BMA 3 n D MAN 4 D 4 MAN A 473 MAN 3 n D MAN 5 D 5 MAN A 474 MAN # 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 22 A CYS 43 1_555 A SG CYS 32 A CYS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 A SG CYS 51 A CYS 72 1_555 A SG CYS 75 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf3 A SG CYS 59 A CYS 80 1_555 A SG CYS 72 A CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf4 A SG CYS 100 A CYS 121 1_555 A SG CYS 133 A CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? disulf ? disulf5 A SG CYS 162 A CYS 183 1_555 A SG CYS 184 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf6 A SG CYS 266 A CYS 287 1_555 A SG CYS 275 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf7 A SG CYS 268 A CYS 289 1_555 A SG CYS 285 A CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf8 A SG CYS 287 A CYS 308 1_555 A SG CYS 296 A CYS 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf9 A SG CYS 299 A CYS 320 1_555 A SG CYS 319 A CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf10 A SG CYS 322 A CYS 343 1_555 A SG CYS 331 A CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? disulf ? disulf11 A SG CYS 324 A CYS 345 1_555 A SG CYS 349 A CYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf12 A SG CYS 352 A CYS 373 1_555 A SG CYS 361 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? disulf ? disulf13 A SG CYS 364 A CYS 385 1_555 A SG CYS 382 A CYS 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? disulf ? disulf14 A SG CYS 385 A CYS 406 1_555 A SG CYS 397 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf15 A SG CYS 387 A CYS 408 1_555 A SG CYS 404 A CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? disulf ? disulf16 A SG CYS 406 A CYS 427 1_555 A SG CYS 415 A CYS 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf17 A SG CYS 418 A CYS 439 1_555 A SG CYS 432 A CYS 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? covale ? covale1 A ND2 ASN 76 A ASN 97 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale2 A ND2 ASN 97 A ASN 118 1_555 E C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 112 A ASN 133 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A ND2 ASN 398 A ASN 419 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale5 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? covale ? covale6 B O6 NAG . B NAG 1 1_555 B C1 FUC . B FUC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale7 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? covale ? covale8 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? covale ? covale9 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale10 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale11 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? covale ? covale12 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale13 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? covale ? covale14 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale15 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale16 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? covale ? covale17 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? metalc ? metalc1 A O PHE 88 A PHE 109 1_555 F CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc2 A OD1 ASP 91 A ASP 112 1_555 F CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc3 A O THR 99 A THR 120 1_555 F CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc4 A OG1 THR 99 A THR 120 1_555 F CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc5 A OD1 ASP 259 A ASP 280 1_555 F CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 MPD sing 308 n n C1 H11 MPD sing 309 n n C1 H12 MPD sing 310 n n C1 H13 MPD sing 311 n n C2 O2 MPD sing 312 n n C2 CM MPD sing 313 n n C2 C3 MPD sing 314 n n O2 HO2 MPD sing 315 n n CM HM1 MPD sing 316 n n CM HM2 MPD sing 317 n n CM HM3 MPD sing 318 n n C3 C4 MPD sing 319 n n C3 H31 MPD sing 320 n n C3 H32 MPD sing 321 n n C4 O4 MPD sing 322 n n C4 C5 MPD sing 323 n n C4 H4 MPD sing 324 n n O4 HO4 MPD sing 325 n n C5 H51 MPD sing 326 n n C5 H52 MPD sing 327 n n C5 H53 MPD sing 328 n n # _atom_sites.entry_id 9D77 _atom_sites.fract_transf_matrix[1][1] 0.005284 _atom_sites.fract_transf_matrix[1][2] 0.003051 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006101 _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] 0.021796 _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 E 4 NAG A 1 501 458 NAG NAG . F 5 CA A 1 502 1 CA CA . G 6 CL A 1 503 1 CL CL . H 7 MPD A 1 504 2 MPD MPD . I 7 MPD A 1 505 3 MPD MPD . J 8 HOH A 1 601 15 HOH HOH . J 8 HOH A 2 602 5 HOH HOH . J 8 HOH A 3 603 13 HOH HOH . J 8 HOH A 4 604 33 HOH HOH . J 8 HOH A 5 605 8 HOH HOH . J 8 HOH A 6 606 7 HOH HOH . J 8 HOH A 7 607 29 HOH HOH . J 8 HOH A 8 608 20 HOH HOH . J 8 HOH A 9 609 18 HOH HOH . J 8 HOH A 10 610 30 HOH HOH . J 8 HOH A 11 611 24 HOH HOH . J 8 HOH A 12 612 2 HOH HOH . J 8 HOH A 13 613 11 HOH HOH . J 8 HOH A 14 614 23 HOH HOH . J 8 HOH A 15 615 3 HOH HOH . J 8 HOH A 16 616 6 HOH HOH . J 8 HOH A 17 617 31 HOH HOH . J 8 HOH A 18 618 35 HOH HOH . J 8 HOH A 19 619 1 HOH HOH . J 8 HOH A 20 620 21 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 MPD . . . I 7 105.661 7.333 -3.792 1 58.74 0 C1 MPD 505 A 1 HETATM 2 C C2 MPD . . . I 7 104.25 7.908 -3.759 1 58.02 0 C2 MPD 505 A 1 HETATM 3 O O2 MPD . . . I 7 104.273 9.171 -4.447 1 64.68 0 O2 MPD 505 A 1 HETATM 4 C CM MPD . . . I 7 103.825 8.218 -2.331 1 61.81 0 CM MPD 505 A 1 HETATM 5 C C3 MPD . . . I 7 103.255 6.975 -4.47 1 52.25 0 C3 MPD 505 A 1 HETATM 6 C C4 MPD . . . I 7 101.78 7.361 -4.393 1 55.8 0 C4 MPD 505 A 1 HETATM 7 O O4 MPD . . . I 7 101.633 8.654 -4.955 1 63.22 0 O4 MPD 505 A 1 HETATM 8 C C5 MPD . . . I 7 100.806 6.43 -5.068 1 55.55 0 C5 MPD 505 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 8 #