data_4ZFY # _model_server_result.job_id vkjsC8FYH3feHgn169-Irw _model_server_result.datetime_utc '2025-09-12 00:28:11' _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 4zfy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 4ZFY # _exptl.entry_id 4ZFY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 194.182 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'methyl alpha-D-galactopyranoside' _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 90 _cell.entry_id 4ZFY _cell.length_a 110.3 _cell.length_b 136.99 _cell.length_c 44.4 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZFY _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 # _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 # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . 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 NAG 1 C 1 NAG B 303 NAG 3 n C NAG 2 C 2 NAG B 304 NAG 3 n C BMA 3 C 3 BMA B 302 BMA # 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 246 A CYS 246 1_555 B SG CYS 4 B CYS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 B SG CYS 20 B CYS 20 1_555 B SG CYS 39 B CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 B SG CYS 61 B CYS 61 1_555 B SG CYS 78 B CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? disulf ? disulf4 B SG CYS 148 B CYS 148 1_555 B SG CYS 163 B CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf5 B SG CYS 189 B CYS 189 1_555 B SG CYS 206 B CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? covale ? covale1 A ND2 ASN 108 A ASN 108 1_555 D C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale2 B ND2 ASN 97 B ASN 97 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.371 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 sing # _chem_comp.formula 'C7 H14 O6' _chem_comp.formula_weight 194.182 _chem_comp.id AMG _chem_comp.mon_nstd_flag n _chem_comp.name 'methyl alpha-D-galactopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'ALPHA-METHYL-D-GALACTOSIDE;methyl alpha-D-galactoside;methyl D-galactoside;methyl galactoside' # 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 AMG sing 13 n n C1 O1 AMG sing 14 n n C1 O5 AMG sing 15 n n C1 H1 AMG sing 16 n n C2 C3 AMG sing 17 n n C2 O2 AMG sing 18 n n C2 H2 AMG sing 19 n n C3 C4 AMG sing 20 n n C3 O3 AMG sing 21 n n C3 H3 AMG sing 22 n n C4 C5 AMG sing 23 n n C4 O4 AMG sing 24 n n C4 H4 AMG sing 25 n n C5 C6 AMG sing 26 n n C5 O5 AMG sing 27 n n C5 H5 AMG sing 28 n n C6 O6 AMG sing 29 n n C6 H61 AMG sing 30 n n C6 H62 AMG sing 31 n n C7 O1 AMG sing 32 n n C7 H71 AMG sing 33 n n C7 H72 AMG sing 34 n n C7 H73 AMG sing 35 n n O2 HO2 AMG sing 36 n n O3 HO3 AMG sing 37 n n O4 HO4 AMG sing 38 n n O6 HO6 AMG sing 39 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 AMG DGalp[1Me]a 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 AMG 1-methyl-a-D-galactopyranose 'COMMON NAME' GMML 1 AMG a-methyl-galactoside 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 # _atom_sites.entry_id 4ZFY _atom_sites.fract_transf_matrix[1][1] 0.009066 _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] 0.0073 _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] 0.022523 _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 1 301 301 NAG NAG . E 5 AMG B 1 301 301 AMG AMG . F 6 HOH A 1 401 401 HOH HOH . F 6 HOH A 2 402 402 HOH HOH . F 6 HOH A 3 403 403 HOH HOH . F 6 HOH A 4 404 404 HOH HOH . F 6 HOH A 5 405 405 HOH HOH . F 6 HOH A 6 406 406 HOH HOH . F 6 HOH A 7 407 407 HOH HOH . F 6 HOH A 8 408 409 HOH HOH . F 6 HOH A 9 409 410 HOH HOH . F 6 HOH A 10 410 411 HOH HOH . F 6 HOH A 11 411 412 HOH HOH . F 6 HOH A 12 412 413 HOH HOH . F 6 HOH A 13 413 414 HOH HOH . F 6 HOH A 14 414 415 HOH HOH . F 6 HOH A 15 415 416 HOH HOH . F 6 HOH A 16 416 417 HOH HOH . F 6 HOH A 17 417 418 HOH HOH . F 6 HOH A 18 418 419 HOH HOH . F 6 HOH A 19 419 420 HOH HOH . F 6 HOH A 20 420 421 HOH HOH . F 6 HOH A 21 421 408 HOH HOH . F 6 HOH A 22 422 422 HOH HOH . F 6 HOH A 23 423 423 HOH HOH . F 6 HOH A 24 424 424 HOH HOH . F 6 HOH A 25 425 425 HOH HOH . F 6 HOH A 26 426 426 HOH HOH . F 6 HOH A 27 427 427 HOH HOH . F 6 HOH A 28 428 428 HOH HOH . F 6 HOH A 29 429 429 HOH HOH . F 6 HOH A 30 430 430 HOH HOH . F 6 HOH A 31 431 431 HOH HOH . F 6 HOH A 32 432 432 HOH HOH . F 6 HOH A 33 433 433 HOH HOH . F 6 HOH A 34 434 434 HOH HOH . F 6 HOH A 35 435 435 HOH HOH . F 6 HOH A 36 436 436 HOH HOH . F 6 HOH A 37 437 437 HOH HOH . F 6 HOH A 38 438 438 HOH HOH . F 6 HOH A 39 439 439 HOH HOH . F 6 HOH A 40 440 440 HOH HOH . F 6 HOH A 41 441 441 HOH HOH . F 6 HOH A 42 442 442 HOH HOH . F 6 HOH A 43 443 443 HOH HOH . F 6 HOH A 44 444 444 HOH HOH . G 6 HOH B 1 401 401 HOH HOH . G 6 HOH B 2 402 402 HOH HOH . G 6 HOH B 3 403 403 HOH HOH . G 6 HOH B 4 404 404 HOH HOH . G 6 HOH B 5 405 405 HOH HOH . G 6 HOH B 6 406 406 HOH HOH . G 6 HOH B 7 407 407 HOH HOH . G 6 HOH B 8 408 408 HOH HOH . G 6 HOH B 9 409 409 HOH HOH . G 6 HOH B 10 410 410 HOH HOH . G 6 HOH B 11 411 411 HOH HOH . G 6 HOH B 12 412 412 HOH HOH . G 6 HOH B 13 413 413 HOH HOH . G 6 HOH B 14 414 414 HOH HOH . G 6 HOH B 15 415 415 HOH HOH . G 6 HOH B 16 416 416 HOH HOH . G 6 HOH B 17 417 417 HOH HOH . G 6 HOH B 18 418 418 HOH HOH . G 6 HOH B 19 419 419 HOH HOH . G 6 HOH B 20 420 420 HOH HOH . G 6 HOH B 21 421 421 HOH HOH . G 6 HOH B 22 422 422 HOH HOH . G 6 HOH B 23 423 423 HOH HOH . G 6 HOH B 24 424 424 HOH HOH . G 6 HOH B 25 425 425 HOH HOH . G 6 HOH B 26 426 426 HOH HOH . G 6 HOH B 27 427 427 HOH HOH . G 6 HOH B 28 428 428 HOH HOH . G 6 HOH B 29 429 429 HOH HOH . G 6 HOH B 30 430 430 HOH HOH . G 6 HOH B 31 431 431 HOH HOH . G 6 HOH B 32 432 432 HOH HOH . G 6 HOH B 33 433 433 HOH HOH . G 6 HOH B 34 434 434 HOH HOH . G 6 HOH B 35 435 435 HOH HOH . G 6 HOH B 36 436 436 HOH HOH . G 6 HOH B 37 437 437 HOH HOH . G 6 HOH B 38 438 438 HOH HOH . G 6 HOH B 39 439 439 HOH HOH . G 6 HOH B 40 440 440 HOH HOH . G 6 HOH B 41 441 441 HOH HOH . G 6 HOH B 42 442 442 HOH HOH . G 6 HOH B 43 443 443 HOH HOH . G 6 HOH B 44 444 444 HOH HOH . G 6 HOH B 45 445 445 HOH HOH . G 6 HOH B 46 446 446 HOH HOH . G 6 HOH B 47 447 447 HOH HOH . G 6 HOH B 48 448 448 HOH HOH . G 6 HOH B 49 449 449 HOH HOH . G 6 HOH B 50 450 450 HOH HOH . G 6 HOH B 51 451 451 HOH HOH . G 6 HOH B 52 452 452 HOH HOH . G 6 HOH B 53 453 453 HOH HOH . G 6 HOH B 54 454 454 HOH HOH . G 6 HOH B 55 455 455 HOH HOH . G 6 HOH B 56 456 456 HOH HOH . G 6 HOH B 57 457 457 HOH HOH . G 6 HOH B 58 458 458 HOH HOH . G 6 HOH B 59 459 459 HOH HOH . G 6 HOH B 60 460 460 HOH HOH . G 6 HOH B 61 461 461 HOH HOH . G 6 HOH B 62 462 462 HOH HOH . G 6 HOH B 63 463 463 HOH HOH . G 6 HOH B 64 464 464 HOH HOH . G 6 HOH B 65 465 465 HOH HOH . G 6 HOH B 66 466 466 HOH HOH . G 6 HOH B 67 467 467 HOH HOH . G 6 HOH B 68 468 468 HOH HOH . G 6 HOH B 69 469 469 HOH HOH . G 6 HOH B 70 470 470 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 AMG . . . E 5 37.513 131.425 17.252 1 34.3 ? C1 AMG 301 B 1 HETATM 2 C C2 AMG . . . E 5 38.035 130.049 16.855 1 35.87 ? C2 AMG 301 B 1 HETATM 3 C C3 AMG . . . E 5 37.715 129.022 17.934 1 35.14 ? C3 AMG 301 B 1 HETATM 4 C C4 AMG . . . E 5 38.183 129.521 19.294 1 33.88 ? C4 AMG 301 B 1 HETATM 5 C C5 AMG . . . E 5 37.655 130.925 19.563 1 34.54 ? C5 AMG 301 B 1 HETATM 6 C C6 AMG . . . E 5 38.171 131.454 20.896 1 34.95 ? C6 AMG 301 B 1 HETATM 7 C C7 AMG . . . E 5 35.55 132.655 17.711 1 36.24 ? C7 AMG 301 B 1 HETATM 8 O O1 AMG . . . E 5 36.091 131.386 17.348 1 35.08 ? O1 AMG 301 B 1 HETATM 9 O O2 AMG . . . E 5 37.439 129.646 15.617 1 37.05 ? O2 AMG 301 B 1 HETATM 10 O O3 AMG . . . E 5 38.368 127.785 17.626 1 38.13 ? O3 AMG 301 B 1 HETATM 11 O O4 AMG . . . E 5 39.614 129.533 19.334 1 32.51 ? O4 AMG 301 B 1 HETATM 12 O O5 AMG . . . E 5 38.065 131.8 18.514 1 33.23 ? O5 AMG 301 B 1 HETATM 13 O O6 AMG . . . E 5 37.636 132.761 21.131 1 36.77 ? O6 AMG 301 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #