data_4I49 # _model_server_result.job_id 5jYHj2t7BcgD_mtEyBb8QQ _model_server_result.datetime_utc '2024-10-19 20:12:56' _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 4i49 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4I49 # _exptl.entry_id 4I49 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 954.684 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-2-({(3S,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14,20-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaicosan-20-yl}amino)pentanedioic acid (non-preferred name)' _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 120 _cell.entry_id 4I49 _cell.length_a 98.521 _cell.length_b 98.521 _cell.length_c 90.009 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4I49 _symmetry.cell_setting ? _symmetry.Int_Tables_number 149 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 1 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_554 -y,-x,-z-1 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 -90.009 5 'crystal symmetry operation' 5_554 -x+y,y,-z-1 -1 0 0 0 1 0 0 0 -1 0 0 -90.009 6 'crystal symmetry operation' 6_554 x,x-y,-z-1 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 -90.009 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C28 H45 N8 O21 P3 S' _chem_comp.formula_weight 954.684 _chem_comp.id 1C4 _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-2-({(3S,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14,20-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaicosan-20-yl}amino)pentanedioic acid (non-preferred name)' _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 O8A P3B 1C4 doub 1 n n P3B O7A 1C4 sing 2 n n P3B O9A 1C4 sing 3 n n P3B O3B 1C4 sing 4 n n O3B C3B 1C4 sing 5 n n O2B C2B 1C4 sing 6 n n C2A N3A 1C4 doub 7 n y C2A N1A 1C4 sing 8 n y C3B C2B 1C4 sing 9 n n C3B C4B 1C4 sing 10 n n N3A C4A 1C4 sing 11 n y C2B C1B 1C4 sing 12 n n C1B O4B 1C4 sing 13 n n C1B N9A 1C4 sing 14 n n C4B O4B 1C4 sing 15 n n C4B C5B 1C4 sing 16 n n N1A C6A 1C4 doub 17 n y C4A N9A 1C4 sing 18 n y C4A C5A 1C4 doub 19 n y N9A C8A 1C4 sing 20 n y C6A C5A 1C4 sing 21 n y C6A N6A 1C4 sing 22 n n C5B O5B 1C4 sing 23 n n C5A N7A 1C4 sing 24 n y C8A N7A 1C4 doub 25 n y O5B P1A 1C4 sing 26 n n O2A P1A 1C4 doub 27 n n O1A P1A 1C4 sing 28 n n P1A O3A 1C4 sing 29 n n O4A P2A 1C4 doub 30 n n O3A P2A 1C4 sing 31 n n CEP CBP 1C4 sing 32 n n P2A O6A 1C4 sing 33 n n P2A O5A 1C4 sing 34 n n CCP O6A 1C4 sing 35 n n CCP CBP 1C4 sing 36 n n OAP CAP 1C4 sing 37 n n CBP CAP 1C4 sing 38 n n CBP CDP 1C4 sing 39 n n CAP C9P 1C4 sing 40 n n N8P C9P 1C4 sing 41 n n N8P C7P 1C4 sing 42 n n O5P C5P 1C4 doub 43 n n C9P O9P 1C4 doub 44 n n S1P C2P 1C4 sing 45 n n S1P C8 1C4 sing 46 n n C7P C6P 1C4 sing 47 n n C5P N4P 1C4 sing 48 n n C5P C6P 1C4 sing 49 n n C2P C3P 1C4 sing 50 n n C3P N4P 1C4 sing 51 n n C8 C7 1C4 sing 52 n n OE2 CD 1C4 doub 53 n n CG CD 1C4 sing 54 n n CG CB 1C4 sing 55 n n CD OE1 1C4 sing 56 n n C7 N2 1C4 sing 57 n n C7 O7 1C4 doub 58 n n N2 CA 1C4 sing 59 n n CB CA 1C4 sing 60 n n CA C 1C4 sing 61 n n C O 1C4 doub 62 n n C OXT 1C4 sing 63 n n C2A H1 1C4 sing 64 n n N6A H2 1C4 sing 65 n n N6A H3 1C4 sing 66 n n C8A H4 1C4 sing 67 n n C1B H5 1C4 sing 68 n n C2B H6 1C4 sing 69 n n O2B H7 1C4 sing 70 n n C3B H8 1C4 sing 71 n n O7A H9 1C4 sing 72 n n O9A H10 1C4 sing 73 n n C4B H11 1C4 sing 74 n n C5B H12 1C4 sing 75 n n C5B H13 1C4 sing 76 n n O1A H14 1C4 sing 77 n n O5A H15 1C4 sing 78 n n CCP H16 1C4 sing 79 n n CCP H17 1C4 sing 80 n n CDP H18 1C4 sing 81 n n CDP H19 1C4 sing 82 n n CDP H20 1C4 sing 83 n n CEP H21 1C4 sing 84 n n CEP H22 1C4 sing 85 n n CEP H23 1C4 sing 86 n n CAP H24 1C4 sing 87 n n OAP H25 1C4 sing 88 n n N8P H26 1C4 sing 89 n n C7P H27 1C4 sing 90 n n C7P H28 1C4 sing 91 n n C6P H29 1C4 sing 92 n n C6P H30 1C4 sing 93 n n N4P H31 1C4 sing 94 n n C3P H32 1C4 sing 95 n n C3P H33 1C4 sing 96 n n C2P H34 1C4 sing 97 n n C2P H35 1C4 sing 98 n n CA H36 1C4 sing 99 n n OXT H37 1C4 sing 100 n n CB H38 1C4 sing 101 n n CB H39 1C4 sing 102 n n CG H40 1C4 sing 103 n n CG H41 1C4 sing 104 n n OE1 H42 1C4 sing 105 n n C8 H43 1C4 sing 106 n n C8 H44 1C4 sing 107 n n N2 H45 1C4 sing 108 n n # _atom_sites.entry_id 4I49 _atom_sites.fract_transf_matrix[1][1] 0.01015 _atom_sites.fract_transf_matrix[1][2] 0.00586 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01172 _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] 0.01111 _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 B 2 1C4 A 1 501 437 1C4 1C4 . C 3 SO4 A 1 502 1 SO4 SO4 . D 4 HOH A 1 601 1 HOH HOH . D 4 HOH A 2 602 2 HOH HOH . D 4 HOH A 3 603 3 HOH HOH . D 4 HOH A 4 604 4 HOH HOH . D 4 HOH A 5 605 5 HOH HOH . D 4 HOH A 6 606 6 HOH HOH . D 4 HOH A 7 607 7 HOH HOH . D 4 HOH A 8 608 8 HOH HOH . D 4 HOH A 9 609 9 HOH HOH . D 4 HOH A 10 610 10 HOH HOH . D 4 HOH A 11 611 11 HOH HOH . D 4 HOH A 12 612 12 HOH HOH . D 4 HOH A 13 613 13 HOH HOH . D 4 HOH A 14 614 14 HOH HOH . D 4 HOH A 15 615 15 HOH HOH . D 4 HOH A 16 616 16 HOH HOH . D 4 HOH A 17 617 17 HOH HOH . D 4 HOH A 18 618 18 HOH HOH . D 4 HOH A 19 619 19 HOH HOH . D 4 HOH A 20 620 20 HOH HOH . D 4 HOH A 21 621 21 HOH HOH . D 4 HOH A 22 622 22 HOH HOH . D 4 HOH A 23 623 23 HOH HOH . D 4 HOH A 24 624 24 HOH HOH . D 4 HOH A 25 625 25 HOH HOH . D 4 HOH A 26 626 26 HOH HOH . D 4 HOH A 27 627 27 HOH HOH . D 4 HOH A 28 628 28 HOH HOH . D 4 HOH A 29 629 29 HOH HOH . D 4 HOH A 30 630 30 HOH HOH . D 4 HOH A 31 631 31 HOH HOH . D 4 HOH A 32 632 32 HOH HOH . D 4 HOH A 33 633 33 HOH HOH . D 4 HOH A 34 634 34 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 N N1A 1C4 . . . B 2 -9.442 28.819 -20.659 1 43.72 ? N1A 1C4 501 A 1 HETATM 2 C C2A 1C4 . . . B 2 -10.136 28.148 -21.581 1 47.79 ? C2A 1C4 501 A 1 HETATM 3 N N3A 1C4 . . . B 2 -10.308 26.817 -21.5 1 50.72 ? N3A 1C4 501 A 1 HETATM 4 C C4A 1C4 . . . B 2 -9.77 26.121 -20.479 1 52.02 ? C4A 1C4 501 A 1 HETATM 5 C C5A 1C4 . . . B 2 -9.038 26.786 -19.499 1 50.07 ? C5A 1C4 501 A 1 HETATM 6 C C6A 1C4 . . . B 2 -8.89 28.168 -19.617 1 45.99 ? C6A 1C4 501 A 1 HETATM 7 N N6A 1C4 . . . B 2 -8.136 28.873 -18.621 1 44.93 ? N6A 1C4 501 A 1 HETATM 8 N N7A 1C4 . . . B 2 -8.611 25.863 -18.597 1 48.47 ? N7A 1C4 501 A 1 HETATM 9 C C8A 1C4 . . . B 2 -9.056 24.649 -18.969 1 48.98 ? C8A 1C4 501 A 1 HETATM 10 N N9A 1C4 . . . B 2 -9.753 24.826 -20.102 1 55.11 ? N9A 1C4 501 A 1 HETATM 11 C C1B 1C4 . . . B 2 -10.423 23.811 -20.924 1 56.19 ? C1B 1C4 501 A 1 HETATM 12 C C2B 1C4 . . . B 2 -9.478 22.713 -21.236 1 61.74 ? C2B 1C4 501 A 1 HETATM 13 O O2B 1C4 . . . B 2 -8.811 23.073 -22.379 1 58.82 ? O2B 1C4 501 A 1 HETATM 14 C C3B 1C4 . . . B 2 -10.334 21.565 -21.502 1 64.45 ? C3B 1C4 501 A 1 HETATM 15 O O3B 1C4 . . . B 2 -10.499 21.584 -22.893 1 68.09 ? O3B 1C4 501 A 1 HETATM 16 P P3B 1C4 . . . B 2 -11.339 20.523 -23.678 1 69.72 ? P3B 1C4 501 A 1 HETATM 17 O O7A 1C4 . . . B 2 -12.835 20.764 -23.419 1 62.31 ? O7A 1C4 501 A 1 HETATM 18 O O8A 1C4 . . . B 2 -11.079 20.715 -25.147 1 62.45 ? O8A 1C4 501 A 1 HETATM 19 O O9A 1C4 . . . B 2 -10.94 19.12 -23.224 1 65.76 ? O9A 1C4 501 A 1 HETATM 20 C C4B 1C4 . . . B 2 -11.596 21.843 -20.773 1 55.66 ? C4B 1C4 501 A 1 HETATM 21 O O4B 1C4 . . . B 2 -11.565 23.225 -20.365 1 55.18 ? O4B 1C4 501 A 1 HETATM 22 C C5B 1C4 . . . B 2 -11.8 21.051 -19.552 1 52.16 ? C5B 1C4 501 A 1 HETATM 23 O O5B 1C4 . . . B 2 -12.89 21.397 -18.771 1 44.15 ? O5B 1C4 501 A 1 HETATM 24 P P1A 1C4 . . . B 2 -13.408 20.484 -17.58 1 49.39 ? P1A 1C4 501 A 1 HETATM 25 O O1A 1C4 . . . B 2 -14.929 20.391 -17.675 1 53.4 ? O1A 1C4 501 A 1 HETATM 26 O O2A 1C4 . . . B 2 -12.872 19.076 -17.734 1 48.4 ? O2A 1C4 501 A 1 HETATM 27 O O3A 1C4 . . . B 2 -13.073 21.069 -16.13 1 47.79 ? O3A 1C4 501 A 1 HETATM 28 P P2A 1C4 . . . B 2 -11.721 20.861 -15.283 1 39.56 ? P2A 1C4 501 A 1 HETATM 29 O O4A 1C4 . . . B 2 -10.553 20.615 -16.239 1 41.88 ? O4A 1C4 501 A 1 HETATM 30 O O5A 1C4 . . . B 2 -11.876 19.753 -14.261 1 42.87 ? O5A 1C4 501 A 1 HETATM 31 O O6A 1C4 . . . B 2 -11.386 22.209 -14.515 1 46.05 ? O6A 1C4 501 A 1 HETATM 32 C CBP 1C4 . . . B 2 -10.883 24.579 -14.462 1 35.9 ? CBP 1C4 501 A 1 HETATM 33 C CCP 1C4 . . . B 2 -11.455 23.417 -15.208 1 41.54 ? CCP 1C4 501 A 1 HETATM 34 C CDP 1C4 . . . B 2 -11.818 24.882 -13.248 1 32.62 ? CDP 1C4 501 A 1 HETATM 35 C CEP 1C4 . . . B 2 -10.812 25.803 -15.376 1 36.47 ? CEP 1C4 501 A 1 HETATM 36 C CAP 1C4 . . . B 2 -9.472 24.136 -13.969 1 41.03 ? CAP 1C4 501 A 1 HETATM 37 O OAP 1C4 . . . B 2 -8.538 24.239 -14.983 1 44.36 ? OAP 1C4 501 A 1 HETATM 38 C C9P 1C4 . . . B 2 -8.871 24.943 -12.809 1 46.78 ? C9P 1C4 501 A 1 HETATM 39 O O9P 1C4 . . . B 2 -9.13 24.69 -11.622 1 45.81 ? O9P 1C4 501 A 1 HETATM 40 N N8P 1C4 . . . B 2 -7.978 26.014 -13.206 1 36.77 ? N8P 1C4 501 A 1 HETATM 41 C C7P 1C4 . . . B 2 -7.385 26.811 -12.139 1 41.36 ? C7P 1C4 501 A 1 HETATM 42 C C6P 1C4 . . . B 2 -8.399 27.601 -11.328 1 37.72 ? C6P 1C4 501 A 1 HETATM 43 C C5P 1C4 . . . B 2 -9.048 28.748 -12.049 1 38.73 ? C5P 1C4 501 A 1 HETATM 44 O O5P 1C4 . . . B 2 -8.65 29.155 -13.143 1 39.32 ? O5P 1C4 501 A 1 HETATM 45 N N4P 1C4 . . . B 2 -10.18 29.357 -11.38 1 44.76 ? N4P 1C4 501 A 1 HETATM 46 C C3P 1C4 . . . B 2 -10.861 30.469 -11.996 1 43.49 ? C3P 1C4 501 A 1 HETATM 47 C C2P 1C4 . . . B 2 -12.322 30.326 -12.004 1 38.5 ? C2P 1C4 501 A 1 HETATM 48 S S1P 1C4 . . . B 2 -13.231 31.835 -12.334 1 49.57 ? S1P 1C4 501 A 1 HETATM 49 C CA 1C4 . . . B 2 -11.33 34.015 -8.43 1 39.26 ? CA 1C4 501 A 1 HETATM 50 C C 1C4 . . . B 2 -11.859 33.711 -7.082 1 43.3 ? C 1C4 501 A 1 HETATM 51 O OXT 1C4 . . . B 2 -11.05 33.764 -6.094 1 39.77 ? OXT 1C4 501 A 1 HETATM 52 O O 1C4 . . . B 2 -13.093 33.407 -6.934 1 40.02 ? O 1C4 501 A 1 HETATM 53 C CB 1C4 . . . B 2 -10.904 35.462 -8.457 1 43.21 ? CB 1C4 501 A 1 HETATM 54 C CG 1C4 . . . B 2 -10.98 36.159 -9.804 1 41.89 ? CG 1C4 501 A 1 HETATM 55 C CD 1C4 . . . B 2 -11.303 37.635 -9.771 1 40.52 ? CD 1C4 501 A 1 HETATM 56 O OE1 1C4 . . . B 2 -12.372 38.055 -9.221 1 40.49 ? OE1 1C4 501 A 1 HETATM 57 O OE2 1C4 . . . B 2 -10.488 38.444 -10.288 1 42.6 ? OE2 1C4 501 A 1 HETATM 58 C C7 1C4 . . . B 2 -12.965 32.523 -9.657 1 40.33 ? C7 1C4 501 A 1 HETATM 59 C C8 1C4 . . . B 2 -13.989 32.392 -10.786 1 38.1 ? C8 1C4 501 A 1 HETATM 60 O O7 1C4 . . . B 2 -12.687 31.538 -8.985 1 41.67 ? O7 1C4 501 A 1 HETATM 61 N N2 1C4 . . . B 2 -12.325 33.805 -9.445 1 36.19 ? N2 1C4 501 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 61 #