data_8KDD # _model_server_result.job_id PHIWDifVB5fsYwaxPwKFVQ _model_server_result.datetime_utc '2025-03-12 17:43:25' _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 8kdd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":601}' # _entry.id 8KDD # _exptl.entry_id 8KDD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 472.321 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Nanvuranlat _entity.pdbx_number_of_molecules 1 _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 8KDD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8KDD _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 211 A CYS 210 1_555 B SG CYS 164 B CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? disulf ? disulf2 C SG CYS 23 L CYS 23 1_555 C SG CYS 94 L CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? disulf ? disulf3 C SG CYS 140 L CYS 140 1_555 C SG CYS 200 L CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 D SG CYS 22 H CYS 22 1_555 D SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf5 D SG CYS 147 H CYS 147 1_555 D SG CYS 202 H CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? covale ? covale1 A ND2 ASN 366 A ASN 365 1_555 G C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 382 A ASN 381 1_555 E C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 A ND2 ASN 425 A ASN 424 1_555 H C1 NAG . A NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 A ND2 ASN 507 A ASN 506 1_555 F C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? # _chem_comp.formula 'C23 H19 Cl2 N3 O4' _chem_comp.formula_weight 472.321 _chem_comp.id VRW _chem_comp.mon_nstd_flag . _chem_comp.name Nanvuranlat _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(2~{S})-2-azanyl-3-[4-[(5-azanyl-2-phenyl-1,3-benzoxazol-7-yl)methoxy]-3,5-bis(chloranyl)phenyl]propanoic acid' # 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 CL2 C16 VRW sing 404 n n C14 O2 VRW sing 405 n n C14 C12 VRW sing 406 n n O2 C15 VRW sing 407 n n C11 C12 VRW doub 408 n y C11 C10 VRW sing 409 n y C16 C15 VRW doub 410 n y C16 C17 VRW sing 411 n y C12 C13 VRW sing 412 n y C15 C20 VRW sing 413 n y N3 C10 VRW sing 414 n n C10 C9 VRW doub 415 n y C17 C18 VRW doub 416 n y C20 CL1 VRW sing 417 n n C20 C19 VRW doub 418 n y C13 O1 VRW sing 419 n y C13 C8 VRW doub 420 n y O1 C7 VRW sing 421 n y C18 C19 VRW sing 422 n y C18 C21 VRW sing 423 n n C9 C8 VRW sing 424 n y N2 C22 VRW sing 425 n n C8 N1 VRW sing 426 n y C22 C21 VRW sing 427 n n C22 C23 VRW sing 428 n n C7 N1 VRW doub 429 n y C7 C4 VRW sing 430 n n C5 C4 VRW doub 431 n y C5 C6 VRW sing 432 n y C23 O3 VRW doub 433 n n C23 O4 VRW sing 434 n n C4 C3 VRW sing 435 n y C6 C1 VRW doub 436 n y C3 C2 VRW doub 437 n y C1 C2 VRW sing 438 n y N3 H1 VRW sing 439 n n N3 H2 VRW sing 440 n n C5 H3 VRW sing 441 n n C6 H4 VRW sing 442 n n C2 H5 VRW sing 443 n n C1 H6 VRW sing 444 n n C3 H7 VRW sing 445 n n C9 H8 VRW sing 446 n n C11 H9 VRW sing 447 n n C14 H10 VRW sing 448 n n C14 H11 VRW sing 449 n n C17 H12 VRW sing 450 n n C19 H13 VRW sing 451 n n C21 H14 VRW sing 452 n n C21 H15 VRW sing 453 n n C22 H16 VRW sing 454 n n O4 H17 VRW sing 455 n n N2 H18 VRW sing 456 n n N2 H19 VRW sing 457 n n # _atom_sites.entry_id 8KDD _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 E 5 NAG A 1 701 631 NAG NAG . F 5 NAG A 1 702 632 NAG NAG . G 5 NAG A 1 703 634 NAG NAG . H 5 NAG A 1 704 635 NAG NAG . I 6 VRW B 1 601 601 VRW JPH . # 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 N N1 VRW . . . I 6 97.682 100.873 87.881 1 189.97 ? N1 VRW 601 B 1 HETATM 2 N N3 VRW . . . I 6 94.246 102.812 84.936 1 265.38 ? N3 VRW 601 B 1 HETATM 3 C C4 VRW . . . I 6 99.569 99.361 88.357 1 174.93 ? C4 VRW 601 B 1 HETATM 4 C C5 VRW . . . I 6 100.538 98.531 87.762 1 199.28 ? C5 VRW 601 B 1 HETATM 5 C C6 VRW . . . I 6 101.563 97.991 88.535 1 238.76 ? C6 VRW 601 B 1 HETATM 6 C C2 VRW . . . I 6 100.681 99.119 90.476 1 214.41 ? C2 VRW 601 B 1 HETATM 7 C C1 VRW . . . I 6 101.636 98.285 89.889 1 239.58 ? C1 VRW 601 B 1 HETATM 8 C C3 VRW . . . I 6 99.65 99.67 89.721 1 138.84 ? C3 VRW 601 B 1 HETATM 9 C C7 VRW . . . I 6 98.52 99.941 87.544 1 168.73 ? C7 VRW 601 B 1 HETATM 10 C C8 VRW . . . I 6 96.918 101.092 86.732 1 210.72 ? C8 VRW 601 B 1 HETATM 11 C C9 VRW . . . I 6 95.87 101.973 86.491 1 217.18 ? C9 VRW 601 B 1 HETATM 12 C C10 VRW . . . I 6 95.295 101.957 85.226 1 260.66 ? C10 VRW 601 B 1 HETATM 13 C C11 VRW . . . I 6 95.757 101.081 84.215 1 291.39 ? C11 VRW 601 B 1 HETATM 14 C C12 VRW . . . I 6 96.808 100.199 84.455 1 284.66 ? C12 VRW 601 B 1 HETATM 15 C C13 VRW . . . I 6 97.371 100.236 85.73 1 212.62 ? C13 VRW 601 B 1 HETATM 16 O O1 VRW . . . I 6 98.408 99.497 86.257 1 172.95 ? O1 VRW 601 B 1 HETATM 17 C C14 VRW . . . I 6 97.29 99.27 83.368 1 313.76 ? C14 VRW 601 B 1 HETATM 18 O O2 VRW . . . I 6 96.679 97.964 83.515 1 228.88 ? O2 VRW 601 B 1 HETATM 19 C C15 VRW . . . I 6 97.2 97.127 84.472 1 138.02 ? C15 VRW 601 B 1 HETATM 20 C C16 VRW . . . I 6 98.436 96.489 84.323 1 143.06 ? C16 VRW 601 B 1 HETATM 21 C C17 VRW . . . I 6 98.96 95.681 85.288 1 157.87 ? C17 VRW 601 B 1 HETATM 22 C C18 VRW . . . I 6 98.282 95.46 86.469 1 179.65 ? C18 VRW 601 B 1 HETATM 23 C C19 VRW . . . I 6 97.054 96.089 86.669 1 215.61 ? C19 VRW 601 B 1 HETATM 24 C C20 VRW . . . I 6 96.519 96.913 85.7 1 215.3 ? C20 VRW 601 B 1 HETATM 25 CL CL1 VRW . . . I 6 94.979 97.667 86.004 1 329.86 ? CL1 VRW 601 B 1 HETATM 26 C C21 VRW . . . I 6 98.892 94.546 87.507 1 215.49 ? C21 VRW 601 B 1 HETATM 27 C C22 VRW . . . I 6 99.45 93.209 86.983 1 195.05 ? C22 VRW 601 B 1 HETATM 28 C C23 VRW . . . I 6 100.317 92.51 88.037 1 216.21 ? C23 VRW 601 B 1 HETATM 29 O O3 VRW . . . I 6 100.139 91.286 88.178 1 207.71 ? O3 VRW 601 B 1 HETATM 30 O O4 VRW . . . I 6 101.162 93.197 88.676 1 258.62 ? O4 VRW 601 B 1 HETATM 31 N N2 VRW . . . I 6 98.342 92.315 86.535 1 167.4 ? N2 VRW 601 B 1 HETATM 32 CL CL2 VRW . . . I 6 99.408 96.659 82.904 1 362.72 ? CL2 VRW 601 B 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 435 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #