data_4YCI # _model_server_result.job_id GLE3KZbr1N0Bek9eLNzShA _model_server_result.datetime_utc '2024-11-24 06:42:26' _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 4yci # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 4YCI # _exptl.entry_id 4YCI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 4YCI _cell.length_a 120.28 _cell.length_b 120.28 _cell.length_c 221.31 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YCI _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,Q,R,S,T _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 4 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 NAG _pdbx_entity_branch_link.comp_id_2 NAG _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 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _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 E NAG 1 E 1 NAG B 3113 NAG 3 n E NAG 2 E 2 NAG B 3114 NAG # 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 133 A CYS 133 1_555 A SG CYS 214 A CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 133 B CYS 133 1_555 B SG CYS 214 B CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 C SG CYS 8 C CYS 305 1_555 C SG CYS 74 C CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 C SG CYS 37 C CYS 334 1_555 C SG CYS 107 C CYS 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 C SG CYS 41 C CYS 338 1_555 C SG CYS 109 C CYS 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 D SG CYS 8 D CYS 305 1_555 D SG CYS 74 D CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 D SG CYS 37 D CYS 334 1_555 D SG CYS 107 D CYS 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 D SG CYS 41 D CYS 338 1_555 D SG CYS 109 D CYS 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 113 A ASN 113 1_555 F C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale2 B ND2 ASN 113 B ASN 113 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? metalc ? metalc1 A OD1 ASP 102 A ASP 102 1_555 M ZN ZN . B ZN 305 5_669 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc2 A OD2 ASP 102 A ASP 102 1_555 M ZN ZN . B ZN 305 5_669 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc3 A NE2 HIS 119 A HIS 119 1_555 H ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc4 A OE2 GLU 120 A GLU 120 1_555 H ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc5 A NE2 HIS 141 A HIS 141 1_555 G ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc6 A OE2 GLU 144 A GLU 144 1_555 J ZN ZN . A ZN 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc7 A OD1 ASP 173 A ASP 173 1_555 I ZN ZN . A ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc8 A OD2 ASP 173 A ASP 173 1_555 I ZN ZN . A ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc9 A ND1 HIS 210 A HIS 210 1_555 J ZN ZN . A ZN 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc10 A OE1 GLU 212 A GLU 212 1_555 G ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc11 A OE2 GLU 212 A GLU 212 1_555 G ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc12 A OE1 GLU 244 A GLU 244 1_555 H ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc13 A OE2 GLU 244 A GLU 244 1_555 H ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc14 G ZN ZN . A ZN 302 4_659 D NE2 HIS 7 D HIS 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc15 G ZN ZN . A ZN 302 4_659 D OD2 ASP 48 D ASP 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc16 H ZN ZN . A ZN 303 1_555 Q O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc17 I ZN ZN . A ZN 304 5_569 B OD1 ASP 102 B ASP 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc18 I ZN ZN . A ZN 304 5_569 B OD2 ASP 102 B ASP 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc19 J ZN ZN . A ZN 305 1_555 Q O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc20 J ZN ZN . A ZN 305 1_555 R O HOH . B HOH 404 5_669 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc21 Q O HOH . A HOH 401 5_569 M ZN ZN . B ZN 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc22 B NE2 HIS 119 B HIS 119 1_555 N ZN ZN . B ZN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc23 B OE2 GLU 120 B GLU 120 1_555 N ZN ZN . B ZN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc24 B OD1 ASP 136 B ASP 136 1_555 L ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc25 B OD2 ASP 136 B ASP 136 1_555 L ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc26 B OE1 GLU 144 B GLU 144 1_555 K ZN ZN . B ZN 301 5_569 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc27 B OE2 GLU 144 B GLU 144 1_555 K ZN ZN . B ZN 301 5_569 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc28 B OD1 ASP 173 B ASP 173 1_555 M ZN ZN . B ZN 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc29 B OD2 ASP 173 B ASP 173 1_555 M ZN ZN . B ZN 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc30 B ND1 HIS 210 B HIS 210 1_555 K ZN ZN . B ZN 301 5_569 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc31 B OD2 ASP 215 B ASP 215 1_555 L ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc32 B OE1 GLU 244 B GLU 244 1_555 N ZN ZN . B ZN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc33 B OE2 GLU 244 B GLU 244 1_555 N ZN ZN . B ZN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc34 K ZN ZN . B ZN 301 1_555 R O HOH . B HOH 401 5_669 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc35 K ZN ZN . B ZN 301 1_555 R O HOH . B HOH 403 5_669 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc36 L ZN ZN . B ZN 304 2_764 D NE2 HIS 62 D HIS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc37 M ZN ZN . B ZN 305 1_555 R O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc38 C NE2 HIS 62 C HIS 359 1_555 P ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc39 C NZ LYS 71 C LYS 368 1_555 P ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc40 C OE2 GLU 100 C GLU 397 1_555 O ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc41 P ZN ZN . C ZN 502 1_555 S O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc42 P ZN ZN . C ZN 502 1_555 S O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 NAG sing 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 4YCI _atom_sites.fract_transf_matrix[1][1] 0.008314 _atom_sites.fract_transf_matrix[1][2] 0.0048 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0096 _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] 0.004519 _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 F 4 NAG A 1 301 3113 NAG NAG . G 5 ZN A 1 302 1 ZN ZN . H 5 ZN A 1 303 4 ZN ZN . I 5 ZN A 1 304 5 ZN ZN . J 5 ZN A 1 305 9 ZN ZN . K 5 ZN B 1 301 7 ZN ZN . L 5 ZN B 1 304 2 ZN ZN . M 5 ZN B 1 305 3 ZN ZN . N 5 ZN B 1 306 6 ZN ZN . O 5 ZN C 1 501 8 ZN ZN . P 5 ZN C 1 502 10 ZN ZN . Q 6 HOH A 1 401 6 HOH WAT . Q 6 HOH A 2 402 9 HOH WAT . Q 6 HOH A 3 403 1 HOH WAT . R 6 HOH B 1 401 8 HOH WAT . R 6 HOH B 2 402 7 HOH WAT . R 6 HOH B 3 403 14 HOH WAT . R 6 HOH B 4 404 10 HOH WAT . R 6 HOH B 5 405 2 HOH WAT . S 6 HOH C 1 601 4 HOH WAT . S 6 HOH C 2 602 11 HOH WAT . S 6 HOH C 3 603 12 HOH WAT . S 6 HOH C 4 604 13 HOH WAT . T 6 HOH D 1 501 3 HOH WAT . T 6 HOH D 2 502 5 HOH WAT . # 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 NAG . . . F 4 96.142 52.528 447.455 1 173.53 ? C1 NAG 301 A 1 HETATM 2 C C2 NAG . . . F 4 96.84 53.445 446.441 1 184.73 ? C2 NAG 301 A 1 HETATM 3 C C3 NAG . . . F 4 97.172 54.796 447.078 1 195.64 ? C3 NAG 301 A 1 HETATM 4 C C4 NAG . . . F 4 95.943 55.404 447.74 1 198.89 ? C4 NAG 301 A 1 HETATM 5 C C5 NAG . . . F 4 95.331 54.405 448.714 1 192.99 ? C5 NAG 301 A 1 HETATM 6 C C6 NAG . . . F 4 94.047 54.897 449.341 1 194.12 ? C6 NAG 301 A 1 HETATM 7 C C7 NAG . . . F 4 98.116 52.214 444.735 1 173.64 ? C7 NAG 301 A 1 HETATM 8 C C8 NAG . . . F 4 99.449 51.635 444.368 1 166.04 ? C8 NAG 301 A 1 HETATM 9 N N2 NAG . . . F 4 98.05 52.822 445.924 1 182.43 ? N2 NAG 301 A 1 HETATM 10 O O3 NAG . . . F 4 97.669 55.682 446.081 1 200.26 ? O3 NAG 301 A 1 HETATM 11 O O4 NAG . . . F 4 96.301 56.585 448.449 1 202.37 ? O4 NAG 301 A 1 HETATM 12 O O5 NAG . . . F 4 95.014 53.198 448.011 1 184.1 ? O5 NAG 301 A 1 HETATM 13 O O6 NAG . . . F 4 94.296 55.578 450.563 1 195 ? O6 NAG 301 A 1 HETATM 14 O O7 NAG . . . F 4 97.145 52.134 443.99 1 172.72 ? O7 NAG 301 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 14 #