data_3VYF # _model_server_result.job_id AWN0altzVCZ0EkvYWj7Wxg _model_server_result.datetime_utc '2025-03-13 17:42:38' _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 3vyf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 3VYF # _exptl.entry_id 3VYF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method man _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 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 3VYF _cell.length_a 141.427 _cell.length_b 141.427 _cell.length_c 141.427 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VYF _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA hexameric 6 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 1 A,B,C,D,E,F,G,H 3 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_577 z+1/2,-x+5/2,-y+2 0 0 1 -1 0 0 0 -1 0 70.7135 353.5675 282.854 3 'crystal symmetry operation' 12_774 -y+5/2,-z+2,x-1/2 0 -1 0 0 0 -1 1 0 0 353.5675 282.854 -70.7135 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E 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 disulf ? disulf1 A SG CYS 51 A CYS 51 1_555 A SG CYS 58 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 217 A CYS 217 1_555 A SG CYS 221 A CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 259 A CYS 259 1_555 A SG CYS 296 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 B SG CYS 51 B CYS 51 1_555 B SG CYS 58 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 B SG CYS 217 B CYS 217 1_555 B SG CYS 221 B CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 B SG CYS 259 B CYS 259 1_555 B SG CYS 296 B CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 75 A ASN 75 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale2 B ND2 ASN 75 B ASN 75 1_555 E C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? # _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 3VYF _atom_sites.fract_transf_matrix[1][1] 0.007071 _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] 0.007071 _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] 0.007071 _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 C 2 NAG A 1 401 401 NAG NAG . D 3 VYF A 1 402 402 VYF UNL . E 2 NAG B 1 401 401 NAG NAG . F 3 VYF B 1 402 403 VYF UNL . G 4 HOH A 1 501 1 HOH HOH . G 4 HOH A 2 502 2 HOH HOH . G 4 HOH A 3 503 4 HOH HOH . G 4 HOH A 4 504 6 HOH HOH . G 4 HOH A 5 505 7 HOH HOH . G 4 HOH A 6 506 9 HOH HOH . G 4 HOH A 7 507 10 HOH HOH . G 4 HOH A 8 508 11 HOH HOH . G 4 HOH A 9 509 12 HOH HOH . G 4 HOH A 10 510 13 HOH HOH . G 4 HOH A 11 511 14 HOH HOH . G 4 HOH A 12 512 15 HOH HOH . G 4 HOH A 13 513 16 HOH HOH . G 4 HOH A 14 514 17 HOH HOH . G 4 HOH A 15 515 19 HOH HOH . G 4 HOH A 16 516 22 HOH HOH . G 4 HOH A 17 517 23 HOH HOH . G 4 HOH A 18 518 24 HOH HOH . G 4 HOH A 19 519 25 HOH HOH . G 4 HOH A 20 520 26 HOH HOH . G 4 HOH A 21 521 28 HOH HOH . G 4 HOH A 22 522 31 HOH HOH . G 4 HOH A 23 523 33 HOH HOH . G 4 HOH A 24 524 34 HOH HOH . G 4 HOH A 25 525 35 HOH HOH . G 4 HOH A 26 526 36 HOH HOH . G 4 HOH A 27 527 38 HOH HOH . G 4 HOH A 28 528 40 HOH HOH . G 4 HOH A 29 529 43 HOH HOH . G 4 HOH A 30 530 44 HOH HOH . G 4 HOH A 31 531 45 HOH HOH . G 4 HOH A 32 532 46 HOH HOH . G 4 HOH A 33 533 51 HOH HOH . G 4 HOH A 34 534 52 HOH HOH . G 4 HOH A 35 535 55 HOH HOH . G 4 HOH A 36 536 56 HOH HOH . G 4 HOH A 37 537 57 HOH HOH . G 4 HOH A 38 538 59 HOH HOH . G 4 HOH A 39 539 60 HOH HOH . G 4 HOH A 40 540 62 HOH HOH . G 4 HOH A 41 541 64 HOH HOH . G 4 HOH A 42 542 66 HOH HOH . G 4 HOH A 43 543 69 HOH HOH . G 4 HOH A 44 544 71 HOH HOH . G 4 HOH A 45 545 72 HOH HOH . G 4 HOH A 46 546 78 HOH HOH . G 4 HOH A 47 547 80 HOH HOH . G 4 HOH A 48 548 81 HOH HOH . G 4 HOH A 49 549 82 HOH HOH . G 4 HOH A 50 550 83 HOH HOH . G 4 HOH A 51 551 86 HOH HOH . G 4 HOH A 52 552 89 HOH HOH . G 4 HOH A 53 553 90 HOH HOH . G 4 HOH A 54 554 92 HOH HOH . G 4 HOH A 55 555 97 HOH HOH . H 4 HOH B 1 501 3 HOH HOH . H 4 HOH B 2 502 5 HOH HOH . H 4 HOH B 3 503 8 HOH HOH . H 4 HOH B 4 504 18 HOH HOH . H 4 HOH B 5 505 20 HOH HOH . H 4 HOH B 6 506 21 HOH HOH . H 4 HOH B 7 507 27 HOH HOH . H 4 HOH B 8 508 29 HOH HOH . H 4 HOH B 9 509 30 HOH HOH . H 4 HOH B 10 510 32 HOH HOH . H 4 HOH B 11 511 37 HOH HOH . H 4 HOH B 12 512 39 HOH HOH . H 4 HOH B 13 513 41 HOH HOH . H 4 HOH B 14 514 42 HOH HOH . H 4 HOH B 15 515 47 HOH HOH . H 4 HOH B 16 516 48 HOH HOH . H 4 HOH B 17 517 49 HOH HOH . H 4 HOH B 18 518 50 HOH HOH . H 4 HOH B 19 519 53 HOH HOH . H 4 HOH B 20 520 54 HOH HOH . H 4 HOH B 21 521 58 HOH HOH . H 4 HOH B 22 522 61 HOH HOH . H 4 HOH B 23 523 63 HOH HOH . H 4 HOH B 24 524 65 HOH HOH . H 4 HOH B 25 525 67 HOH HOH . H 4 HOH B 26 526 68 HOH HOH . H 4 HOH B 27 527 70 HOH HOH . H 4 HOH B 28 528 73 HOH HOH . H 4 HOH B 29 529 74 HOH HOH . H 4 HOH B 30 530 75 HOH HOH . H 4 HOH B 31 531 76 HOH HOH . H 4 HOH B 32 532 77 HOH HOH . H 4 HOH B 33 533 79 HOH HOH . H 4 HOH B 34 534 84 HOH HOH . H 4 HOH B 35 535 85 HOH HOH . H 4 HOH B 36 536 87 HOH HOH . H 4 HOH B 37 537 88 HOH HOH . H 4 HOH B 38 538 91 HOH HOH . H 4 HOH B 39 539 93 HOH HOH . H 4 HOH B 40 540 94 HOH HOH . H 4 HOH B 41 541 95 HOH HOH . H 4 HOH B 42 542 96 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 . . . C 2 199.016 188.562 104.442 1 52.82 ? C1 NAG 401 A 1 HETATM 2 C C2 NAG . . . C 2 199.931 187.459 104.994 1 54.3 ? C2 NAG 401 A 1 HETATM 3 C C3 NAG . . . C 2 200.404 187.813 106.412 1 56.83 ? C3 NAG 401 A 1 HETATM 4 C C4 NAG . . . C 2 201.062 189.194 106.415 1 58.57 ? C4 NAG 401 A 1 HETATM 5 C C5 NAG . . . C 2 200.102 190.234 105.82 1 57.83 ? C5 NAG 401 A 1 HETATM 6 C C6 NAG . . . C 2 200.769 191.594 105.703 1 57.36 ? C6 NAG 401 A 1 HETATM 7 C C7 NAG . . . C 2 199.916 185.059 104.819 1 55.95 ? C7 NAG 401 A 1 HETATM 8 C C8 NAG . . . C 2 200.136 184.186 106.044 1 56.02 ? C8 NAG 401 A 1 HETATM 9 N N2 NAG . . . C 2 199.236 186.188 105 1 54.16 ? N2 NAG 401 A 1 HETATM 10 O O3 NAG . . . C 2 201.345 186.846 106.861 1 57.73 ? O3 NAG 401 A 1 HETATM 11 O O4 NAG . . . C 2 201.425 189.562 107.742 1 58.83 ? O4 NAG 401 A 1 HETATM 12 O O5 NAG . . . C 2 199.696 189.836 104.482 1 56.09 ? O5 NAG 401 A 1 HETATM 13 O O6 NAG . . . C 2 199.866 192.576 105.217 1 58.98 ? O6 NAG 401 A 1 HETATM 14 O O7 NAG . . . C 2 200.367 184.709 103.723 1 56.52 ? O7 NAG 401 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #