data_7KHR # _model_server_result.job_id tX4rU5p57Ro37vyq_MzExQ _model_server_result.datetime_utc '2024-10-20 19:10:53' _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 7khr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"GB","auth_seq_id":201}' # _entry.id 7KHR # _exptl.entry_id 7KHR _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 622.83 _entity.id 25 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 32-meric _pdbx_struct_assembly.oligomeric_count 32 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? _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 ? 25 AB N N ? 25 BB N N ? 25 DB N N ? 25 EB N N ? 25 FB N N ? 25 GB N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 17 oligosaccharide 18 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 17 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 17 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 17 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 17 5 4 MAN MAN C1 O1 . O2 HO2 . sing 5 ? 17 6 5 MAN MAN C1 O1 . O2 HO2 . sing 6 ? 17 7 6 GLC MAN C1 O1 . O3 HO3 . sing 7 ? 17 8 7 GLC GLC C1 O1 . O3 HO3 . sing 8 ? 17 9 8 GLC GLC C1 O1 . O2 HO2 . sing 9 ? 18 2 1 MAN MAN C1 O1 . O6 HO6 . 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 17 n GA NAG 1 t 1 NAG t 1 NAG 17 n GA NAG 2 t 2 NAG t 2 NAG 17 n GA BMA 3 t 3 BMA t 3 BMA 17 n GA MAN 4 t 4 MAN t 4 MAN 17 n GA MAN 5 t 5 MAN t 5 MAN 17 n GA MAN 6 t 6 MAN t 6 MAN 17 n GA GLC 7 t 7 GLC t 7 GLC 17 n GA GLC 8 t 8 GLC t 8 GLC 17 n GA GLC 9 t 9 GLC t 9 GLC 18 n HA MAN 1 Q 1 MAN t 10 MAN 18 n HA MAN 2 Q 2 MAN t 11 MAN # 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 U SG CYS 369 s CYS 369 1_555 U SG CYS 416 s CYS 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 U ND2 ASN 258 s ASN 258 1_555 VA C1 NAG . s NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 U ND2 ASN 271 s ASN 271 1_555 PA C1 NAG . s NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 U ND2 ASN 301 s ASN 301 1_555 RA C1 NAG . s NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.305 ? covale ? covale4 U ND2 ASN 348 s ASN 348 1_555 SA C1 NAG . s NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale5 U ND2 ASN 355 s ASN 355 1_555 TA C1 NAG . s NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.545 ? covale ? covale6 GA O4 NAG . t NAG 1 1_555 GA C1 NAG . t NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale7 GA O4 NAG . t NAG 2 1_555 GA C1 BMA . t BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 GA O3 BMA . t BMA 3 1_555 GA C1 MAN . t MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 GA O2 MAN . t MAN 4 1_555 GA C1 MAN . t MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale10 GA O2 MAN . t MAN 5 1_555 GA C1 MAN . t MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale11 GA O3 MAN . t MAN 6 1_555 GA C1 GLC . t GLC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale12 GA O3 GLC . t GLC 7 1_555 GA C1 GLC . t GLC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale13 GA O2 GLC . t GLC 8 1_555 GA C1 GLC . t GLC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale14 HA O6 MAN . Q MAN 1 1_555 HA C1 MAN . Q MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? metalc ? metalc1 C OG1 THR 257 C THR 257 1_555 IA MG MG . C MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc2 C OE1 GLU 283 C GLU 283 1_555 IA MG MG . C MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? metalc ? metalc3 C OE2 GLU 283 C GLU 283 1_555 IA MG MG . C MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc4 IA MG MG . C MG 701 1_555 JA O3B ADP . C ADP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? # _chem_comp.formula 'C35 H58 O9' _chem_comp.formula_weight 622.83 _chem_comp.id WEV _chem_comp.mon_nstd_flag . _chem_comp.name (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 7KHR _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 IA 19 MG C 1 701 1 MG MG . JA 20 ADP C 1 702 2 ADP ADP . KA 21 WJP a 1 901 46 WJP WJP . LA 22 POV b 1 301 7 POV POV . MA 22 POV b 1 302 8 POV POV . NA 22 POV s 1 501 2 POV POV . OA 22 POV s 1 502 3 POV POV . PA 23 NAG s 1 503 501 NAG NAG . QA 23 NAG s 1 504 502 NAG NAG . RA 23 NAG s 1 505 503 NAG NAG . SA 23 NAG s 1 506 504 NAG NAG . TA 23 NAG s 1 507 505 NAG NAG . UA 23 NAG s 1 508 506 NAG NAG . VA 23 NAG s 1 509 507 NAG NAG . WA 22 POV r 1 401 1 POV POV . XA 22 POV r 1 402 4 POV POV . YA 22 POV r 1 403 5 POV POV . ZA 24 OLA r 1 404 102 OLA OLA . AB 25 WEV g 1 201 2 WEV OCN . BB 25 WEV g 1 202 3 WEV OCN . CB 22 POV l 1 201 6 POV POV . DB 25 WEV l 1 202 4 WEV OCN . EB 25 WEV m 1 201 5 WEV OCN . FB 25 WEV o 1 201 6 WEV OCN . GB 25 WEV p 1 201 7 WEV OCN . # 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 C43 WEV . . . GB 25 261.307 262.9 196.483 1 37.4 ? C43 WEV 201 p 1 HETATM 2 C C01 WEV . . . GB 25 261.487 262.827 189.025 1 37.4 ? C01 WEV 201 p 1 HETATM 3 C C02 WEV . . . GB 25 261.842 264.297 189.104 1 37.4 ? C02 WEV 201 p 1 HETATM 4 C C03 WEV . . . GB 25 262.48 264.549 190.438 1 37.4 ? C03 WEV 201 p 1 HETATM 5 C C04 WEV . . . GB 25 263.045 263.337 191.058 1 37.4 ? C04 WEV 201 p 1 HETATM 6 C C05 WEV . . . GB 25 262.689 263.22 192.292 1 37.4 ? C05 WEV 201 p 1 HETATM 7 C C06 WEV . . . GB 25 261.802 264.244 192.969 1 37.4 ? C06 WEV 201 p 1 HETATM 8 C C07 WEV . . . GB 25 261.24 263.646 193.93 1 37.4 ? C07 WEV 201 p 1 HETATM 9 C C08 WEV . . . GB 25 260.245 264.194 194.938 1 37.4 ? C08 WEV 201 p 1 HETATM 10 C C09 WEV . . . GB 25 258.902 263.357 195.175 1 37.4 ? C09 WEV 201 p 1 HETATM 11 C C11 WEV . . . GB 25 257.562 265.028 193.934 1 37.4 ? C11 WEV 201 p 1 HETATM 12 C C13 WEV . . . GB 25 257.49 265.406 192.468 1 37.4 ? C13 WEV 201 p 1 HETATM 13 C C14 WEV . . . GB 25 258.494 265.734 191.675 1 37.4 ? C14 WEV 201 p 1 HETATM 14 C C15 WEV . . . GB 25 258.343 266.215 190.217 1 37.4 ? C15 WEV 201 p 1 HETATM 15 C C16 WEV . . . GB 25 259.099 266.599 189.265 1 37.4 ? C16 WEV 201 p 1 HETATM 16 C C17 WEV . . . GB 25 260.485 266.328 188.71 1 37.4 ? C17 WEV 201 p 1 HETATM 17 C C18 WEV . . . GB 25 260.502 264.95 189.068 1 37.4 ? C18 WEV 201 p 1 HETATM 18 C C20 WEV . . . GB 25 261.725 266.987 189.231 1 37.4 ? C20 WEV 201 p 1 HETATM 19 C C21 WEV . . . GB 25 257.022 266.763 189.869 1 37.4 ? C21 WEV 201 p 1 HETATM 20 C C23 WEV . . . GB 25 255.425 266.242 192.854 1 37.4 ? C23 WEV 201 p 1 HETATM 21 C C24 WEV . . . GB 25 258.462 262.97 196.593 1 37.4 ? C24 WEV 201 p 1 HETATM 22 C C25 WEV . . . GB 25 258.92 264.094 197.491 1 37.4 ? C25 WEV 201 p 1 HETATM 23 C C26 WEV . . . GB 25 256.935 262.812 196.797 1 37.4 ? C26 WEV 201 p 1 HETATM 24 C C27 WEV . . . GB 25 256.39 261.799 197.774 1 37.4 ? C27 WEV 201 p 1 HETATM 25 C C28 WEV . . . GB 25 255.642 262.706 198.677 1 37.4 ? C28 WEV 201 p 1 HETATM 26 C C29 WEV . . . GB 25 257.376 261.105 198.711 1 37.4 ? C29 WEV 201 p 1 HETATM 27 C C30 WEV . . . GB 25 256.738 260.703 200.015 1 37.4 ? C30 WEV 201 p 1 HETATM 28 C C31 WEV . . . GB 25 257.66 259.938 200.899 1 37.4 ? C31 WEV 201 p 1 HETATM 29 C C32 WEV . . . GB 25 258.333 258.884 200.145 1 37.4 ? C32 WEV 201 p 1 HETATM 30 C C33 WEV . . . GB 25 259.097 259.621 199.116 1 37.4 ? C33 WEV 201 p 1 HETATM 31 C C35 WEV . . . GB 25 260.231 258.981 198.488 1 37.4 ? C35 WEV 201 p 1 HETATM 32 C C36 WEV . . . GB 25 260.684 259.959 197.44 1 37.4 ? C36 WEV 201 p 1 HETATM 33 C C37 WEV . . . GB 25 261.401 259.046 199.424 1 37.4 ? C37 WEV 201 p 1 HETATM 34 C C38 WEV . . . GB 25 259.314 258.185 201.134 1 37.4 ? C38 WEV 201 p 1 HETATM 35 C C44 WEV . . . GB 25 263.951 262.414 190.313 1 37.4 ? C44 WEV 201 p 1 HETATM 36 O O10 WEV . . . GB 25 257.678 263.786 194.516 1 37.4 ? O10 WEV 201 p 1 HETATM 37 O O12 WEV . . . GB 25 257.403 265.89 194.651 1 37.4 ? O12 WEV 201 p 1 HETATM 38 O O19 WEV . . . GB 25 259.918 264.591 187.899 1 37.4 ? O19 WEV 201 p 1 HETATM 39 O O22 WEV . . . GB 25 256.206 265.431 192.03 1 37.4 ? O22 WEV 201 p 1 HETATM 40 O O34 WEV . . . GB 25 258.136 260.039 198.111 1 37.4 ? O34 WEV 201 p 1 HETATM 41 O O39 WEV . . . GB 25 256.968 259.444 202.089 1 37.4 ? O39 WEV 201 p 1 HETATM 42 O O40 WEV . . . GB 25 258.163 262.084 199.129 1 37.4 ? O40 WEV 201 p 1 HETATM 43 O O41 WEV . . . GB 25 256.452 262.538 195.591 1 37.4 ? O41 WEV 201 p 1 HETATM 44 O O42 WEV . . . GB 25 261.203 264.136 195.897 1 37.4 ? O42 WEV 201 p 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 401 _model_server_stats.query_time_ms 406 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 44 #