data_3P70 # _model_server_result.job_id gEg05mKNMt_IL0xU_QvDjg _model_server_result.datetime_utc '2024-11-29 22:07:35' _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 3p70 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":1416}' # _entry.id 3P70 # _exptl.entry_id 3P70 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 72.57 _cell.angle_beta 84.05 _cell.angle_gamma 80.45 _cell.entry_id 3P70 _cell.length_a 62.243 _cell.length_b 68.227 _cell.length_c 98.972 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3P70 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 PISA trimeric 3 author_and_software_defined_assembly 3 PISA trimeric 3 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,O,P,Q,R,S,EA,FA 1 1 C,D,J,T,U,V,W,GA,JA 2 1 E,F,K,M,X,Y,Z,HA 3 1 G,H,L,N,AA,BA,CA,DA,IA 4 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 ? 5 O N N ? 5 U N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 4 n M NAG 1 I 1 NAG F 1416 NAG 4 n M NAG 2 I 2 NAG F 1417 NAG 4 n N NAG 1 J 1 NAG H 1416 NAG 4 n N NAG 2 J 2 NAG H 1417 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 9 A CYS 336 1_555 B SG CYS 119 B CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 B SG CYS 28 B CYS 391 1_555 B SG CYS 44 B CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf3 B SG CYS 173 B CYS 536 1_555 B SG CYS 187 B CYS 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf4 B SG CYS 201 B CYS 564 1_555 B SG CYS 231 B CYS 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf5 C SG CYS 9 C CYS 336 1_555 D SG CYS 119 D CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf6 D SG CYS 28 D CYS 391 1_555 D SG CYS 44 D CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf7 D SG CYS 173 D CYS 536 1_555 D SG CYS 187 D CYS 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf8 D SG CYS 201 D CYS 564 1_555 D SG CYS 231 D CYS 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? disulf ? disulf9 E SG CYS 9 E CYS 336 1_555 F SG CYS 119 F CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 F SG CYS 28 F CYS 391 1_555 F SG CYS 44 F CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 F SG CYS 173 F CYS 536 1_555 F SG CYS 187 F CYS 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf12 F SG CYS 201 F CYS 564 1_555 F SG CYS 231 F CYS 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf13 G SG CYS 9 G CYS 336 1_555 H SG CYS 119 H CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf14 H SG CYS 28 H CYS 391 1_555 H SG CYS 44 H CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf15 H SG CYS 173 H CYS 536 1_555 H SG CYS 187 H CYS 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf16 H SG CYS 201 H CYS 564 1_555 H SG CYS 231 H CYS 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? covale ? covale1 B ND2 ASN 53 B ASN 416 1_555 O C1 NAG . B NAG 1416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 D ND2 ASN 53 D ASN 416 1_555 U C1 NAG . D NAG 1416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 F ND2 ASN 53 F ASN 416 1_555 M C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale4 H ND2 ASN 53 H ASN 416 1_555 N C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 M O4 NAG . I NAG 1 1_555 M C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? covale ? covale6 N O4 NAG . J NAG 1 1_555 N C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? metalc ? metalc1 B O LEU 39 B LEU 402 1_555 R NA NA . B NA 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? metalc ? metalc2 B O GLY 206 B GLY 569 1_555 R NA NA . B NA 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc3 B O ARG 233 B ARG 596 1_555 Q NA NA . B NA 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? metalc ? metalc4 Q NA NA . B NA 1500 1_555 FA O HOH . B HOH 3503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc5 Q NA NA . B NA 1500 1_555 FA O HOH . B HOH 3517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc6 C O TYR 32 C TYR 359 1_555 T NA NA . C NA 3200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc7 T NA NA . C NA 3200 1_555 GA O HOH . C HOH 3511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? metalc ? metalc8 T NA NA . C NA 3200 1_555 D OH TYR 134 D TYR 497 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc9 D O ARG 233 D ARG 596 1_555 W NA NA . D NA 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc10 D O LYS 236 D LYS 599 1_555 W NA NA . D NA 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? metalc ? metalc11 F O ARG 233 F ARG 596 1_555 Y NA NA . F NA 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc12 F O LYS 236 F LYS 599 1_555 Y NA NA . F NA 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.095 ? metalc ? metalc13 Y NA NA . F NA 1500 1_555 HA O HOH . F HOH 3505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.827 ? metalc ? metalc14 G O TYR 32 G TYR 359 1_555 AA NA NA . G NA 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? metalc ? metalc15 AA NA NA . G NA 1501 1_555 H OH TYR 134 H TYR 497 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc16 H O ARG 233 H ARG 596 1_555 CA NA NA . H NA 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc17 H O LYS 236 H LYS 599 1_555 CA NA NA . H NA 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.732 ? metalc ? metalc18 CA NA NA . H NA 1500 1_555 IA O HOH . H HOH 3501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.784 ? metalc ? metalc19 CA NA NA . H NA 1500 1_555 IA O HOH . H HOH 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.177 ? # _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 278 n n C1 O1 NAG sing 279 n n C1 O5 NAG sing 280 n n C1 H1 NAG sing 281 n n C2 C3 NAG sing 282 n n C2 N2 NAG sing 283 n n C2 H2 NAG sing 284 n n C3 C4 NAG sing 285 n n C3 O3 NAG sing 286 n n C3 H3 NAG sing 287 n n C4 C5 NAG sing 288 n n C4 O4 NAG sing 289 n n C4 H4 NAG sing 290 n n C5 C6 NAG sing 291 n n C5 O5 NAG sing 292 n n C5 H5 NAG sing 293 n n C6 O6 NAG sing 294 n n C6 H61 NAG sing 295 n n C6 H62 NAG sing 296 n n C7 C8 NAG sing 297 n n C7 N2 NAG sing 298 n n C7 O7 NAG doub 299 n n C8 H81 NAG sing 300 n n C8 H82 NAG sing 301 n n C8 H83 NAG sing 302 n n N2 HN2 NAG sing 303 n n O1 HO1 NAG sing 304 n n O3 HO3 NAG sing 305 n n O4 HO4 NAG sing 306 n n O6 HO6 NAG sing 307 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 3P70 _atom_sites.fract_transf_matrix[1][1] 0.016066 _atom_sites.fract_transf_matrix[1][2] -0.002703 _atom_sites.fract_transf_matrix[1][3] -0.000936 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014863 _atom_sites.fract_transf_matrix[2][3] -0.004466 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.010607 _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 O 5 NAG B 1 1416 1416 NAG NAG . P 6 BEN B 1 2001 2001 BEN BEN . Q 7 NA B 1 1500 1500 NA NA . R 7 NA B 1 1501 1501 NA NA . S 8 BGC B 1 4202 4202 BGC BGC . T 7 NA C 1 3200 3200 NA NA . U 5 NAG D 1 1416 1416 NAG NAG . V 6 BEN D 1 2001 2001 BEN BEN . W 7 NA D 1 1500 1500 NA NA . X 6 BEN F 1 2001 2001 BEN BEN . Y 7 NA F 1 1500 1500 NA NA . Z 8 BGC F 1 4203 4203 BGC BGC . AA 7 NA G 1 1501 1501 NA NA . BA 6 BEN H 1 2001 2001 BEN BEN . CA 7 NA H 1 1500 1500 NA NA . DA 8 BGC H 1 4201 4201 BGC BGC . EA 9 HOH A 1 3500 3500 HOH HOH . FA 9 HOH B 1 3503 3503 HOH HOH . FA 9 HOH B 2 3504 3504 HOH HOH . FA 9 HOH B 3 3506 3506 HOH HOH . FA 9 HOH B 4 3513 3513 HOH HOH . FA 9 HOH B 5 3515 3515 HOH HOH . FA 9 HOH B 6 3516 3516 HOH HOH . FA 9 HOH B 7 3517 3517 HOH HOH . FA 9 HOH B 8 3518 3518 HOH HOH . FA 9 HOH B 9 3519 3519 HOH HOH . FA 9 HOH B 10 3520 3520 HOH HOH . FA 9 HOH B 11 3524 3524 HOH HOH . GA 9 HOH C 1 3508 3508 HOH HOH . GA 9 HOH C 2 3511 3511 HOH HOH . HA 9 HOH F 1 3505 3505 HOH HOH . HA 9 HOH F 2 3510 3510 HOH HOH . HA 9 HOH F 3 3512 3512 HOH HOH . HA 9 HOH F 4 3514 3514 HOH HOH . HA 9 HOH F 5 3521 3521 HOH HOH . HA 9 HOH F 6 3523 3523 HOH HOH . IA 9 HOH H 1 3501 3501 HOH HOH . IA 9 HOH H 2 3502 3502 HOH HOH . IA 9 HOH H 3 3522 3522 HOH HOH . JA 9 HOH N 1 3509 3509 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 . . . O 5 10.755 8.196 83.756 1 92.93 ? C1 NAG 1416 B 1 HETATM 2 C C2 NAG . . . O 5 10.501 7.611 82.354 1 101.43 ? C2 NAG 1416 B 1 HETATM 3 C C3 NAG . . . O 5 9.641 6.315 82.291 1 107.22 ? C3 NAG 1416 B 1 HETATM 4 C C4 NAG . . . O 5 9.728 5.461 83.564 1 107.51 ? C4 NAG 1416 B 1 HETATM 5 C C5 NAG . . . O 5 9.62 6.389 84.787 1 102.34 ? C5 NAG 1416 B 1 HETATM 6 C C6 NAG . . . O 5 9.52 5.634 86.105 1 104.34 ? C6 NAG 1416 B 1 HETATM 7 C C7 NAG . . . O 5 9.008 9.574 81.797 1 100.25 ? C7 NAG 1416 B 1 HETATM 8 C C8 NAG . . . O 5 8.359 9.638 83.161 1 98.38 ? C8 NAG 1416 B 1 HETATM 9 N N2 NAG . . . O 5 9.949 8.661 81.499 1 101.03 ? N2 NAG 1416 B 1 HETATM 10 O O3 NAG . . . O 5 9.991 5.493 81.185 1 110.77 ? O3 NAG 1416 B 1 HETATM 11 O O4 NAG . . . O 5 8.757 4.421 83.539 1 112.23 ? O4 NAG 1416 B 1 HETATM 12 O O5 NAG . . . O 5 10.763 7.239 84.81 1 96.45 ? O5 NAG 1416 B 1 HETATM 13 O O6 NAG . . . O 5 10.65 4.797 86.259 1 106.89 ? O6 NAG 1416 B 1 HETATM 14 O O7 NAG . . . O 5 8.656 10.391 80.951 1 100.46 ? O7 NAG 1416 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #