data_6DY2 # _model_server_result.job_id rRim8aMVZNw2l3y6oaMqwQ _model_server_result.datetime_utc '2024-11-15 00:31:40' _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 6dy2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":202}' # _entry.id 6DY2 # _exptl.entry_id 6DY2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 6 _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 6DY2 _cell.length_a 71.885 _cell.length_b 98.863 _cell.length_c 117.761 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DY2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # 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,F,G,H,I,J,K,L,M,N,O,Z,AA 1 1 C,D,P,Q,R,S,T,U,V,W,X,Y,BA,CA 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N ? 3 H N N ? 3 P N N ? 3 Q N N ? 3 T 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 covale ? covale1 A ND2 ASN 17 A ASN 35 1_555 E C1 NAG . A NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 87 A ASN 105 1_555 F C1 NAG . A NAG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 B SG CYS 1 B CYS 124 1_555 O C18 HJA . B HJA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? covale ? covale4 B ND2 ASN 185 B ASN 308 1_555 H C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale5 C ND2 ASN 17 C ASN 35 1_555 P C1 NAG . C NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 C ND2 ASN 87 C ASN 105 1_555 Q C1 NAG . C NAG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale7 D SG CYS 1 D CYS 124 1_555 Y C18 HJA . D HJA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? covale ? covale8 D ND2 ASN 185 D ASN 308 1_555 T C1 NAG . D NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 6DY2 _atom_sites.fract_transf_matrix[1][1] 0.013911 _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] 0.010115 _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] 0.008492 _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 E 3 NAG A 1 201 1 NAG NAG . F 3 NAG A 1 202 3 NAG NAG . G 4 CL A 1 203 3 CL CL . H 3 NAG B 1 401 5 NAG NAG . I 5 PO4 B 1 402 1 PO4 PO4 . J 4 CL B 1 403 1 CL CL . K 4 CL B 1 404 5 CL CL . L 4 CL B 1 405 6 CL CL . M 4 CL B 1 406 7 CL CL . N 4 CL B 1 407 8 CL CL . O 6 HJA B 1 408 1 HJA WTF . P 3 NAG C 1 201 2 NAG NAG . Q 3 NAG C 1 202 4 NAG NAG . R 4 CL C 1 203 9 CL CL . S 4 CL C 1 204 10 CL CL . T 3 NAG D 1 401 6 NAG NAG . U 5 PO4 D 1 402 2 PO4 PO4 . V 4 CL D 1 403 2 CL CL . W 4 CL D 1 404 4 CL CL . X 4 CL D 1 405 11 CL CL . Y 6 HJA D 1 406 2 HJA WTF . Z 7 HOH A 1 301 5 HOH HOH . Z 7 HOH A 2 302 25 HOH HOH . Z 7 HOH A 3 303 115 HOH HOH . Z 7 HOH A 4 304 103 HOH HOH . Z 7 HOH A 5 305 18 HOH HOH . Z 7 HOH A 6 306 27 HOH HOH . Z 7 HOH A 7 307 110 HOH HOH . Z 7 HOH A 8 308 130 HOH HOH . Z 7 HOH A 9 309 111 HOH HOH . Z 7 HOH A 10 310 102 HOH HOH . Z 7 HOH A 11 311 80 HOH HOH . Z 7 HOH A 12 312 19 HOH HOH . Z 7 HOH A 13 313 52 HOH HOH . Z 7 HOH A 14 314 39 HOH HOH . Z 7 HOH A 15 315 76 HOH HOH . Z 7 HOH A 16 316 33 HOH HOH . Z 7 HOH A 17 317 63 HOH HOH . Z 7 HOH A 18 318 22 HOH HOH . Z 7 HOH A 19 319 93 HOH HOH . Z 7 HOH A 20 320 42 HOH HOH . Z 7 HOH A 21 321 124 HOH HOH . Z 7 HOH A 22 322 125 HOH HOH . Z 7 HOH A 23 323 31 HOH HOH . Z 7 HOH A 24 324 94 HOH HOH . Z 7 HOH A 25 325 104 HOH HOH . Z 7 HOH A 26 326 32 HOH HOH . Z 7 HOH A 27 327 106 HOH HOH . Z 7 HOH A 28 328 68 HOH HOH . Z 7 HOH A 29 329 113 HOH HOH . Z 7 HOH A 30 330 132 HOH HOH . Z 7 HOH A 31 331 120 HOH HOH . AA 7 HOH B 1 501 81 HOH HOH . AA 7 HOH B 2 502 1 HOH HOH . AA 7 HOH B 3 503 26 HOH HOH . AA 7 HOH B 4 504 7 HOH HOH . AA 7 HOH B 5 505 12 HOH HOH . AA 7 HOH B 6 506 14 HOH HOH . AA 7 HOH B 7 507 2 HOH HOH . AA 7 HOH B 8 508 11 HOH HOH . AA 7 HOH B 9 509 6 HOH HOH . AA 7 HOH B 10 510 28 HOH HOH . AA 7 HOH B 11 511 105 HOH HOH . AA 7 HOH B 12 512 24 HOH HOH . AA 7 HOH B 13 513 23 HOH HOH . AA 7 HOH B 14 514 17 HOH HOH . AA 7 HOH B 15 515 99 HOH HOH . AA 7 HOH B 16 516 16 HOH HOH . AA 7 HOH B 17 517 73 HOH HOH . AA 7 HOH B 18 518 78 HOH HOH . AA 7 HOH B 19 519 41 HOH HOH . AA 7 HOH B 20 520 46 HOH HOH . AA 7 HOH B 21 521 121 HOH HOH . AA 7 HOH B 22 522 8 HOH HOH . AA 7 HOH B 23 523 108 HOH HOH . AA 7 HOH B 24 524 49 HOH HOH . AA 7 HOH B 25 525 118 HOH HOH . AA 7 HOH B 26 526 44 HOH HOH . AA 7 HOH B 27 527 74 HOH HOH . AA 7 HOH B 28 528 83 HOH HOH . AA 7 HOH B 29 529 43 HOH HOH . AA 7 HOH B 30 530 48 HOH HOH . AA 7 HOH B 31 531 109 HOH HOH . AA 7 HOH B 32 532 67 HOH HOH . AA 7 HOH B 33 533 114 HOH HOH . AA 7 HOH B 34 534 37 HOH HOH . AA 7 HOH B 35 535 91 HOH HOH . AA 7 HOH B 36 536 90 HOH HOH . AA 7 HOH B 37 537 51 HOH HOH . AA 7 HOH B 38 538 95 HOH HOH . AA 7 HOH B 39 539 75 HOH HOH . AA 7 HOH B 40 540 101 HOH HOH . AA 7 HOH B 41 541 36 HOH HOH . AA 7 HOH B 42 542 122 HOH HOH . AA 7 HOH B 43 543 38 HOH HOH . AA 7 HOH B 44 544 40 HOH HOH . AA 7 HOH B 45 545 96 HOH HOH . AA 7 HOH B 46 546 50 HOH HOH . AA 7 HOH B 47 547 53 HOH HOH . AA 7 HOH B 48 548 70 HOH HOH . AA 7 HOH B 49 549 47 HOH HOH . AA 7 HOH B 50 550 60 HOH HOH . AA 7 HOH B 51 551 92 HOH HOH . AA 7 HOH B 52 552 35 HOH HOH . AA 7 HOH B 53 553 123 HOH HOH . AA 7 HOH B 54 554 69 HOH HOH . AA 7 HOH B 55 555 21 HOH HOH . AA 7 HOH B 56 556 129 HOH HOH . AA 7 HOH B 57 557 100 HOH HOH . AA 7 HOH B 58 558 71 HOH HOH . AA 7 HOH B 59 559 89 HOH HOH . AA 7 HOH B 60 560 131 HOH HOH . BA 7 HOH C 1 301 9 HOH HOH . BA 7 HOH C 2 302 13 HOH HOH . BA 7 HOH C 3 303 116 HOH HOH . BA 7 HOH C 4 304 117 HOH HOH . BA 7 HOH C 5 305 62 HOH HOH . BA 7 HOH C 6 306 82 HOH HOH . CA 7 HOH D 1 501 20 HOH HOH . CA 7 HOH D 2 502 3 HOH HOH . CA 7 HOH D 3 503 15 HOH HOH . CA 7 HOH D 4 504 45 HOH HOH . CA 7 HOH D 5 505 54 HOH HOH . CA 7 HOH D 6 506 72 HOH HOH . CA 7 HOH D 7 507 127 HOH HOH . CA 7 HOH D 8 508 58 HOH HOH . CA 7 HOH D 9 509 4 HOH HOH . CA 7 HOH D 10 510 10 HOH HOH . CA 7 HOH D 11 511 57 HOH HOH . CA 7 HOH D 12 512 133 HOH HOH . CA 7 HOH D 13 513 64 HOH HOH . CA 7 HOH D 14 514 119 HOH HOH . CA 7 HOH D 15 515 30 HOH HOH . CA 7 HOH D 16 516 56 HOH HOH . CA 7 HOH D 17 517 34 HOH HOH . CA 7 HOH D 18 518 84 HOH HOH . CA 7 HOH D 19 519 29 HOH HOH . CA 7 HOH D 20 520 79 HOH HOH . CA 7 HOH D 21 521 55 HOH HOH . CA 7 HOH D 22 522 107 HOH HOH . CA 7 HOH D 23 523 126 HOH HOH . CA 7 HOH D 24 524 65 HOH HOH . CA 7 HOH D 25 525 59 HOH HOH . CA 7 HOH D 26 526 128 HOH HOH . CA 7 HOH D 27 527 66 HOH HOH . CA 7 HOH D 28 528 77 HOH HOH . CA 7 HOH D 29 529 112 HOH HOH . CA 7 HOH D 30 530 88 HOH HOH . CA 7 HOH D 31 531 85 HOH HOH . CA 7 HOH D 32 532 87 HOH HOH . CA 7 HOH D 33 533 86 HOH HOH . CA 7 HOH D 34 534 61 HOH HOH . CA 7 HOH D 35 535 97 HOH HOH . CA 7 HOH D 36 536 98 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 . . . Q 3 138.87 90.94 59.962 1 62.21 ? C1 NAG 202 C 1 HETATM 2 C C2 NAG . . . Q 3 139.521 90.677 58.612 1 62.9 ? C2 NAG 202 C 1 HETATM 3 C C3 NAG . . . Q 3 139.557 91.963 57.801 1 65.95 ? C3 NAG 202 C 1 HETATM 4 C C4 NAG . . . Q 3 138.144 92.506 57.638 1 74.85 ? C4 NAG 202 C 1 HETATM 5 C C5 NAG . . . Q 3 137.473 92.679 59.002 1 77.57 ? C5 NAG 202 C 1 HETATM 6 C C6 NAG . . . Q 3 136.013 93.058 58.885 1 58.72 ? C6 NAG 202 C 1 HETATM 7 C C7 NAG . . . Q 3 141.081 88.821 58.979 1 60.34 ? C7 NAG 202 C 1 HETATM 8 C C8 NAG . . . Q 3 142.518 88.412 59.091 1 53.29 ? C8 NAG 202 C 1 HETATM 9 N N2 NAG . . . Q 3 140.857 90.12 58.757 1 64.18 ? N2 NAG 202 C 1 HETATM 10 O O3 NAG . . . Q 3 140.14 91.718 56.526 1 79.78 ? O3 NAG 202 C 1 HETATM 11 O O4 NAG . . . Q 3 138.179 93.763 56.971 1 68.43 ? O4 NAG 202 C 1 HETATM 12 O O5 NAG . . . Q 3 137.528 91.456 59.759 1 84.09 ? O5 NAG 202 C 1 HETATM 13 O O6 NAG . . . Q 3 135.162 91.93 59.031 1 52.72 ? O6 NAG 202 C 1 HETATM 14 O O7 NAG . . . Q 3 140.165 88.013 59.09 1 58.51 ? O7 NAG 202 C 1 HETATM 15 H H1 NAG . . . Q 3 139.398 91.599 60.451 1 74.65 ? H1 NAG 202 C 1 HETATM 16 H H2 NAG . . . Q 3 138.97 90.033 58.129 1 75.49 ? H2 NAG 202 C 1 HETATM 17 H H3 NAG . . . Q 3 140.097 92.623 58.276 1 79.14 ? H3 NAG 202 C 1 HETATM 18 H H4 NAG . . . Q 3 137.622 91.878 57.104 1 89.83 ? H4 NAG 202 C 1 HETATM 19 H H5 NAG . . . Q 3 137.941 93.378 59.496 1 93.08 ? H5 NAG 202 C 1 HETATM 20 H H61 NAG . . . Q 3 135.859 93.461 58.01 1 70.47 ? H61 NAG 202 C 1 HETATM 21 H H62 NAG . . . Q 3 135.798 93.71 59.578 1 70.47 ? H62 NAG 202 C 1 HETATM 22 H H81 NAG . . . Q 3 142.935 88.89 59.833 1 63.95 ? H81 NAG 202 C 1 HETATM 23 H H82 NAG . . . Q 3 142.984 88.63 58.262 1 63.95 ? H82 NAG 202 C 1 HETATM 24 H H83 NAG . . . Q 3 142.571 87.451 59.252 1 63.95 ? H83 NAG 202 C 1 HETATM 25 H HN2 NAG . . . Q 3 141.573 90.68 58.679 1 77.01 ? HN2 NAG 202 C 1 HETATM 26 H HO3 NAG . . . Q 3 140.449 92.48 56.191 1 95.74 ? HO3 NAG 202 C 1 HETATM 27 H HO4 NAG . . . Q 3 137.64 93.739 56.265 1 82.11 ? HO4 NAG 202 C 1 HETATM 28 H HO6 NAG . . . Q 3 134.468 92.01 58.483 1 63.27 ? HO6 NAG 202 C 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 227 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #