data_5SVK # _model_server_result.job_id S7_9NgM5HZ8MN-Tn99qLJg _model_server_result.datetime_utc '2024-11-04 22:42:41' _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 5svk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":404}' # _entry.id 5SVK # _exptl.entry_id 5SVK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 7 _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 5SVK _cell.length_a 173.15 _cell.length_b 173.15 _cell.length_c 173.15 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SVK _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 PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,C,D,G,H,I,J,K,L,M,S 1 1,2,4 B,E,F,N,O,P,Q,R,T 2 1,3,5 # 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 6_577 z+1/2,-x+5/2,-y+2 0 0 1 -1 0 0 0 -1 0 86.575 432.875 346.3 4 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 5 'crystal symmetry operation' 12_774 -y+5/2,-z+2,x-1/2 0 -1 0 0 0 -1 1 0 0 432.875 346.3 -86.575 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 O N N ? 4 P N N ? 4 Q N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 GLC _pdbx_entity_branch_link.comp_id_2 GLC _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 2 n C GLC 1 C 1 GLC A 504 MAL 2 n C GLC 2 C 2 GLC A 504 MAL 2 n D GLC 1 D 1 GLC J 2 MAL 2 n D GLC 2 D 2 GLC J 2 MAL 2 n E GLC 1 E 1 GLC B 503 MAL 2 n E GLC 2 E 2 GLC B 503 MAL 2 n F GLC 1 F 1 GLC J 1 MAL 2 n F GLC 2 F 2 GLC J 1 MAL # 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 106 A CYS 107 1_555 A SG CYS 152 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 121 A CYS 122 1_555 A SG CYS 146 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 202 A CYS 203 1_555 A SG CYS 212 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 246 A CYS 247 1_555 A SG CYS 255 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 B SG CYS 106 B CYS 107 1_555 B SG CYS 152 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 B SG CYS 115 B CYS 116 1_555 B SG CYS 136 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 B SG CYS 121 B CYS 122 1_555 B SG CYS 146 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 B SG CYS 202 B CYS 203 1_555 B SG CYS 212 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf10 B SG CYS 246 B CYS 247 1_555 B SG CYS 255 B CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 138 A ASN 139 1_555 K C1 NAG . A NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 A ND2 ASN 169 A ASN 170 1_555 H C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale3 A ND2 ASN 193 A ASN 194 1_555 I C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 A ND2 ASN 289 A ASN 290 1_555 J C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 B ND2 ASN 169 B ASN 170 1_555 O C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale6 B ND2 ASN 193 B ASN 194 1_555 P C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale7 B ND2 ASN 289 B ASN 290 1_555 Q C1 NAG . B NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale8 C O4 GLC . C GLC 1 1_555 C C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 sing covale ? covale9 D O4 GLC . D GLC 1 1_555 D C1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 sing covale ? covale10 E O4 GLC . E GLC 1 1_555 E C1 GLC . E GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 sing covale ? covale11 F O4 GLC . F GLC 1 1_555 F C1 GLC . F GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 sing # _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 ? # 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 5SVK _atom_sites.fract_transf_matrix[1][1] 0.005775 _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] 0.005775 _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] 0.005775 _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 G 3 ATP A 1 401 402 ATP ATP . H 4 NAG A 1 402 500 NAG NAG . I 4 NAG A 1 403 501 NAG NAG . J 4 NAG A 1 404 502 NAG NAG . K 4 NAG A 1 405 503 NAG NAG . L 5 EDO A 1 408 1 EDO EDO . M 6 MHA A 1 409 1 MHA LIG . N 3 ATP B 1 401 402 ATP ATP . O 4 NAG B 1 402 500 NAG NAG . P 4 NAG B 1 403 501 NAG NAG . Q 4 NAG B 1 404 502 NAG NAG . R 5 EDO B 1 407 2 EDO EDO . S 7 HOH A 1 501 33 HOH HOH . S 7 HOH A 2 502 60 HOH HOH . S 7 HOH A 3 503 23 HOH HOH . S 7 HOH A 4 504 22 HOH HOH . S 7 HOH A 5 505 8 HOH HOH . S 7 HOH A 6 506 1 HOH HOH . S 7 HOH A 7 507 55 HOH HOH . S 7 HOH A 8 508 4 HOH HOH . S 7 HOH A 9 509 81 HOH HOH . S 7 HOH A 10 510 64 HOH HOH . S 7 HOH A 11 511 12 HOH HOH . S 7 HOH A 12 512 27 HOH HOH . S 7 HOH A 13 513 34 HOH HOH . S 7 HOH A 14 514 17 HOH HOH . S 7 HOH A 15 515 53 HOH HOH . S 7 HOH A 16 516 14 HOH HOH . S 7 HOH A 17 517 68 HOH HOH . S 7 HOH A 18 518 5 HOH HOH . S 7 HOH A 19 519 13 HOH HOH . S 7 HOH A 20 520 16 HOH HOH . S 7 HOH A 21 521 56 HOH HOH . S 7 HOH A 22 522 28 HOH HOH . S 7 HOH A 23 523 26 HOH HOH . S 7 HOH A 24 524 31 HOH HOH . S 7 HOH A 25 525 9 HOH HOH . S 7 HOH A 26 526 80 HOH HOH . S 7 HOH A 27 527 3 HOH HOH . S 7 HOH A 28 528 32 HOH HOH . S 7 HOH A 29 529 20 HOH HOH . S 7 HOH A 30 530 6 HOH HOH . S 7 HOH A 31 531 57 HOH HOH . S 7 HOH A 32 532 10 HOH HOH . S 7 HOH A 33 533 62 HOH HOH . S 7 HOH A 34 534 7 HOH HOH . S 7 HOH A 35 535 71 HOH HOH . S 7 HOH A 36 536 19 HOH HOH . S 7 HOH A 37 537 70 HOH HOH . S 7 HOH A 38 538 54 HOH HOH . S 7 HOH A 39 539 11 HOH HOH . T 7 HOH B 1 501 66 HOH HOH . T 7 HOH B 2 502 75 HOH HOH . T 7 HOH B 3 503 36 HOH HOH . T 7 HOH B 4 504 47 HOH HOH . T 7 HOH B 5 505 45 HOH HOH . T 7 HOH B 6 506 42 HOH HOH . T 7 HOH B 7 507 82 HOH HOH . T 7 HOH B 8 508 46 HOH HOH . T 7 HOH B 9 509 41 HOH HOH . T 7 HOH B 10 510 39 HOH HOH . T 7 HOH B 11 511 61 HOH HOH . T 7 HOH B 12 512 63 HOH HOH . T 7 HOH B 13 513 49 HOH HOH . T 7 HOH B 14 514 67 HOH HOH . T 7 HOH B 15 515 74 HOH HOH . T 7 HOH B 16 516 59 HOH HOH . T 7 HOH B 17 517 48 HOH HOH . T 7 HOH B 18 518 77 HOH HOH . T 7 HOH B 19 519 43 HOH HOH . T 7 HOH B 20 520 65 HOH HOH . T 7 HOH B 21 521 69 HOH HOH . T 7 HOH B 22 522 72 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 4 207.871 228.853 132.13 1 133.98 ? C1 NAG 404 B 1 HETATM 2 C C2 NAG . . . Q 4 206.993 229.7 133.055 1 139.21 ? C2 NAG 404 B 1 HETATM 3 C C3 NAG . . . Q 4 205.768 228.873 133.462 1 134.47 ? C3 NAG 404 B 1 HETATM 4 C C4 NAG . . . Q 4 205.026 228.42 132.209 1 137.9 ? C4 NAG 404 B 1 HETATM 5 C C5 NAG . . . Q 4 205.973 227.611 131.318 1 136.41 ? C5 NAG 404 B 1 HETATM 6 C C6 NAG . . . Q 4 205.275 227.197 130.027 1 131.33 ? C6 NAG 404 B 1 HETATM 7 C C7 NAG . . . Q 4 208.876 231.006 133.925 1 147.38 ? C7 NAG 404 B 1 HETATM 8 C C8 NAG . . . Q 4 209.747 231.547 135.062 1 142.76 ? C8 NAG 404 B 1 HETATM 9 N N2 NAG . . . Q 4 207.808 230.21 134.167 1 145.53 ? N2 NAG 404 B 1 HETATM 10 O O3 NAG . . . Q 4 204.905 229.629 134.323 1 117.39 ? O3 NAG 404 B 1 HETATM 11 O O4 NAG . . . Q 4 203.865 227.653 132.566 1 133.05 ? O4 NAG 404 B 1 HETATM 12 O O5 NAG . . . Q 4 207.139 228.378 130.994 1 141.2 ? O5 NAG 404 B 1 HETATM 13 O O6 NAG . . . Q 4 206.213 226.561 129.152 1 137.59 ? O6 NAG 404 B 1 HETATM 14 O O7 NAG . . . Q 4 209.146 231.295 132.762 1 149.53 ? O7 NAG 404 B 1 HETATM 15 H H1 NAG . . . Q 4 208.262 227.994 132.696 1 160.78 ? H1 NAG 404 B 1 HETATM 16 H H2 NAG . . . Q 4 206.637 230.571 132.482 1 167.05 ? H2 NAG 404 B 1 HETATM 17 H H3 NAG . . . Q 4 206.128 227.982 133.999 1 161.37 ? H3 NAG 404 B 1 HETATM 18 H H4 NAG . . . Q 4 204.696 229.312 131.652 1 165.48 ? H4 NAG 404 B 1 HETATM 19 H H5 NAG . . . Q 4 206.28 226.694 131.847 1 163.69 ? H5 NAG 404 B 1 HETATM 20 H H61 NAG . . . Q 4 204.852 228.076 129.537 1 157.6 ? H61 NAG 404 B 1 HETATM 21 H H62 NAG . . . Q 4 204.458 226.509 130.255 1 157.6 ? H62 NAG 404 B 1 HETATM 22 H H81 NAG . . . Q 4 210.747 231.218 134.929 1 171.31 ? H81 NAG 404 B 1 HETATM 23 H H82 NAG . . . Q 4 209.435 231.243 136.033 1 171.31 ? H82 NAG 404 B 1 HETATM 24 H H83 NAG . . . Q 4 209.737 232.608 135.04 1 171.31 ? H83 NAG 404 B 1 HETATM 25 H HN2 NAG . . . Q 4 207.573 229.962 135.126 1 174.63 ? HN2 NAG 404 B 1 HETATM 26 H HO3 NAG . . . Q 4 204.912 229.242 135.209 1 140.87 ? HO3 NAG 404 B 1 HETATM 27 H HO4 NAG . . . Q 4 203.193 228.24 132.939 1 159.66 ? HO4 NAG 404 B 1 HETATM 28 H HO6 NAG . . . Q 4 206.306 227.085 128.344 1 165.11 ? HO6 NAG 404 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #