data_5VRN # _model_server_result.job_id WPczY1_O7pzOqWH1Pl_ocQ _model_server_result.datetime_utc '2024-10-19 22:18:19' _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 5vrn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":300}' # _entry.id 5VRN # _exptl.entry_id 5VRN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 957.495 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-4-[[5-[4-cyano-2-[(~{E})-hydroxyiminomethyl]phenoxy]-1-oxidanyl-3~{H}-2,1$l^{4}-benzoxaborol-1-yl]oxy]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate' _entity.pdbx_number_of_molecules 6 _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 5VRN _cell.length_a 81.66 _cell.length_b 100.94 _cell.length_c 377.82 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VRN _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # 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 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 ? monomeric 1 author_defined_assembly 5 ? monomeric 1 author_defined_assembly 6 PISA tetrameric 4 software_defined_assembly 7 PISA tetrameric 4 software_defined_assembly 8 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,G,M 1 1 B,H,N 2 1 C,I,O 3 1 D,J,P 4 1 E,K,Q 5 1 F,L,R 6 1 A,B,G,H,M,N 7 1,2 C,D,E,F,I,J,K,L,O,P,Q,R 8 1 # 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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 188.91 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N # _chem_comp.formula 'C36 H38 B N9 O18 P2 1' _chem_comp.formula_weight 957.495 _chem_comp.id 9JM _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-4-[[5-[4-cyano-2-[(~{E})-hydroxyiminomethyl]phenoxy]-1-oxidanyl-3~{H}-2,1$l^{4}-benzoxaborol-1-yl]oxy]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O2B C2B 9JM sing 1 n n O3B C3B 9JM sing 2 n n O1A PA 9JM doub 3 n n C3B C2B 9JM sing 4 n n C3B C4B 9JM sing 5 n n C2B C1B 9JM sing 6 n n PA O2A 9JM sing 7 n n PA O5B 9JM sing 8 n n PA O3 9JM sing 9 n n O5B C5B 9JM sing 10 n n C4B C5B 9JM sing 11 n n C4B O4B 9JM sing 12 n n C1B N9A 9JM sing 13 n n C1B O4B 9JM sing 14 n n O3 PN 9JM sing 15 n n O2N PN 9JM doub 16 n n N3A C4A 9JM doub 17 n y N3A C2A 9JM sing 18 n y N9A C4A 9JM sing 19 n y N9A C8A 9JM sing 20 n y C4A C5A 9JM sing 21 n y C2A N1A 9JM doub 22 n y C8A N7A 9JM doub 23 n y PN O1N 9JM sing 24 n n PN O5D 9JM sing 25 n n N1A C6A 9JM sing 26 n y C5A N7A 9JM sing 27 n y C5A C6A 9JM doub 28 n y C6A N6A 9JM sing 29 n n O5D C5D 9JM sing 30 n n C5D C4D 9JM sing 31 n n N7N C7N 9JM sing 32 n n O6 N2 9JM sing 33 n n C4D O4D 9JM sing 34 n n C4D C3D 9JM sing 35 n n C7N O7N 9JM doub 36 n n C7N C3N 9JM sing 37 n n N2 C1 9JM doub 38 e n C3 O2 9JM sing 39 n n C3 C4 9JM sing 40 n n O4D C1D 9JM sing 41 n n C1 C18 9JM sing 42 n n C3D C2D 9JM sing 43 n n C3D O3D 9JM sing 44 n n C2N C3N 9JM doub 45 n y C2N N1N 9JM sing 46 n y C15 C4 9JM doub 47 n y C15 C14 9JM sing 48 n y C3N C4N 9JM sing 49 n y O2 B1 9JM sing 50 n n C4 C5 9JM sing 51 n y C2D C1D 9JM sing 52 n n C2D O2D 9JM sing 53 n n C1D N1N 9JM sing 54 n n O4 C14 9JM sing 55 n n O4 C17 9JM sing 56 n n N1N C6N 9JM doub 57 n y C18 C17 9JM doub 58 n y C18 C19 9JM sing 59 n y C14 C13 9JM doub 60 n y C4N C5N 9JM doub 61 n y C5 B1 9JM sing 62 n n C5 C12 9JM doub 63 n y B1 O2D 9JM sing 64 n n B1 O1 9JM sing 65 n n C17 C22 9JM sing 66 n y C19 C20 9JM doub 67 n y C13 C12 9JM sing 68 n y C6N C5N 9JM sing 69 n y C22 C21 9JM doub 70 n y C20 C21 9JM sing 71 n y C20 C23 9JM sing 72 n n C23 N7 9JM trip 73 n n C3 H1 9JM sing 74 n n C3 H2 9JM sing 75 n n C12 H3 9JM sing 76 n n C13 H4 9JM sing 77 n n C19 H5 9JM sing 78 n n C21 H6 9JM sing 79 n n O2A H7 9JM sing 80 n n C5B H8 9JM sing 81 n n C5B H9 9JM sing 82 n n C4B H10 9JM sing 83 n n C1B H11 9JM sing 84 n n C8A H12 9JM sing 85 n n N6A H13 9JM sing 86 n n N6A H14 9JM sing 87 n n C2A H15 9JM sing 88 n n C2B H16 9JM sing 89 n n O2B H17 9JM sing 90 n n C3B H18 9JM sing 91 n n O3B H19 9JM sing 92 n n O1N H20 9JM sing 93 n n C5D H21 9JM sing 94 n n C5D H22 9JM sing 95 n n C4D H23 9JM sing 96 n n C3D H24 9JM sing 97 n n O3D H25 9JM sing 98 n n C2D H26 9JM sing 99 n n C1D H27 9JM sing 100 n n C2N H28 9JM sing 101 n n C6N H29 9JM sing 102 n n C5N H30 9JM sing 103 n n C4N H31 9JM sing 104 n n N7N H32 9JM sing 105 n n N7N H33 9JM sing 106 n n C15 H34 9JM sing 107 n n C22 H35 9JM sing 108 n n O1 H36 9JM sing 109 n n C1 H37 9JM sing 110 n n O6 H38 9JM sing 111 n n # _atom_sites.entry_id 5VRN _atom_sites.fract_transf_matrix[1][1] 0.012246 _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] 0.009907 _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] 0.002647 _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 2 9JM A 1 300 300 9JM 438 . H 2 9JM B 1 300 300 9JM 438 . I 2 9JM C 1 300 300 9JM 438 . J 2 9JM D 1 300 300 9JM 438 . K 2 9JM E 1 300 300 9JM 438 . L 2 9JM F 1 300 300 9JM 438 . M 3 HOH A 1 401 16 HOH HOH . M 3 HOH A 2 402 9 HOH HOH . M 3 HOH A 3 403 88 HOH HOH . M 3 HOH A 4 404 94 HOH HOH . M 3 HOH A 5 405 81 HOH HOH . M 3 HOH A 6 406 83 HOH HOH . M 3 HOH A 7 407 3 HOH HOH . M 3 HOH A 8 408 8 HOH HOH . M 3 HOH A 9 409 18 HOH HOH . M 3 HOH A 10 410 10 HOH HOH . M 3 HOH A 11 411 20 HOH HOH . M 3 HOH A 12 412 17 HOH HOH . M 3 HOH A 13 413 87 HOH HOH . M 3 HOH A 14 414 84 HOH HOH . M 3 HOH A 15 415 7 HOH HOH . M 3 HOH A 16 416 24 HOH HOH . M 3 HOH A 17 417 19 HOH HOH . M 3 HOH A 18 418 21 HOH HOH . M 3 HOH A 19 419 11 HOH HOH . M 3 HOH A 20 420 22 HOH HOH . M 3 HOH A 21 421 82 HOH HOH . M 3 HOH A 22 422 4 HOH HOH . M 3 HOH A 23 423 1 HOH HOH . M 3 HOH A 24 424 6 HOH HOH . M 3 HOH A 25 425 86 HOH HOH . M 3 HOH A 26 426 5 HOH HOH . M 3 HOH A 27 427 85 HOH HOH . M 3 HOH A 28 428 15 HOH HOH . M 3 HOH A 29 429 2 HOH HOH . M 3 HOH A 30 430 108 HOH HOH . M 3 HOH A 31 431 46 HOH HOH . M 3 HOH A 32 432 92 HOH HOH . N 3 HOH B 1 401 27 HOH HOH . N 3 HOH B 2 402 28 HOH HOH . N 3 HOH B 3 403 33 HOH HOH . N 3 HOH B 4 404 95 HOH HOH . N 3 HOH B 5 405 38 HOH HOH . N 3 HOH B 6 406 30 HOH HOH . N 3 HOH B 7 407 42 HOH HOH . N 3 HOH B 8 408 36 HOH HOH . N 3 HOH B 9 409 13 HOH HOH . N 3 HOH B 10 410 35 HOH HOH . N 3 HOH B 11 411 89 HOH HOH . N 3 HOH B 12 412 104 HOH HOH . N 3 HOH B 13 413 37 HOH HOH . N 3 HOH B 14 414 29 HOH HOH . N 3 HOH B 15 415 45 HOH HOH . N 3 HOH B 16 416 98 HOH HOH . N 3 HOH B 17 417 47 HOH HOH . N 3 HOH B 18 418 32 HOH HOH . N 3 HOH B 19 419 44 HOH HOH . N 3 HOH B 20 420 109 HOH HOH . N 3 HOH B 21 421 40 HOH HOH . N 3 HOH B 22 422 43 HOH HOH . N 3 HOH B 23 423 41 HOH HOH . N 3 HOH B 24 424 26 HOH HOH . N 3 HOH B 25 425 25 HOH HOH . N 3 HOH B 26 426 39 HOH HOH . N 3 HOH B 27 427 96 HOH HOH . N 3 HOH B 28 428 23 HOH HOH . N 3 HOH B 29 429 34 HOH HOH . N 3 HOH B 30 430 31 HOH HOH . N 3 HOH B 31 431 97 HOH HOH . O 3 HOH C 1 401 52 HOH HOH . O 3 HOH C 2 402 100 HOH HOH . O 3 HOH C 3 403 93 HOH HOH . O 3 HOH C 4 404 70 HOH HOH . O 3 HOH C 5 405 91 HOH HOH . O 3 HOH C 6 406 57 HOH HOH . O 3 HOH C 7 407 60 HOH HOH . O 3 HOH C 8 408 99 HOH HOH . O 3 HOH C 9 409 68 HOH HOH . O 3 HOH C 10 410 55 HOH HOH . O 3 HOH C 11 411 51 HOH HOH . O 3 HOH C 12 412 48 HOH HOH . O 3 HOH C 13 413 50 HOH HOH . O 3 HOH C 14 414 64 HOH HOH . O 3 HOH C 15 415 49 HOH HOH . O 3 HOH C 16 416 54 HOH HOH . O 3 HOH C 17 417 105 HOH HOH . O 3 HOH C 18 418 53 HOH HOH . O 3 HOH C 19 419 59 HOH HOH . P 3 HOH D 1 401 69 HOH HOH . P 3 HOH D 2 402 66 HOH HOH . P 3 HOH D 3 403 65 HOH HOH . P 3 HOH D 4 404 101 HOH HOH . P 3 HOH D 5 405 58 HOH HOH . P 3 HOH D 6 406 62 HOH HOH . P 3 HOH D 7 407 67 HOH HOH . P 3 HOH D 8 408 107 HOH HOH . P 3 HOH D 9 409 63 HOH HOH . P 3 HOH D 10 410 12 HOH HOH . P 3 HOH D 11 411 106 HOH HOH . Q 3 HOH E 1 401 71 HOH HOH . Q 3 HOH E 2 402 76 HOH HOH . Q 3 HOH E 3 403 75 HOH HOH . Q 3 HOH E 4 404 72 HOH HOH . Q 3 HOH E 5 405 77 HOH HOH . Q 3 HOH E 6 406 102 HOH HOH . Q 3 HOH E 7 407 74 HOH HOH . Q 3 HOH E 8 408 14 HOH HOH . Q 3 HOH E 9 409 73 HOH HOH . Q 3 HOH E 10 410 56 HOH HOH . R 3 HOH F 1 401 78 HOH HOH . R 3 HOH F 2 402 80 HOH HOH . R 3 HOH F 3 403 103 HOH HOH . R 3 HOH F 4 404 61 HOH HOH . R 3 HOH F 5 405 90 HOH HOH . R 3 HOH F 6 406 79 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 O O2A 9JM . . . L 2 10.681 65.84 46.64 1 37.49 ? O2A 9JM 300 F 1 HETATM 2 P PA 9JM . . . L 2 9.286 65.401 47.052 1 35.88 ? PA 9JM 300 F 1 HETATM 3 O O1A 9JM . . . L 2 8.381 66.335 47.818 1 34.62 ? O1A 9JM 300 F 1 HETATM 4 O O5B 9JM . . . L 2 9.455 64.068 47.883 1 36.07 ? O5B 9JM 300 F 1 HETATM 5 C C5B 9JM . . . L 2 10.644 63.332 47.809 1 36.05 ? C5B 9JM 300 F 1 HETATM 6 C C4B 9JM . . . L 2 11.04 63.038 49.212 1 37.45 ? C4B 9JM 300 F 1 HETATM 7 O O4B 9JM . . . L 2 12.172 62.194 49.213 1 37.82 ? O4B 9JM 300 F 1 HETATM 8 C C1B 9JM . . . L 2 