data_3T4M # _model_server_result.job_id K0YYIsWDk5RO6DzWzBsITA _model_server_result.datetime_utc '2024-11-28 13:13:59' _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 3t4m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":250}' # _entry.id 3T4M # _exptl.entry_id 3T4M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 90 _cell.entry_id 3T4M _cell.length_a 108.922 _cell.length_b 152.22 _cell.length_c 176.775 _cell.Z_PDB 40 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3T4M _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA pentameric 5 author_and_software_defined_assembly 1 PISA pentameric 5 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,K,L,M,N,O,P,Q,R,S,T,FA,GA,HA,IA,JA 1 1 F,G,H,I,J,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,KA,LA,MA,NA,OA 2 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 V _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 136 A CYS 127 1_555 A SG CYS 149 A CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? disulf ? disulf2 A SG CYS 199 A CYS 190 1_555 A SG CYS 200 A CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf3 B SG CYS 136 B CYS 127 1_555 B SG CYS 149 B CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? disulf ? disulf4 B SG CYS 199 B CYS 190 1_555 B SG CYS 200 B CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf5 C SG CYS 136 C CYS 127 1_555 C SG CYS 149 C CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.857 ? disulf ? disulf6 C SG CYS 199 C CYS 190 1_555 C SG CYS 200 C CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf7 D SG CYS 136 D CYS 127 1_555 D SG CYS 149 D CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? disulf ? disulf8 D SG CYS 199 D CYS 190 1_555 D SG CYS 200 D CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf9 E SG CYS 136 E CYS 127 1_555 E SG CYS 149 E CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? disulf ? disulf10 F SG CYS 136 F CYS 127 1_555 F SG CYS 149 F CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? disulf ? disulf11 F SG CYS 199 F CYS 190 1_555 F SG CYS 200 F CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf12 G SG CYS 136 G CYS 127 1_555 G SG CYS 149 G CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? disulf ? disulf13 G SG CYS 199 G CYS 190 1_555 G SG CYS 200 G CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf14 H SG CYS 136 H CYS 127 1_555 H SG CYS 149 H CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? disulf ? disulf15 H SG CYS 199 H CYS 190 1_555 H SG CYS 200 H CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf16 I SG CYS 136 I CYS 127 1_555 I SG CYS 149 I CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? disulf ? disulf17 I SG CYS 199 I CYS 190 1_555 I SG CYS 200 I CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf18 J SG CYS 136 J CYS 127 1_555 J SG CYS 149 J CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? disulf ? disulf19 J SG CYS 199 J CYS 190 1_555 J SG CYS 200 J CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 Q CA CA . D CA 225 1_555 IA O HOH . D HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.119 ? metalc ? metalc2 U CA CA . F CA 225 1_555 KA O HOH . F HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? # _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 279 n n C1 O1 NAG sing 280 n n C1 O5 NAG sing 281 n n C1 H1 NAG sing 282 n n C2 C3 NAG sing 283 n n C2 N2 NAG sing 284 n n C2 H2 NAG sing 285 n n C3 C4 NAG sing 286 n n C3 O3 NAG sing 287 n n C3 H3 NAG sing 288 n n C4 C5 NAG sing 289 n n C4 O4 NAG sing 290 n n C4 H4 NAG sing 291 n n C5 C6 NAG sing 292 n n C5 O5 NAG sing 293 n n C5 H5 NAG sing 294 n n C6 O6 NAG sing 295 n n C6 H61 NAG sing 296 n n C6 H62 NAG sing 297 n n C7 C8 NAG sing 298 n n C7 N2 NAG sing 299 n n C7 O7 NAG doub 300 n n C8 H81 NAG sing 301 n n C8 H82 NAG sing 302 n n C8 H83 NAG sing 303 n n N2 HN2 NAG sing 304 n n O1 HO1 NAG sing 305 n n O3 HO3 NAG sing 306 n n O4 HO4 NAG sing 307 n n O6 HO6 NAG sing 308 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 3T4M _atom_sites.fract_transf_matrix[1][1] 0.009181 _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] 0.006569 _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] 0.005657 _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 K 2 CA A 1 225 225 CA CA . L 3 MRD A 1 275 275 MRD MRD . M 2 CA B 1 225 225 CA CA . N 4 MPD B 1 275 275 MPD MPD . O 3 MRD B 1 222 222 MRD MRD . P 2 CA C 1 225 225 CA CA . Q 2 CA D 1 225 225 CA CA . R 3 MRD D 1 275 275 MRD MRD . S 2 CA E 1 225 225 CA CA . T 3 MRD E 1 275 275 MRD MRD . U 2 CA F 1 225 225 CA CA . V 5 NAG F 1 250 250 NAG NAG . W 3 MRD F 1 275 275 MRD MRD . X 2 CA G 1 225 225 CA CA . Y 4 MPD G 1 275 275 MPD MPD . Z 3 MRD G 1 222 222 MRD MRD . AA 2 CA H 1 225 225 CA CA . BA 3 MRD H 1 276 276 MRD MRD . CA 3 MRD H 1 275 275 MRD MRD . DA 3 MRD I 1 275 275 MRD MRD . EA 2 CA J 1 225 225 CA CA . FA 6 HOH A 1 300 300 HOH HOH . FA 6 HOH A 2 303 303 HOH HOH . FA 6 HOH A 3 307 307 HOH HOH . FA 6 HOH A 4 308 308 HOH HOH . FA 6 HOH A 5 310 310 HOH HOH . FA 6 HOH A 6 312 312 HOH HOH . FA 6 HOH A 7 313 313 HOH HOH . FA 6 HOH A 8 314 314 HOH HOH . GA 6 HOH B 1 302 302 HOH HOH . GA 6 HOH B 2 303 303 HOH HOH . GA 6 HOH B 3 304 304 HOH HOH . GA 6 HOH B 4 305 305 HOH HOH . GA 6 HOH B 5 307 307 HOH HOH . GA 6 HOH B 6 310 310 HOH HOH . GA 6 HOH B 7 311 311 HOH HOH . GA 6 HOH B 8 313 313 HOH HOH . GA 6 HOH B 9 320 320 HOH HOH . GA 6 HOH B 10 321 321 HOH HOH . HA 6 HOH C 1 300 300 HOH HOH . HA 6 HOH C 2 301 301 HOH HOH . HA 6 HOH C 3 302 302 HOH HOH . HA 6 HOH C 4 304 304 HOH HOH . HA 6 HOH C 5 306 306 HOH HOH . HA 6 HOH C 6 307 307 HOH HOH . HA 6 HOH C 7 308 308 HOH HOH . HA 6 HOH C 8 313 313 HOH HOH . HA 6 HOH C 9 316 316 HOH HOH . HA 6 HOH C 10 317 317 HOH HOH . HA 6 HOH C 11 320 320 HOH HOH . HA 6 HOH C 12 321 321 HOH HOH . IA 6 HOH D 1 300 300 HOH HOH . IA 6 HOH D 2 301 301 HOH HOH . IA 6 HOH D 3 302 302 HOH HOH . IA 6 HOH D 4 303 303 HOH HOH . IA 6 HOH D 5 304 304 HOH HOH . IA 6 HOH D 6 305 305 HOH HOH . IA 6 HOH D 7 306 306 HOH HOH . IA 6 HOH D 8 307 307 HOH HOH . IA 6 HOH D 9 308 308 HOH HOH . IA 6 HOH D 10 309 309 HOH HOH . IA 6 HOH D 11 310 310 HOH HOH . IA 6 HOH D 12 311 311 HOH HOH . IA 6 HOH D 13 312 312 HOH HOH . IA 6 HOH D 14 313 313 HOH HOH . IA 6 HOH D 15 314 314 HOH HOH . IA 6 HOH D 16 318 318 HOH HOH . IA 6 HOH D 17 319 319 HOH HOH . IA 6 HOH D 18 321 321 HOH HOH . IA 6 HOH D 19 325 325 HOH HOH . IA 6 HOH D 20 326 326 HOH HOH . JA 6 HOH E 1 301 301 HOH HOH . JA 6 HOH E 2 302 302 HOH HOH . JA 6 HOH E 3 303 303 HOH HOH . JA 6 HOH E 4 305 305 HOH HOH . JA 6 HOH E 5 307 307 HOH HOH . JA 6 HOH E 6 310 310 HOH HOH . JA 6 HOH E 7 314 314 HOH HOH . JA 6 HOH E 8 315 315 HOH HOH . JA 6 HOH E 9 316 316 HOH HOH . JA 6 HOH E 10 317 317 HOH HOH . JA 6 HOH E 11 322 322 HOH HOH . KA 6 HOH F 1 300 300 HOH HOH . KA 6 HOH F 2 301 301 HOH HOH . KA 6 HOH F 3 303 303 HOH HOH . KA 6 HOH F 4 304 304 HOH HOH . KA 6 HOH F 5 305 305 HOH HOH . KA 6 HOH F 6 306 306 HOH HOH . KA 6 HOH F 7 307 307 HOH HOH . KA 6 HOH F 8 309 309 HOH HOH . KA 6 HOH F 9 310 310 HOH HOH . KA 6 HOH F 10 311 311 HOH HOH . KA 6 HOH F 11 312 312 HOH HOH . KA 6 HOH F 12 313 313 HOH HOH . KA 6 HOH F 13 314 314 HOH HOH . KA 6 HOH F 14 315 315 HOH HOH . LA 6 HOH G 1 300 300 HOH HOH . LA 6 HOH G 2 302 302 HOH HOH . LA 6 HOH G 3 306 306 HOH HOH . LA 6 HOH G 4 307 307 HOH HOH . LA 6 HOH G 5 312 312 HOH HOH . MA 6 HOH H 1 300 300 HOH HOH . MA 6 HOH H 2 303 303 HOH HOH . MA 6 HOH H 3 304 304 HOH HOH . NA 6 HOH I 1 225 225 HOH HOH . NA 6 HOH I 2 300 300 HOH HOH . NA 6 HOH I 3 303 303 HOH HOH . OA 6 HOH J 1 302 302 HOH HOH . OA 6 HOH J 2 303 303 HOH HOH . OA 6 HOH J 3 304 304 HOH HOH . OA 6 HOH J 4 307 307 HOH HOH . OA 6 HOH J 5 308 308 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 NAG . A . V 5 0.125 2.146 -51.928 0.5 48.47 ? C1 NAG 250 F 1 HETATM 2 C C1 NAG . B . V 5 0.252 -2.57 -47.819 0.5 51.19 ? C1 NAG 250 F 1 HETATM 3 C C2 NAG . A . V 5 -1.138 1.644 -51.249 0.5 52.48 ? C2 NAG 250 F 1 HETATM 4 C C2 NAG . B . V 5 -0.779 -2.88 -46.744 0.5 56.83 ? C2 NAG 250 F 1 HETATM 5 C C3 NAG . A . V 5 -2.291 2.534 -51.681 0.5 55.74 ? C3 NAG 250 F 1 HETATM 6 C C3 NAG . B . V 5 -0.903 -4.395 -46.583 0.5 59.09 ? C3 NAG 250 F 1 HETATM 7 C C4 NAG . A . V 5 -1.972 4.017 -51.451 0.5 53.56 ? C4 NAG 250 F 1 HETATM 8 C C4 NAG . B . V 5 -1.227 -5.024 -47.931 0.5 54.66 ? C4 NAG 250 F 1 HETATM 9 C C5 NAG . A . V 5 -0.505 4.404 -51.679 0.5 53.14 ? C5 NAG 250 F 1 HETATM 10 C C5 NAG . B . V 5 -0.193 -4.575 -48.965 0.5 58.9 ? C5 NAG 250 F 1 HETATM 11 C C6 NAG . A . V 5 -0.172 5.696 -50.928 0.5 51.54 ? C6 NAG 250 F 1 HETATM 12 C C6 NAG . B . V 5 -0.514 -5.147 -50.339 0.5 54.8 ? C6 NAG 250 F 1 HETATM 13 C C7 NAG . A . V 5 -1.629 -0.671 -50.621 0.5 58.89 ? C7 NAG 250 F 1 HETATM 14 C C7 NAG . B . V 5 -1.299 -1.486 -44.814 0.5 56.09 ? C7 NAG 250 F 1 HETATM 15 C C8 NAG . A . V 5 -0.798 -0.601 -49.371 0.5 53.89 ? C8 NAG 250 F 1 HETATM 16 C C8 NAG . B . V 5 -2.509 -0.961 -45.541 0.5 49.3 ? C8 NAG 250 F 1 HETATM 17 N N2 NAG . A . V 5 -1.407 0.253 -51.561 0.5 56.33 ? N2 NAG 250 F 1 HETATM 18 N N2 NAG . B . V 5 -0.421 -2.223 -45.5 0.5 54.82 ? N2 NAG 250 F 1 HETATM 19 O O3 NAG . A . V 5 -3.437 2.148 -50.954 0.5 47.85 ? O3 NAG 250 F 1 HETATM 20 O O3 NAG . B . V 5 -1.879 -4.758 -45.627 0.5 59.32 ? O3 NAG 250 F 1 HETATM 21 O O4 NAG . A . V 5 -2.74 4.794 -52.343 0.5 38.88 ? O4 NAG 250 F 1 HETATM 22 O O4 NAG . B . V 5 -1.235 -6.431 -47.798 0.5 52.07 ? O4 NAG 250 F 1 HETATM 23 O O5 NAG . A . V 5 0.418 3.387 -51.325 0.5 51.22 ? O5 NAG 250 F 1 HETATM 24 O O5 NAG . B . V 5 -0.129 -3.164 -49.042 0.5 54.41 ? O5 NAG 250 F 1 HETATM 25 O O6 NAG . A . V 5 -0.61 5.614 -49.59 0.5 50.25 ? O6 NAG 250 F 1 HETATM 26 O O6 NAG . B . V 5 -1.857 -4.847 -50.639 0.5 48.51 ? O6 NAG 250 F 1 HETATM 27 O O7 NAG . A . V 5 -2.469 -1.564 -50.747 0.5 60.38 ? O7 NAG 250 F 1 HETATM 28 O O7 NAG . B . V 5 -1.144 -1.241 -43.62 0.5 54.2 ? O7 NAG 250 F 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 538 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #