data_3MA7 # _model_server_result.job_id rXKTXRME8o9DQ4lNLJwzNQ _model_server_result.datetime_utc '2025-01-10 07:32:33' _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 3ma7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 3MA7 # _exptl.entry_id 3MA7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _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 102.15 _cell.angle_beta 92.22 _cell.angle_gamma 106.21 _cell.entry_id 3MA7 _cell.length_a 46.773 _cell.length_b 50.921 _cell.length_c 103.165 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3MA7 _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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,E,H,I,J,M,N 1 1 C,D,F,G,K,L,O,P 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 6 _struct_asym.id J _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 C 511 NAG 3 n E NAG 2 E 2 NAG C 512 NAG 3 n F NAG 1 F 1 NAG A 501 NAG 3 n F NAG 2 F 2 NAG A 502 NAG 3 n G NAG 1 G 1 NAG A 511 NAG 3 n G NAG 2 G 2 NAG A 512 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 104 C CYS 104 1_555 A SG CYS 168 C CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? disulf ? disulf2 A SG CYS 208 C CYS 208 1_555 A SG CYS 263 C CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf3 B SG CYS 25 D CYS 25 1_555 B SG CYS 80 D CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 C SG CYS 104 A CYS 104 1_555 C SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? disulf ? disulf5 C SG CYS 208 A CYS 208 1_555 C SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 D SG CYS 25 B CYS 25 1_555 D SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 42 C ASN 42 1_555 J C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 A ND2 ASN 165 C ASN 165 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 C ND2 ASN 42 A ASN 42 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 C ND2 ASN 165 A ASN 165 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? # _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 446 n n C1 O1 NAG sing 447 n n C1 O5 NAG sing 448 n n C1 H1 NAG sing 449 n n C2 C3 NAG sing 450 n n C2 N2 NAG sing 451 n n C2 H2 NAG sing 452 n n C3 C4 NAG sing 453 n n C3 O3 NAG sing 454 n n C3 H3 NAG sing 455 n n C4 C5 NAG sing 456 n n C4 O4 NAG sing 457 n n C4 H4 NAG sing 458 n n C5 C6 NAG sing 459 n n C5 O5 NAG sing 460 n n C5 H5 NAG sing 461 n n C6 O6 NAG sing 462 n n C6 H61 NAG sing 463 n n C6 H62 NAG sing 464 n n C7 C8 NAG sing 465 n n C7 N2 NAG sing 466 n n C7 O7 NAG doub 467 n n C8 H81 NAG sing 468 n n C8 H82 NAG sing 469 n n C8 H83 NAG sing 470 n n N2 HN2 NAG sing 471 n n O1 HO1 NAG sing 472 n n O3 HO3 NAG sing 473 n n O4 HO4 NAG sing 474 n n O6 HO6 NAG sing 475 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 3MA7 _atom_sites.fract_transf_matrix[1][1] 0.02138 _atom_sites.fract_transf_matrix[1][2] 0.006215 _atom_sites.fract_transf_matrix[1][3] 0.002325 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020451 _atom_sites.fract_transf_matrix[2][3] 0.004847 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009969 _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 H 4 CD4 C 1 2089 2089 CD4 CD4 . I 5 PLM C 1 286 286 PLM PLM . J 6 NAG C 1 501 501 NAG NAG . K 4 CD4 A 1 2089 2089 CD4 CD4 . L 5 PLM A 1 286 286 PLM PLM . M 7 HOH C 1 287 287 HOH HOH . M 7 HOH C 2 288 288 HOH HOH . M 7 HOH C 3 289 289 HOH HOH . M 7 HOH C 4 290 290 HOH HOH . M 7 HOH C 5 291 291 HOH HOH . M 7 HOH C 6 292 292 HOH HOH . M 7 HOH C 7 293 293 HOH HOH . M 7 HOH C 8 294 294 HOH HOH . M 7 HOH C 9 295 295 HOH HOH . M 7 HOH C 10 296 296 HOH HOH . M 7 HOH C 11 297 297 HOH HOH . M 7 HOH C 12 298 298 HOH HOH . M 7 HOH C 13 299 299 HOH HOH . M 7 HOH C 14 300 300 HOH HOH . M 7 HOH C 15 301 301 HOH HOH . M 7 HOH C 16 302 302 HOH HOH . M 7 HOH C 17 303 303 HOH HOH . M 7 HOH C 18 304 304 HOH HOH . M 7 HOH C 19 305 305 HOH HOH . M 7 HOH C 20 306 306 HOH HOH . M 7 HOH C 21 307 307 HOH HOH . M 7 HOH C 22 308 308 HOH HOH . M 7 HOH C 23 309 309 HOH HOH . M 7 HOH C 24 310 310 HOH HOH . M 7 HOH C 25 311 311 HOH HOH . M 7 HOH C 26 312 312 HOH HOH . M 7 HOH C 27 313 313 HOH HOH . M 7 HOH C 28 314 314 HOH HOH . M 7 HOH C 29 315 315 HOH HOH . M 7 HOH C 30 316 316 HOH HOH . M 7 HOH C 31 317 317 HOH HOH . M 7 HOH C 32 318 318 HOH HOH . M 7 HOH C 33 319 319 HOH HOH . M 7 HOH C 34 320 320 HOH HOH . M 7 HOH C 35 321 321 HOH HOH . M 7 HOH C 36 322 322 HOH HOH . M 7 HOH C 37 323 323 HOH HOH . M 7 HOH C 38 324 324 HOH HOH . M 7 HOH C 39 325 325 HOH HOH . M 7 HOH C 40 326 326 HOH HOH . M 7 HOH C 41 327 327 HOH HOH . M 7 HOH C 42 328 328 HOH HOH . M 7 HOH C 43 329 329 HOH HOH . M 7 HOH C 44 330 330 HOH HOH . M 7 HOH C 45 331 331 HOH HOH . M 7 HOH C 46 332 332 HOH HOH . M 7 HOH C 47 333 333 HOH HOH . M 7 HOH C 48 334 334 HOH HOH . M 7 HOH C 49 335 335 HOH HOH . M 7 HOH C 50 336 336 HOH HOH . M 7 HOH C 51 337 337 HOH HOH . M 7 HOH C 52 338 338 HOH HOH . M 7 HOH C 53 339 339 HOH HOH . M 7 HOH C 54 340 340 HOH HOH . M 7 HOH C 55 341 341 HOH HOH . M 7 HOH C 56 342 342 HOH HOH . M 7 HOH C 57 343 343 HOH HOH . M 7 HOH C 58 344 344 HOH HOH . M 7 HOH C 59 345 345 HOH HOH . M 7 HOH C 60 346 346 HOH HOH . M 7 HOH C 61 347 347 HOH HOH . M 7 HOH C 62 348 348 HOH HOH . N 7 HOH D 1 100 100 HOH HOH . N 7 HOH D 2 101 101 HOH HOH . N 7 HOH D 3 102 102 HOH HOH . N 7 HOH D 4 103 103 HOH HOH . N 7 HOH D 5 104 104 HOH HOH . N 7 HOH D 6 105 105 HOH HOH . N 7 HOH D 7 106 106 HOH HOH . N 7 HOH D 8 107 107 HOH HOH . N 7 HOH D 9 108 108 HOH HOH . N 7 HOH D 10 109 109 HOH HOH . N 7 HOH D 11 110 110 HOH HOH . N 7 HOH D 12 111 111 HOH HOH . N 7 HOH D 13 112 112 HOH HOH . N 7 HOH D 14 113 113 HOH HOH . N 7 HOH D 15 114 114 HOH HOH . N 7 HOH D 16 115 115 HOH HOH . N 7 HOH D 17 116 116 HOH HOH . N 7 HOH D 18 117 117 HOH HOH . N 7 HOH D 19 118 118 HOH HOH . N 7 HOH D 20 119 119 HOH HOH . N 7 HOH D 21 120 120 HOH HOH . N 7 HOH D 22 121 121 HOH HOH . N 7 HOH D 23 122 122 HOH HOH . N 7 HOH D 24 124 124 HOH HOH . N 7 HOH D 25 135 135 HOH HOH . N 7 HOH D 26 136 136 HOH HOH . N 7 HOH D 27 141 141 HOH HOH . N 7 HOH D 28 144 144 HOH HOH . N 7 HOH D 29 151 151 HOH HOH . N 7 HOH D 30 152 152 HOH HOH . N 7 HOH D 31 154 154 HOH HOH . N 7 HOH D 32 157 157 HOH HOH . N 7 HOH D 33 158 158 HOH HOH . N 7 HOH D 34 160 160 HOH HOH . N 7 HOH D 35 163 163 HOH HOH . N 7 HOH D 36 195 195 HOH HOH . O 7 HOH A 1 287 287 HOH HOH . O 7 HOH A 2 288 288 HOH HOH . O 7 HOH A 3 289 289 HOH HOH . O 7 HOH A 4 290 290 HOH HOH . O 7 HOH A 5 291 291 HOH HOH . O 7 HOH A 6 292 292 HOH HOH . O 7 HOH A 7 293 293 HOH HOH . O 7 HOH A 8 294 294 HOH HOH . O 7 HOH A 9 295 295 HOH HOH . O 7 HOH A 10 296 296 HOH HOH . O 7 HOH A 11 297 297 HOH HOH . O 7 HOH A 12 298 298 HOH HOH . O 7 HOH A 13 299 299 HOH HOH . O 7 HOH A 14 300 300 HOH HOH . O 7 HOH A 15 301 301 HOH HOH . O 7 HOH A 16 302 302 HOH HOH . O 7 HOH A 17 303 303 HOH HOH . O 7 HOH A 18 304 304 HOH HOH . O 7 HOH A 19 305 305 HOH HOH . O 7 HOH A 20 306 306 HOH HOH . O 7 HOH A 21 307 307 HOH HOH . O 7 HOH A 22 308 308 HOH HOH . O 7 HOH A 23 309 309 HOH HOH . O 7 HOH A 24 310 310 HOH HOH . O 7 HOH A 25 311 311 HOH HOH . O 7 HOH A 26 312 312 HOH HOH . O 7 HOH A 27 313 313 HOH HOH . O 7 HOH A 28 314 314 HOH HOH . O 7 HOH A 29 315 315 HOH HOH . O 7 HOH A 30 316 316 HOH HOH . O 7 HOH A 31 317 317 HOH HOH . O 7 HOH A 32 318 318 HOH HOH . O 7 HOH A 33 319 319 HOH HOH . O 7 HOH A 34 320 320 HOH HOH . O 7 HOH A 35 321 321 HOH HOH . O 7 HOH A 36 322 322 HOH HOH . O 7 HOH A 37 323 323 HOH HOH . O 7 HOH A 38 324 324 HOH HOH . O 7 HOH A 39 325 325 HOH HOH . O 7 HOH A 40 326 326 HOH HOH . O 7 HOH A 41 327 327 HOH HOH . O 7 HOH A 42 328 328 HOH HOH . O 7 HOH A 43 329 329 HOH HOH . P 7 HOH B 1 100 100 HOH HOH . P 7 HOH B 2 101 101 HOH HOH . P 7 HOH B 3 102 102 HOH HOH . P 7 HOH B 4 103 103 HOH HOH . P 7 HOH B 5 104 104 HOH HOH . P 7 HOH B 6 105 105 HOH HOH . P 7 HOH B 7 106 106 HOH HOH . P 7 HOH B 8 107 107 HOH HOH . P 7 HOH B 9 108 108 HOH HOH . P 7 HOH B 10 109 109 HOH HOH . P 7 HOH B 11 110 110 HOH HOH . P 7 HOH B 12 112 112 HOH HOH . P 7 HOH B 13 122 122 HOH HOH . P 7 HOH B 14 147 147 HOH HOH . P 7 HOH B 15 149 149 HOH HOH . P 7 HOH B 16 194 194 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 . . . J 6 18.926 -1.048 13.597 1 58.25 ? C1 NAG 501 C 1 HETATM 2 C C2 NAG . . . J 6 19.088 -2.119 14.673 1 62.12 ? C2 NAG 501 C 1 HETATM 3 C C3 NAG . . . J 6 20.051 -1.692 15.762 1 65.18 ? C3 NAG 501 C 1 HETATM 4 C C4 NAG . . . J 6 21.405 -1.466 15.095 1 66.74 ? C4 NAG 501 C 1 HETATM 5 C C5 NAG . . . J 6 21.29 -0.412 13.997 1 63.25 ? C5 NAG 501 C 1 HETATM 6 C C6 NAG . . . J 6 22.577 -0.425 13.186 1 63.9 ? C6 NAG 501 C 1 HETATM 7 C C7 NAG . . . J 6 17.434 -3.741 15.183 1 63.5 ? C7 NAG 501 C 1 HETATM 8 C C8 NAG . . . J 6 16.057 -4.047 15.698 1 64.08 ? C8 NAG 501 C 1 HETATM 9 N N2 NAG . . . J 6 17.78 -2.464 15.178 1 62.12 ? N2 NAG 501 C 1 HETATM 10 O O3 NAG . . . J 6 20.104 -2.686 16.753 1 66.88 ? O3 NAG 501 C 1 HETATM 11 O O4 NAG . . . J 6 22.392 -1.048 16.023 1 72.94 ? O4 NAG 501 C 1 HETATM 12 O O5 NAG . . . J 6 20.191 -0.609 13.112 1 58.75 ? O5 NAG 501 C 1 HETATM 13 O O6 NAG . . . J 6 22.352 -1.199 12.031 1 65.8 ? O6 NAG 501 C 1 HETATM 14 O O7 NAG . . . J 6 18.196 -4.629 14.79 1 63.52 ? O7 NAG 501 C 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 234 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #