data_5SVK # _model_server_result.job_id 3TfZfenMHOD7bWQeTDV6bQ _model_server_result.datetime_utc '2024-11-26 21:47:12' _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":"H","auth_seq_id":402}' # _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 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 341 n n C1 O1 NAG sing 342 n n C1 O5 NAG sing 343 n n C1 H1 NAG sing 344 n n C2 C3 NAG sing 345 n n C2 N2 NAG sing 346 n n C2 H2 NAG sing 347 n n C3 C4 NAG sing 348 n n C3 O3 NAG sing 349 n n C3 H3 NAG sing 350 n n C4 C5 NAG sing 351 n n C4 O4 NAG sing 352 n n C4 H4 NAG sing 353 n n C5 C6 NAG sing 354 n n C5 O5 NAG sing 355 n n C5 H5 NAG sing 356 n n C6 O6 NAG sing 357 n n C6 H61 NAG sing 358 n n C6 H62 NAG sing 359 n n C7 C8 NAG sing 360 n n C7 N2 NAG sing 361 n n C7 O7 NAG doub 362 n n C8 H81 NAG sing 363 n n C8 H82 NAG sing 364 n n C8 H83 NAG sing 365 n n N2 HN2 NAG sing 366 n n O1 HO1 NAG sing 367 n n O3 HO3 NAG sing 368 n n O4 HO4 NAG sing 369 n n O6 HO6 NAG sing 370 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 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 . . . H 4 211.521 196.987 170.632 1 53.01 ? C1 NAG 402 A 1 HETATM 2 C C2 NAG . . . H 4 211.895 195.651 170.009 1 62.86 ? C2 NAG 402 A 1 HETATM 3 C C3 NAG . . . H 4 212.898 195.86 168.879 1 69.99 ? C3 NAG 402 A 1 HETATM 4 C C4 NAG . . . H 4 212.355 196.851 167.859 1 59.23 ? C4 NAG 402 A 1 HETATM 5 C C5 NAG . . . H 4 211.915 198.144 168.541 1 65.39 ? C5 NAG 402 A 1 HETATM 6 C C6 NAG . . . H 4 211.174 199.071 167.605 1 58.96 ? C6 NAG 402 A 1 HETATM 7 C C7 NAG . . . H 4 211.931 193.515 171.219 1 73.88 ? C7 NAG 402 A 1 HETATM 8 C C8 NAG . . . H 4 212.613 192.702 172.277 1 87.53 ? C8 NAG 402 A 1 HETATM 9 N N2 NAG . . . H 4 212.433 194.736 171.003 1 64.62 ? N2 NAG 402 A 1 HETATM 10 O O3 NAG . . . H 4 213.166 194.614 168.247 1 77.52 ? O3 NAG 402 A 1 HETATM 11 O O4 NAG . . . H 4 213.367 197.159 166.907 1 91.44 ? O4 NAG 402 A 1 HETATM 12 O O5 NAG . . . H 4 211.017 197.863 169.624 1 64.09 ? O5 NAG 402 A 1 HETATM 13 O O6 NAG . . . H 4 210.4 200.025 168.321 1 86.74 ? O6 NAG 402 A 1 HETATM 14 O O7 NAG . . . H 4 210.967 193.087 170.59 1 79 ? O7 NAG 402 A 1 HETATM 15 H H1 NAG . . . H 4 212.313 197.386 171.039 1 63.62 ? H1 NAG 402 A 1 HETATM 16 H H2 NAG . . . H 4 211.089 195.255 169.626 1 75.43 ? H2 NAG 402 A 1 HETATM 17 H H3 NAG . . . H 4 213.729 196.212 169.253 1 83.99 ? H3 NAG 402 A 1 HETATM 18 H H4 NAG . . . H 4 211.591 196.454 167.4 1 71.07 ? H4 NAG 402 A 1 HETATM 19 H H5 NAG . . . H 4 212.702 198.604 168.889 1 78.47 ? H5 NAG 402 A 1 HETATM 20 H H61 NAG . . . H 4 210.583 198.544 167.036 1 70.76 ? H61 NAG 402 A 1 HETATM 21 H H62 NAG . . . H 4 211.821 199.541 167.045 1 70.76 ? H62 NAG 402 A 1 HETATM 22 H H81 NAG . . . H 4 212.562 193.171 173.132 1 105.03 ? H81 NAG 402 A 1 HETATM 23 H H82 NAG . . . H 4 212.173 191.835 172.355 1 105.03 ? H82 NAG 402 A 1 HETATM 24 H H83 NAG . . . H 4 213.549 192.572 172.034 1 105.03 ? H83 NAG 402 A 1 HETATM 25 H HN2 NAG . . . H 4 213.151 195.004 171.497 1 77.55 ? HN2 NAG 402 A 1 HETATM 26 H HO3 NAG . . . H 4 213.385 194.011 168.861 1 93.02 ? HO3 NAG 402 A 1 HETATM 27 H HO4 NAG . . . H 4 213.91 197.778 167.241 1 109.72 ? HO4 NAG 402 A 1 HETATM 28 H HO6 NAG . . . H 4 210.301 199.755 169.161 1 104.08 ? HO6 NAG 402 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #