data_4D90 # _model_server_result.job_id oFWu4yKKPaH0zypnqQeyTA _model_server_result.datetime_utc '2024-11-05 01:26:22' _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 4d90 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":601}' # _entry.id 4D90 # _exptl.entry_id 4D90 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-galactopyranose _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 4D90 _cell.length_a 82.68 _cell.length_b 82.68 _cell.length_c 56.422 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D90 _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,K 1 1 B,G,H,I,J,L 2 1 A,B,C,D,E,F,G,H,I,J,K,L 3 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 ? 2 C N N ? 2 G N 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 3 A CYS 26 1_555 A SG CYS 14 A CYS 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 8 A CYS 31 1_555 A SG CYS 25 A CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 27 A CYS 50 1_555 A SG CYS 36 A CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf4 A SG CYS 55 A CYS 78 1_555 A SG CYS 66 A CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf5 A SG CYS 60 A CYS 83 1_555 A SG CYS 82 A CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 A SG CYS 84 A CYS 107 1_555 A SG CYS 93 A CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? disulf ? disulf7 A SG CYS 100 A CYS 123 1_555 A SG CYS 111 A CYS 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf8 A SG CYS 105 A CYS 128 1_555 A SG CYS 120 A CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf9 A SG CYS 122 A CYS 145 1_555 A SG CYS 131 A CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? disulf ? disulf10 B SG CYS 3 B CYS 26 1_555 B SG CYS 14 B CYS 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 B SG CYS 8 B CYS 31 1_555 B SG CYS 25 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf12 B SG CYS 27 B CYS 50 1_555 B SG CYS 36 B CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf13 B SG CYS 55 B CYS 78 1_555 B SG CYS 66 B CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf14 B SG CYS 60 B CYS 83 1_555 B SG CYS 82 B CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf15 B SG CYS 84 B CYS 107 1_555 B SG CYS 93 B CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? disulf ? disulf16 B SG CYS 100 B CYS 123 1_555 B SG CYS 111 B CYS 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? disulf ? disulf17 B SG CYS 105 B CYS 128 1_555 B SG CYS 120 B CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf18 B SG CYS 122 B CYS 145 1_555 B SG CYS 131 B CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? covale ? covale1 A OG1 THR 50 A THR 73 1_555 C C1 NGA . A NGA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale2 A OG1 THR 65 A THR 88 1_555 E C1 FUC . A FUC 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale3 A ND2 ASN 117 A ASN 140 1_555 D C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale4 B OG1 THR 50 B THR 73 1_555 G C1 NGA . B NGA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 B OG1 THR 65 B THR 88 1_555 I C1 FUC . B FUC 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale6 B ND2 ASN 117 B ASN 140 1_555 H C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? metalc ? metalc1 A OD1 ASN 96 A ASN 119 1_555 F CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc2 A O ILE 97 A ILE 120 1_555 F CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? metalc ? metalc3 A OE1 GLU 99 A GLU 122 1_555 F CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc4 A OD2 ASP 113 A ASP 136 1_555 F CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc5 A OD1 ASP 113 A ASP 136 1_555 F CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? metalc ? metalc6 A O LEU 114 A LEU 137 1_555 F CA CA . A CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? metalc ? metalc7 F CA CA . A CA 604 1_555 K O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc8 B OD1 ASN 96 B ASN 119 1_555 J CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc9 B O ILE 97 B ILE 120 1_555 J CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc10 B OE1 GLU 99 B GLU 122 1_555 J CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc11 B OD1 ASP 113 B ASP 136 1_555 J CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? metalc ? metalc12 B OD2 ASP 113 B ASP 136 1_555 J CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc13 B O LEU 114 B LEU 137 1_555 J CA CA . B CA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? metalc ? metalc14 J CA CA . B CA 604 1_555 L O HOH . B HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NGA _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-galactopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-galactosamine;2-acetamido-2-deoxy-beta-D-galactose;2-acetamido-2-deoxy-D-galactose;2-acetamido-2-deoxy-galactose;N-ACETYL-D-GALACTOSAMINE # 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 NGA sing 290 n n C1 O1 NGA sing 291 n n C1 O5 NGA sing 292 n n C1 H1 NGA sing 293 n n C2 C3 NGA sing 294 n n C2 N2 NGA sing 295 n n C2 H2 NGA sing 296 n n C3 C4 NGA sing 297 n n C3 O3 NGA sing 298 n n C3 H3 NGA sing 299 n n C4 C5 NGA sing 300 n n C4 O4 NGA sing 301 n n C4 H4 NGA sing 302 n n C5 C6 NGA sing 303 n n C5 O5 NGA sing 304 n n C5 H5 NGA sing 305 n n C6 O6 NGA sing 306 n n C6 H61 NGA sing 307 n n C6 H62 NGA sing 308 n n C7 C8 NGA sing 309 n n C7 N2 NGA sing 310 n n C7 O7 NGA doub 311 n n C8 H81 NGA sing 312 n n C8 H82 NGA sing 313 n n C8 H83 NGA sing 314 n n N2 HN2 NGA sing 315 n n O1 HO1 NGA sing 316 n n O3 HO3 NGA sing 317 n n O4 HO4 NGA sing 318 n n O6 HO6 NGA sing 319 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 NGA DGalpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NGA N-acetyl-b-D-galactopyranosamine 'COMMON NAME' GMML 1 NGA b-D-GalpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NGA GalNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 4D90 _atom_sites.fract_transf_matrix[1][1] 0.012095 _atom_sites.fract_transf_matrix[1][2] 0.006983 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013966 _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] 0.017724 _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 C 2 NGA A 1 601 601 NGA NGA . D 3 NAG A 1 602 701 NAG NAG . E 4 FUC A 1 603 801 FUC FUC . F 5 CA A 1 604 901 CA CA . G 2 NGA B 1 601 601 NGA NGA . H 3 NAG B 1 602 701 NAG NAG . I 4 FUC B 1 603 801 FUC FUC . J 5 CA B 1 604 901 CA CA . K 6 HOH A 1 701 1 HOH HOH . K 6 HOH A 2 702 9 HOH HOH . K 6 HOH A 3 703 10 HOH HOH . K 6 HOH A 4 704 11 HOH HOH . K 6 HOH A 5 705 12 HOH HOH . K 6 HOH A 6 706 13 HOH HOH . K 6 HOH A 7 707 14 HOH HOH . K 6 HOH A 8 708 15 HOH HOH . K 6 HOH A 9 709 16 HOH HOH . K 6 HOH A 10 710 19 HOH HOH . K 6 HOH A 11 711 20 HOH HOH . K 6 HOH A 12 712 21 HOH HOH . K 6 HOH A 13 713 22 HOH HOH . K 6 HOH A 14 714 23 HOH HOH . K 6 HOH A 15 715 24 HOH HOH . K 6 HOH A 16 716 25 HOH HOH . K 6 HOH A 17 717 26 HOH HOH . K 6 HOH A 18 718 27 HOH HOH . K 6 HOH A 19 719 35 HOH HOH . K 6 HOH A 20 720 36 HOH HOH . K 6 HOH A 21 721 38 HOH HOH . K 6 HOH A 22 722 39 HOH HOH . K 6 HOH A 23 723 41 HOH HOH . K 6 HOH A 24 724 42 HOH HOH . K 6 HOH A 25 725 44 HOH HOH . K 6 HOH A 26 726 45 HOH HOH . K 6 HOH A 27 727 46 HOH HOH . K 6 HOH A 28 728 47 HOH HOH . K 6 HOH A 29 729 48 HOH HOH . K 6 HOH A 30 730 49 HOH HOH . K 6 HOH A 31 731 50 HOH HOH . L 6 HOH B 1 701 2 HOH HOH . L 6 HOH B 2 702 3 HOH HOH . L 6 HOH B 3 703 4 HOH HOH . L 6 HOH B 4 704 5 HOH HOH . L 6 HOH B 5 705 6 HOH HOH . L 6 HOH B 6 706 7 HOH HOH . L 6 HOH B 7 707 8 HOH HOH . L 6 HOH B 8 708 17 HOH HOH . L 6 HOH B 9 709 18 HOH HOH . L 6 HOH B 10 710 28 HOH HOH . L 6 HOH B 11 711 29 HOH HOH . L 6 HOH B 12 712 30 HOH HOH . L 6 HOH B 13 713 31 HOH HOH . L 6 HOH B 14 714 32 HOH HOH . L 6 HOH B 15 715 33 HOH HOH . L 6 HOH B 16 716 34 HOH HOH . L 6 HOH B 17 717 37 HOH HOH . L 6 HOH B 18 718 40 HOH HOH . L 6 HOH B 19 719 43 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 NGA . . . G 2 19.639 15.492 6.903 1 96.22 ? C1 NGA 601 B 1 HETATM 2 C C2 NGA . . . G 2 19.641 16.395 5.664 1 99.83 ? C2 NGA 601 B 1 HETATM 3 C C3 NGA . . . G 2 20.122 17.838 5.881 1 104.29 ? C3 NGA 601 B 1 HETATM 4 C C4 NGA . . . G 2 19.803 18.409 7.261 1 103.64 ? C4 NGA 601 B 1 HETATM 5 C C5 NGA . . . G 2 20.09 17.374 8.343 1 97.11 ? C5 NGA 601 B 1 HETATM 6 C C6 NGA . . . G 2 19.74 17.941 9.715 1 96.93 ? C6 NGA 601 B 1 HETATM 7 C C7 NGA . . . G 2 20.025 15.417 3.484 1 102.64 ? C7 NGA 601 B 1 HETATM 8 C C8 NGA . . . G 2 20.996 14.739 2.558 1 102.73 ? C8 NGA 601 B 1 HETATM 9 N N2 NGA . . . G 2 20.501 15.786 4.664 1 100.02 ? N2 NGA 601 B 1 HETATM 10 O O3 NGA . . . G 2 19.542 18.691 4.881 1 102.74 ? O3 NGA 601 B 1 HETATM 11 O O4 NGA . . . G 2 18.438 18.866 7.327 1 101.28 ? O4 NGA 601 B 1 HETATM 12 O O5 NGA . . . G 2 19.308 16.206 8.1 1 97.48 ? O5 NGA 601 B 1 HETATM 13 O O6 NGA . . . G 2 18.738 17.135 10.349 1 93.74 ? O6 NGA 601 B 1 HETATM 14 O O7 NGA . . . G 2 18.862 15.627 3.185 1 103.78 ? O7 NGA 601 B 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #