data_5KYK # _model_server_result.job_id M7S9zDSpVfsVLinS7wltgQ _model_server_result.datetime_utc '2024-11-05 21:01:44' _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 5kyk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5KYK # _exptl.entry_id 5KYK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.876 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(R)-[({2-[(chloroacetyl)amino]ethyl}sulfamoyl)methyl](hydroxy)phosphoryl]guanosine" _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 112.98 _cell.angle_gamma 90 _cell.entry_id 5KYK _cell.length_a 114.83 _cell.length_b 66.155 _cell.length_c 98.006 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KYK _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G 1 1 B,E,H 2 1 C,F,I 3 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 x,y,z _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 ? 2 D N N ? 2 E N N ? 2 F 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 covale ? covale1 A SG CYS 13 A CYS 12 1_555 D C32 6ZD . A 6ZD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.805 ? covale ? covale2 A OD2 ASP 120 A ASP 119 1_555 D N21 6ZD . A 6ZD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale3 A N ALA 147 A ALA 146 1_555 D O23 6ZD . A 6ZD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.301 ? covale ? covale4 B SG CYS 13 B CYS 12 1_555 E C32 6ZD . B 6ZD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.807 ? covale ? covale5 B OD2 ASP 120 B ASP 119 1_555 E N21 6ZD . B 6ZD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale6 B N ALA 147 B ALA 146 1_555 E O23 6ZD . B 6ZD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? covale ? covale7 C SG CYS 13 C CYS 12 1_555 F C32 6ZD . C 6ZD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.801 ? covale ? covale8 C OD2 ASP 120 C ASP 119 1_555 F N21 6ZD . C 6ZD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? covale ? covale9 C N ALA 147 C ALA 146 1_555 F O23 6ZD . C 6ZD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.299 ? # _chem_comp.formula 'C15 H23 Cl N7 O10 P S' _chem_comp.formula_weight 559.876 _chem_comp.id 6ZD _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(R)-[({2-[(chloroacetyl)amino]ethyl}sulfamoyl)methyl](hydroxy)phosphoryl]guanosine" _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 O01 S02 6ZD doub 1 n n C28 C29 6ZD sing 2 n n C28 N27 6ZD sing 3 n n C29 N30 6ZD sing 4 n n S02 C03 6ZD sing 5 n n S02 N27 6ZD sing 6 n n S02 O35 6ZD doub 7 n n O34 C31 6ZD doub 8 n n C03 P04 6ZD sing 9 n n N30 C31 6ZD sing 10 n n O25 P04 6ZD doub 11 n n C31 C32 6ZD sing 12 n n P04 O26 6ZD sing 13 n n P04 O05 6ZD sing 14 n n O05 C06 6ZD sing 15 n n N15 C14 6ZD doub 16 n y N15 C17 6ZD sing 17 n y C14 N13 6ZD sing 18 n y O23 C18 6ZD doub 19 n n O11 C10 6ZD sing 20 n n C10 C08 6ZD sing 21 n n C10 C12 6ZD sing 22 n n C06 C07 6ZD sing 23 n n C17 C18 6ZD sing 24 n n C17 C16 6ZD doub 25 n y C08 C07 6ZD sing 26 n n C08 O09 6ZD sing 27 n n C18 N19 6ZD sing 28 n n N13 C16 6ZD sing 29 n y N13 C12 6ZD sing 30 n n C16 N22 6ZD sing 31 n n C07 O24 6ZD sing 32 n n C12 O24 6ZD sing 33 n n N19 C20 6ZD doub 34 n n N22 C20 6ZD sing 35 n n C20 N21 6ZD sing 36 n n C10 H1 6ZD sing 37 n n C28 H2 6ZD sing 38 n n C28 H3 6ZD sing 39 n n C03 H4 6ZD sing 40 n n C03 H5 6ZD sing 41 n n C06 H6 6ZD sing 42 n n C06 H7 6ZD sing 43 n n C07 H8 6ZD sing 44 n n C08 H9 6ZD sing 45 n n O09 H10 6ZD sing 46 n n O11 H11 6ZD sing 47 n n C12 H12 6ZD sing 48 n n C14 H13 6ZD sing 49 n n N21 H14 6ZD sing 50 n n N21 H15 6ZD sing 51 n n N22 H16 6ZD sing 52 n n O26 H17 6ZD sing 53 n n N27 H18 6ZD sing 54 n n C29 H19 6ZD sing 55 n n C29 H20 6ZD sing 56 n n N30 H21 6ZD sing 57 n n C32 H22 6ZD sing 58 n n C32 H23 6ZD sing 59 n n C32 CL1 6ZD sing 60 n n # _atom_sites.entry_id 5KYK _atom_sites.fract_transf_matrix[1][1] 0.008709 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003693 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015116 _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] 0.011083 _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 D 2 6ZD A 1 201 1 6ZD LIG . E 2 6ZD B 1 201 2 6ZD LIG . F 2 6ZD C 1 201 3 6ZD LIG . G 3 HOH A 1 301 1 HOH HOH . G 3 HOH A 2 302 17 HOH HOH . G 3 HOH A 3 303 18 HOH HOH . G 3 HOH A 4 304 14 HOH HOH . G 3 HOH A 5 305 10 HOH HOH . G 3 HOH A 6 306 16 HOH HOH . G 3 HOH A 7 307 15 HOH HOH . H 3 HOH B 1 301 5 HOH HOH . H 3 HOH B 2 302 2 HOH HOH . H 3 HOH B 3 303 27 HOH HOH . H 3 HOH B 4 304 20 HOH HOH . H 3 HOH B 5 305 22 HOH HOH . H 3 HOH B 6 306 13 HOH HOH . H 3 HOH B 7 307 19 HOH HOH . H 3 HOH B 8 308 23 HOH HOH . H 3 HOH B 9 309 21 HOH HOH . H 3 HOH B 10 310 26 HOH HOH . H 3 HOH B 11 311 25 HOH HOH . H 3 HOH B 12 312 24 HOH HOH . I 3 HOH C 1 301 7 HOH HOH . I 3 HOH C 2 302 30 HOH HOH . I 3 HOH C 3 303 31 HOH HOH . I 3 HOH C 4 304 4 HOH HOH . I 3 HOH C 5 305 3 HOH HOH . I 3 HOH C 6 306 6 HOH HOH . I 3 HOH C 7 307 12 HOH HOH . I 3 HOH C 8 308 28 HOH HOH . I 3 HOH C 9 309 11 HOH HOH . I 3 HOH C 10 310 9 HOH HOH . I 3 HOH C 11 311 29 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 C C10 6ZD . . . E 2 7.856 -53.003 119.114 1 82.51 ? C10 6ZD 201 B 1 HETATM 2 C C17 6ZD . . . E 2 7.949 -48.52 118.459 1 94.51 ? C17 6ZD 201 B 1 HETATM 3 C C20 6ZD . . . E 2 6.389 -47.667 120.444 1 106.94 ? C20 6ZD 201 B 1 HETATM 4 C C28 6ZD . . . E 2 12.787 -57.116 115.355 1 81.61 ? C28 6ZD 201 B 1 HETATM 5 O O01 6ZD . . . E 2 10.12 -57.103 114.343 1 86.7 ? O01 6ZD 201 B 1 HETATM 6 S S02 6ZD . . . E 2 10.185 -56.499 115.641 1 85.06 ? S02 6ZD 201 B 1 HETATM 7 C C03 6ZD . . . E 2 9.858 -54.722 115.43 1 88.15 ? C03 6ZD 201 B 1 HETATM 8 P P04 6ZD . . . E 2 11.041 -53.757 116.457 1 86.48 ? P04 6ZD 201 B 1 HETATM 9 O O05 6ZD . . . E 2 10.814 -54.291 117.921 1 72.03 ? O05 6ZD 201 B 1 HETATM 10 C C06 6ZD . . . E 2 11.129 -53.412 118.985 1 72.34 ? C06 6ZD 201 B 1 HETATM 11 C C07 6ZD . . . E 2 10.045 -53.48 120.031 1 78.18 ? C07 6ZD 201 B 1 HETATM 12 C C08 6ZD . . . E 2 8.788 -54.15 119.484 1 81.6 ? C08 6ZD 201 B 1 HETATM 13 O O09 6ZD . . . E 2 8.201 -54.967 120.501 1 80.2 ? O09 6ZD 201 B 1 HETATM 14 O O11 6ZD . . . E 2 6.506 -53.365 119.426 1 83.4 ? O11 6ZD 201 B 1 HETATM 15 C C12 6ZD . . . E 2 8.338 -51.828 120.014 1 83.28 ? C12 6ZD 201 B 1 HETATM 16 N N13 6ZD . . . E 2 8.322 -50.561 119.218 1 85.49 ? N13 6ZD 201 B 1 HETATM 17 C C14 6ZD . . . E 2 8.967 -50.386 118.032 1 83.5 ? C14 6ZD 201 B 1 HETATM 18 N N15 6ZD . . . E 2 8.763 -49.155 117.554 1 87.35 ? N15 6ZD 201 B 1 HETATM 19 C C16 6ZD . . . E 2 7.666 -49.391 119.504 1 95.16 ? C16 6ZD 201 B 1 HETATM 20 C C18 6ZD . . . E 2 7.41 -47.215 118.474 1 100.24 ? C18 6ZD 201 B 1 HETATM 21 N N19 6ZD . . . E 2 6.631 -46.785 119.461 1 102.75 ? N19 6ZD 201 B 1 HETATM 22 N N21 6ZD . . . E 2 5.608 -47.266 121.458 1 108.97 ? N21 6ZD 201 B 1 HETATM 23 N N22 6ZD . . . E 2 6.859 -48.967 120.545 1 97.23 ? N22 6ZD 201 B 1 HETATM 24 O O23 6ZD . . . E 2 7.676 -46.455 117.518 1 84.48 ? O23 6ZD 201 B 1 HETATM 25 O O24 6ZD . . . E 2 9.666 -52.136 120.444 1 85.06 ? O24 6ZD 201 B 1 HETATM 26 O O25 6ZD . . . E 2 12.523 -54.058 116.077 1 62.1 ? O25 6ZD 201 B 1 HETATM 27 O O26 6ZD . . . E 2 10.737 -52.244 116.269 1 104.61 ? O26 6ZD 201 B 1 HETATM 28 N N27 6ZD . . . E 2 11.726 -56.654 116.225 1 84.98 ? N27 6ZD 201 B 1 HETATM 29 C C29 6ZD . . . E 2 14.144 -56.983 116.074 1 83.5 ? C29 6ZD 201 B 1 HETATM 30 N N30 6ZD . . . E 2 15.122 -56.341 115.199 1 88.21 ? N30 6ZD 201 B 1 HETATM 31 C C31 6ZD . . . E 2 16.417 -56.656 115.28 1 93.67 ? C31 6ZD 201 B 1 HETATM 32 C C32 6ZD . . . E 2 16.833 -57.677 116.297 1 67.94 ? C32 6ZD 201 B 1 HETATM 33 O O34 6ZD . . . E 2 17.247 -56.117 114.543 1 106.01 ? O34 6ZD 201 B 1 HETATM 34 O O35 6ZD . . . E 2 9.281 -56.99 116.635 1 84.67 ? O35 6ZD 201 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 209 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 34 #