data_4KH5 # _model_server_result.job_id HClkITJoSR8X1-pvU0zF_A _model_server_result.datetime_utc '2024-11-22 20:04:44' _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 4kh5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":700}' # _entry.id 4KH5 # _exptl.entry_id 4KH5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 426.216 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(R)-hydroxy(phosphonoamino)phosphoryl]adenosine" _entity.pdbx_number_of_molecules 2 _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 4KH5 _cell.length_a 73.537 _cell.length_b 150.25 _cell.length_c 240.967 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KH5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -120.4835 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 35 A CYS 59 1_555 A SG CYS 64 A CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 317 A CYS 341 1_555 A SG CYS 328 A CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 332 A CYS 356 1_555 A SG CYS 421 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 341 A CYS 365 1_555 A SG CYS 409 A CYS 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 372 A CYS 396 1_555 A SG CYS 389 A CYS 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 A SG CYS 502 A CYS 526 1_555 A SG CYS 534 A CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 35 B CYS 59 1_555 B SG CYS 64 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 B SG CYS 317 B CYS 341 1_555 B SG CYS 328 B CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 B SG CYS 332 B CYS 356 1_555 B SG CYS 421 B CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 B SG CYS 341 B CYS 365 1_555 B SG CYS 409 B CYS 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf11 B SG CYS 372 B CYS 396 1_555 B SG CYS 389 B CYS 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf12 B SG CYS 502 B CYS 526 1_555 B SG CYS 534 B CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 C O3B AU1 . A AU1 700 1_555 D MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc2 C O5' AU1 . A AU1 700 1_555 D MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? metalc ? metalc3 E O2A AU1 . B AU1 700 1_555 F MG MG . B MG 701 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc4 E O2A AU1 . B AU1 700 1_555 F MG MG . B MG 701 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc5 E O2B AU1 . B AU1 700 1_555 F MG MG . B MG 701 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc6 E O2B AU1 . B AU1 700 1_555 F MG MG . B MG 701 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.499 ? # _chem_comp.formula 'C10 H16 N6 O9 P2' _chem_comp.formula_weight 426.216 _chem_comp.id AU1 _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(R)-hydroxy(phosphonoamino)phosphoryl]adenosine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Adenosine 5-(alpha,beta-imido)diphosphate' # 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 O2A PA AU1 doub 70 n n O2B PB AU1 doub 71 n n O1B PB AU1 sing 72 n n O1A PA AU1 sing 73 n n PB N3A AU1 sing 74 n n PB O3B AU1 sing 75 n n PA N3A AU1 sing 76 n n PA O5' AU1 sing 77 n n N6 C6 AU1 sing 78 n n N1 C6 AU1 doub 79 n y N1 C2 AU1 sing 80 n y O5' C5' AU1 sing 81 n n C5' C4' AU1 sing 82 n n C6 C5 AU1 sing 83 n y C2 N3 AU1 doub 84 n y N3 C4 AU1 sing 85 n y C5 C4 AU1 doub 86 n y C5 N7 AU1 sing 87 n y O4' C4' AU1 sing 88 n n O4' C1' AU1 sing 89 n n C4 N9 AU1 sing 90 n y N7 C8 AU1 doub 91 n y C4' C3' AU1 sing 92 n n N9 C8 AU1 sing 93 n y N9 C1' AU1 sing 94 n n C1' C2' AU1 sing 95 n n C3' C2' AU1 sing 96 n n C3' O3' AU1 sing 97 n n C2' O2' AU1 sing 98 n n O1A H1 AU1 sing 99 n n N3A H2 AU1 sing 100 n n O1B H3 AU1 sing 101 n n O3B H4 AU1 sing 102 n n C5' H5 AU1 sing 103 n n C5' H6 AU1 sing 104 n n C4' H7 AU1 sing 105 n n C3' H8 AU1 sing 106 n n O3' H9 AU1 sing 107 n n C2' H10 AU1 sing 108 n n O2' H11 AU1 sing 109 n n C1' H12 AU1 sing 110 n n C8 H13 AU1 sing 111 n n C2 H14 AU1 sing 112 n n N6 H15 AU1 sing 113 n n N6 H16 AU1 sing 114 n n # _atom_sites.entry_id 4KH5 _atom_sites.fract_transf_matrix[1][1] 0.013599 _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] 0.006656 _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] 0.00415 _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 C 2 AU1 A 1 700 700 AU1 19P . D 3 MG A 1 701 701 MG MG . E 2 AU1 B 1 700 700 AU1 AU1 . F 3 MG B 1 701 701 MG MG . # 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 O1A AU1 . A . E 2 -5.59 14.726 -26.56 0.8 46.92 ? O1A AU1 700 B 1 HETATM 2 O O1A AU1 . B . E 2 -5.687 14.749 -26.409 0 59.91 ? O1A AU1 700 B 1 HETATM 3 P PA AU1 . A . E 2 -4.733 13.483 -26.466 0.8 47.42 ? PA AU1 700 B 1 HETATM 4 P PA AU1 . B . E 2 -4.822 13.519 -26.569 0 59.91 ? PA AU1 700 B 1 HETATM 5 O O2A AU1 . A . E 2 -4.092 12.963 -27.73 0.8 47.72 ? O2A AU1 700 B 1 HETATM 6 O O2A AU1 . B . E 2 -4.472 13.082 -27.971 0 59.91 ? O2A AU1 700 B 1 HETATM 7 N N3A AU1 . A . E 2 -5.722 12.227 -25.748 0.8 48.35 ? N3A AU1 700 B 1 HETATM 8 N N3A AU1 . B . E 2 -5.641 12.206 -25.748 0 59.91 ? N3A AU1 700 B 1 HETATM 9 P PB AU1 . A . E 2 -6.199 10.737 -26.537 0.8 49.44 ? PB AU1 700 B 1 HETATM 10 P PB AU1 . B . E 2 -6.032 10.679 -26.51 0 59.91 ? PB AU1 700 B 1 HETATM 11 O O2B AU1 . A . E 2 -5.05 10.316 -27.422 0.8 50.16 ? O2B AU1 700 B 1 HETATM 12 O O2B AU1 . B . E 2 -4.811 10.289 -27.309 0 59.91 ? O2B AU1 700 B 1 HETATM 13 O O1B AU1 . A . E 2 -7.456 11.093 -27.294 0.8 49.23 ? O1B AU1 700 B 1 HETATM 14 O O1B AU1 . B . E 2 -7.253 10.984 -27.343 0 59.91 ? O1B AU1 700 B 1 HETATM 15 O O3B AU1 . A . E 2 -6.423 9.799 -25.375 0.8 49.42 ? O3B AU1 700 B 1 HETATM 16 O O3B AU1 . B . E 2 -6.31 9.748 -25.354 0 59.91 ? O3B AU1 700 B 1 HETATM 17 O O5' AU1 . A . E 2 -3.525 13.771 -25.436 0.8 47.69 ? O5' AU1 700 B 1 HETATM 18 O O5' AU1 . B . E 2 -3.421 13.763 -25.8 0 59.91 ? O5' AU1 700 B 1 HETATM 19 C C5' AU1 . A . E 2 -3.006 15.08 -25.205 0.8 48.6 ? C5' AU1 700 B 1 HETATM 20 C C5' AU1 . B . E 2 -2.947 15.058 -25.423 0 59.91 ? C5' AU1 700 B 1 HETATM 21 C C4' AU1 . A . E 2 -1.945 15.023 -24.113 0.8 49.86 ? C4' AU1 700 B 1 HETATM 22 C C4' AU1 . B . E 2 -2.426 15.01 -23.989 0 59.91 ? C4' AU1 700 B 1 HETATM 23 C C3' AU1 . A . E 2 -2.482 15.484 -22.759 0.8 50.51 ? C3' AU1 700 B 1 HETATM 24 C C3' AU1 . B . E 2 -2.935 16.181 -23.159 0 59.91 ? C3' AU1 700 B 1 HETATM 25 O O3' AU1 . A . E 2 -2.395 14.396 -21.826 0.8 50.24 ? O3' AU1 700 B 1 HETATM 26 O O3' AU1 . B . E 2 -4.037 15.784 -22.335 0 59.91 ? O3' AU1 700 B 1 HETATM 27 C C2' AU1 . A . E 2 -1.585 16.64 -22.33 0.8 51.19 ? C2' AU1 700 B 1 HETATM 28 C C2' AU1 . B . E 2 -1.743 16.632 -22.328 0 59.91 ? C2' AU1 700 B 1 HETATM 29 O O2' AU1 . A . E 2 -1.072 16.457 -21.001 0.8 51.9 ? O2' AU1 700 B 1 HETATM 30 O O2' AU1 . B . E 2 -1.794 16.088 -21.003 0 59.91 ? O2' AU1 700 B 1 HETATM 31 C C1' AU1 . A . E 2 -0.438 16.646 -23.337 0.8 50.71 ? C1' AU1 700 B 1 HETATM 32 C C1' AU1 . B . E 2 -0.523 16.063 -23.049 0 59.91 ? C1' AU1 700 B 1 HETATM 33 O O4' AU1 . A . E 2 -0.857 15.88 -24.466 0.8 50.2 ? O4' AU1 700 B 1 HETATM 34 O O4' AU1 . B . E 2 -0.997 15.09 -23.988 0 59.91 ? O4' AU1 700 B 1 HETATM 35 N N9 AU1 . A . E 2 0.007 18.002 -23.771 0.8 50.78 ? N9 AU1 700 B 1 HETATM 36 N N9 AU1 . B . E 2 0.355 17.055 -23.748 0 59.91 ? N9 AU1 700 B 1 HETATM 37 C C4 AU1 . A . E 2 1.201 18.264 -24.314 0.8 51.19 ? C4 AU1 700 B 1 HETATM 38 C C4 AU1 . B . E 2 0.204 18.386 -23.918 0 59.91 ? C4 AU1 700 B 1 HETATM 39 C C5 AU1 . A . E 2 1.227 19.715 -24.591 0.8 51.3 ? C5 AU1 700 B 1 HETATM 40 C C5 AU1 . B . E 2 1.382 18.839 -24.691 0 59.91 ? C5 AU1 700 B 1 HETATM 41 N N7 AU1 . A . E 2 0.035 20.201 -24.196 0.8 51.18 ? N7 AU1 700 B 1 HETATM 42 N N7 AU1 . B . E 2 2.135 17.752 -24.923 0 59.91 ? N7 AU1 700 B 1 HETATM 43 C C8 AU1 . A . E 2 -0.689 19.158 -23.715 0.8 50.89 ? C8 AU1 700 B 1 HETATM 44 C C8 AU1 . B . E 2 1.505 16.696 -24.353 0 59.91 ? C8 AU1 700 B 1 HETATM 45 N N3 AU1 . A . E 2 2.304 17.522 -24.618 0.8 51.78 ? N3 AU1 700 B 1 HETATM 46 N N3 AU1 . B . E 2 -0.719 19.326 -23.559 0 59.91 ? N3 AU1 700 B 1 HETATM 47 C C2 AU1 . A . E 2 3.405 18.088 -25.163 0.8 52.15 ? C2 AU1 700 B 1 HETATM 48 C C2 AU1 . B . E 2 -0.581 20.629 -23.888 0 59.91 ? C2 AU1 700 B 1 HETATM 49 N N1 AU1 . A . E 2 3.494 19.408 -25.447 0.8 51.85 ? N1 AU1 700 B 1 HETATM 50 N N1 AU1 . B . E 2 0.47 21.103 -24.592 0 59.91 ? N1 AU1 700 B 1 HETATM 51 C C6 AU1 . A . E 2 2.473 20.266 -25.195 0.8 51.41 ? C6 AU1 700 B 1 HETATM 52 C C6 AU1 . B . E 2 1.469 20.289 -25.019 0 59.91 ? C6 AU1 700 B 1 HETATM 53 N N6 AU1 . A . E 2 2.588 21.584 -25.49 0.8 51.24 ? N6 AU1 700 B 1 HETATM 54 N N6 AU1 . B . E 2 2.516 20.782 -25.725 0 59.91 ? N6 AU1 700 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 54 #