12.881 62.511 50.402 1 38.13 ? C1B 9JM 300 F 1 HETATM 9 N N9A 9JM . . . L 2 14.231 61.973 50.394 1 37.46 ? N9A 9JM 300 F 1 HETATM 10 C C8A 9JM . . . L 2 15.138 62.047 49.398 1 37.18 ? C8A 9JM 300 F 1 HETATM 11 N N7A 9JM . . . L 2 16.305 61.398 49.8 1 37.88 ? N7A 9JM 300 F 1 HETATM 12 C C5A 9JM . . . L 2 16.096 60.929 51.047 1 37.34 ? C5A 9JM 300 F 1 HETATM 13 C C6A 9JM . . . L 2 16.891 60.18 52.021 1 38.42 ? C6A 9JM 300 F 1 HETATM 14 N N6A 9JM . . . L 2 18.297 59.755 51.712 1 39.81 ? N6A 9JM 300 F 1 HETATM 15 N N1A 9JM . . . L 2 16.324 59.881 53.21 1 38.37 ? N1A 9JM 300 F 1 HETATM 16 C C2A 9JM . . . L 2 15.038 60.27 53.499 1 39.9 ? C2A 9JM 300 F 1 HETATM 17 N N3A 9JM . . . L 2 14.272 60.969 52.617 1 38.17 ? N3A 9JM 300 F 1 HETATM 18 C C4A 9JM . . . L 2 14.752 61.307 51.414 1 37.39 ? C4A 9JM 300 F 1 HETATM 19 C C2B 9JM . . . L 2 12.842 63.999 50.488 1 38.18 ? C2B 9JM 300 F 1 HETATM 20 O O2B 9JM . . . L 2 13.06 64.444 51.827 1 40.93 ? O2B 9JM 300 F 1 HETATM 21 C C3B 9JM . . . L 2 11.446 64.294 50.016 1 38.88 ? C3B 9JM 300 F 1 HETATM 22 O O3B 9JM . . . L 2 10.549 64.48 51.142 1 38.77 ? O3B 9JM 300 F 1 HETATM 23 O O3 9JM . . . L 2 8.491 64.897 45.737 1 35.58 ? O3 9JM 300 F 1 HETATM 24 P PN 9JM . . . L 2 7.183 63.949 45.822 1 33.48 ? PN 9JM 300 F 1 HETATM 25 O O1N 9JM . . . L 2 6.334 64.192 44.596 1 33.03 ? O1N 9JM 300 F 1 HETATM 26 O O2N 9JM . . . L 2 6.561 64.12 47.213 1 36.3 ? O2N 9JM 300 F 1 HETATM 27 O O5D 9JM . . . L 2 7.823 62.482 45.757 1 30.67 ? O5D 9JM 300 F 1 HETATM 28 C C5D 9JM . . . L 2 7.58 61.548 46.832 1 28.81 ? C5D 9JM 300 F 1 HETATM 29 C C4D 9JM . . . L 2 7.342 60.203 46.223 1 27.35 ? C4D 9JM 300 F 1 HETATM 30 O O4D 9JM . . . L 2 6.218 60.271 45.355 1 26.59 ? O4D 9JM 300 F 1 HETATM 31 C C3D 9JM . . . L 2 8.512 59.784 45.348 1 27.44 ? C3D 9JM 300 F 1 HETATM 32 O O3D 9JM . . . L 2 8.757 58.4 45.536 1 28.39 ? O3D 9JM 300 F 1 HETATM 33 C C2D 9JM . . . L 2 8.052 60.05 43.94 1 26.93 ? C2D 9JM 300 F 1 HETATM 34 O O2D 9JM . . . L 2 8.698 59.271 42.939 1 26.8 ? O2D 9JM 300 F 1 HETATM 35 C C1D 9JM . . . L 2 6.616 59.716 44.066 1 26.59 ? C1D 9JM 300 F 1 HETATM 36 N N1N 9JM . . . L 2 5.831 60.212 42.944 1 26.03 ? N1N 9JM 300 F 1 HETATM 37 C C2N 9JM . . . L 2 5.806 61.515 42.683 1 26.25 ? C2N 9JM 300 F 1 HETATM 38 C C6N 9JM . . . L 2 5.089 59.212 42.145 1 25.26 ? C6N 9JM 300 F 1 HETATM 39 C C5N 9JM . . . L 2 4.327 59.785 41.039 1 25.06 ? C5N 9JM 300 F 1 HETATM 40 C C4N 9JM . . . L 2 4.322 61.14 40.804 1 26.03 ? C4N 9JM 300 F 1 HETATM 41 C C3N 9JM . . . L 2 5.063 62.008 41.626 1 27.16 ? C3N 9JM 300 F 1 HETATM 42 C C7N 9JM . . . L 2 5.045 63.467 41.358 1 28.16 ? C7N 9JM 300 F 1 HETATM 43 O O7N 9JM . . . L 2 4.398 63.907 40.414 1 30.32 ? O7N 9JM 300 F 1 HETATM 44 N N7N 9JM . . . L 2 5.761 64.324 42.205 1 28.32 ? N7N 9JM 300 F 1 # _model_server_stats.io_time_ms 127 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 44 #