data_8VEV # _model_server_result.job_id 4VJmbEbcMXYFmoDv6g5Nog _model_server_result.datetime_utc '2024-11-07 10:38:36' _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 8vev # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":301}' # _entry.id 8VEV # _exptl.entry_id 8VEV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 281.268 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-methyladenosine _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 8VEV _cell.length_a 83.64 _cell.length_b 128.377 _cell.length_c 150.476 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VEV _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 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,B,G,H,I,W,X 1 1 C,D,J,K,L,M,N,Y,Z 2 1 E,F,O,P,Q,R,S,T,U,V,AA,BA 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 ? 5 J N N ? 5 R 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 22 A CYS 22 1_555 A SG CYS 98 A CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 145 A CYS 145 1_555 A SG CYS 200 A CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 B SG CYS 22 B CYS 22 1_555 B SG CYS 90 B CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 B SG CYS 137 B CYS 137 1_555 B SG CYS 196 B CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 C SG CYS 22 C CYS 22 1_555 C SG CYS 98 C CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 C SG CYS 145 C CYS 145 1_555 C SG CYS 200 C CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 D SG CYS 22 D CYS 22 1_555 D SG CYS 90 D CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 D SG CYS 137 D CYS 137 1_555 D SG CYS 196 D CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 E SG CYS 22 H CYS 22 1_555 E SG CYS 98 H CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf10 E SG CYS 145 H CYS 145 1_555 E SG CYS 200 H CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf11 F SG CYS 22 L CYS 22 1_555 F SG CYS 90 L CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf12 F SG CYS 137 L CYS 137 1_555 F SG CYS 196 L CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _chem_comp.formula 'C11 H15 N5 O4' _chem_comp.formula_weight 281.268 _chem_comp.id 6MD _chem_comp.mon_nstd_flag . _chem_comp.name N-methyladenosine _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 C2 N1 6MD doub 1 n y C2 N3 6MD sing 2 n y N1 C6 6MD sing 3 n y N3 C4 6MD doub 4 n y CZ N6 6MD sing 5 n n C6 N6 6MD sing 6 n n C6 C5 6MD doub 7 n y C4 C5 6MD sing 8 n y C4 N9 6MD sing 9 n y C4' O4' 6MD sing 10 n n C4' C5' 6MD sing 11 n n C4' C3' 6MD sing 12 n n O4' C1' 6MD sing 13 n n C5 N7 6MD sing 14 n y C5' O5' 6MD sing 15 n n O3' C3' 6MD sing 16 n n C1' N9 6MD sing 17 n n C1' C2' 6MD sing 18 n n N9 C8 6MD sing 19 n y C3' C2' 6MD sing 20 n n C2' O2' 6MD sing 21 n n N7 C8 6MD doub 22 n y O5' H1 6MD sing 23 n n C5' H2 6MD sing 24 n n C5' H3 6MD sing 25 n n C4' H4 6MD sing 26 n n C3' H5 6MD sing 27 n n O3' H6 6MD sing 28 n n C2' H7 6MD sing 29 n n O2' H8 6MD sing 30 n n C1' H9 6MD sing 31 n n C8 H10 6MD sing 32 n n N6 H11 6MD sing 33 n n C2 H12 6MD sing 34 n n CZ H13 6MD sing 35 n n CZ H14 6MD sing 36 n n CZ H15 6MD sing 37 n n # _atom_sites.entry_id 8VEV _atom_sites.fract_transf_matrix[1][1] 0.011956 _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] 0.00779 _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] 0.006646 _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 3 PEG A 1 301 219 PEG PEG . H 4 SO4 B 1 301 214 SO4 SO4 . I 4 SO4 B 1 302 215 SO4 SO4 . J 5 6MD C 1 301 219 6MD 6MD . K 4 SO4 C 1 302 220 SO4 SO4 . L 4 SO4 D 1 301 211 SO4 SO4 . M 4 SO4 D 1 302 212 SO4 SO4 . N 4 SO4 D 1 303 213 SO4 SO4 . O 4 SO4 H 1 301 218 SO4 SO4 . P 4 SO4 H 1 302 219 SO4 SO4 . Q 4 SO4 H 1 303 220 SO4 SO4 . R 5 6MD H 1 304 221 6MD 6MD . S 6 CL H 1 305 222 CL CL . T 4 SO4 L 1 301 213 SO4 SO4 . U 4 SO4 L 1 302 214 SO4 SO4 . V 4 SO4 L 1 303 215 SO4 SO4 . W 7 HOH A 1 401 221 HOH HOH . W 7 HOH A 2 402 220 HOH HOH . X 7 HOH B 1 401 219 HOH HOH . X 7 HOH B 2 402 217 HOH HOH . X 7 HOH B 3 403 216 HOH HOH . X 7 HOH B 4 404 218 HOH HOH . Y 7 HOH C 1 401 225 HOH HOH . Y 7 HOH C 2 402 224 HOH HOH . Y 7 HOH C 3 403 223 HOH HOH . Y 7 HOH C 4 404 222 HOH HOH . Y 7 HOH C 5 405 221 HOH HOH . Z 7 HOH D 1 401 220 HOH HOH . Z 7 HOH D 2 402 218 HOH HOH . Z 7 HOH D 3 403 214 HOH HOH . Z 7 HOH D 4 404 217 HOH HOH . Z 7 HOH D 5 405 226 HOH HOH . Z 7 HOH D 6 406 215 HOH HOH . Z 7 HOH D 7 407 221 HOH HOH . Z 7 HOH D 8 408 216 HOH HOH . Z 7 HOH D 9 409 225 HOH HOH . Z 7 HOH D 10 410 219 HOH HOH . Z 7 HOH D 11 411 227 HOH HOH . Z 7 HOH D 12 412 229 HOH HOH . Z 7 HOH D 13 413 223 HOH HOH . Z 7 HOH D 14 414 225 HOH HOH . Z 7 HOH D 15 415 224 HOH HOH . AA 7 HOH H 1 401 229 HOH HOH . AA 7 HOH H 2 402 227 HOH HOH . AA 7 HOH H 3 403 228 HOH HOH . AA 7 HOH H 4 404 223 HOH HOH . AA 7 HOH H 5 405 226 HOH HOH . AA 7 HOH H 6 406 224 HOH HOH . AA 7 HOH H 7 407 225 HOH HOH . BA 7 HOH L 1 401 216 HOH HOH . BA 7 HOH L 2 402 217 HOH HOH . BA 7 HOH L 3 403 224 HOH HOH . BA 7 HOH L 4 404 223 HOH HOH . BA 7 HOH L 5 405 219 HOH HOH . BA 7 HOH L 6 406 233 HOH HOH . BA 7 HOH L 7 407 231 HOH HOH . BA 7 HOH L 8 408 222 HOH HOH . BA 7 HOH L 9 409 220 HOH HOH . BA 7 HOH L 10 410 232 HOH HOH . BA 7 HOH L 11 411 228 HOH HOH . BA 7 HOH L 12 412 218 HOH HOH . BA 7 HOH L 13 413 226 HOH HOH . BA 7 HOH L 14 414 230 HOH HOH . BA 7 HOH L 15 415 227 HOH HOH . BA 7 HOH L 16 416 221 HOH HOH . BA 7 HOH L 17 417 222 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 O5' 6MD . . . J 5 22.927 55.953 -23.428 1 85.27 ? O5' 6MD 301 C 1 HETATM 2 C C5' 6MD . . . J 5 22.289 54.759 -23.001 1 82.33 ? C5' 6MD 301 C 1 HETATM 3 C C4' 6MD . . . J 5 20.785 54.913 -22.978 1 82.57 ? C4' 6MD 301 C 1 HETATM 4 O O4' 6MD . . . J 5 20.169 53.614 -23.137 1 79.96 ? O4' 6MD 301 C 1 HETATM 5 C C3' 6MD . . . J 5 20.215 55.46 -21.681 1 82.59 ? C3' 6MD 301 C 1 HETATM 6 O O3' 6MD . . . J 5 18.914 55.989 -21.919 1 83.64 ? O3' 6MD 301 C 1 HETATM 7 C C2' 6MD . . . J 5 20.096 54.2 -20.832 1 81.09 ? C2' 6MD 301 C 1 HETATM 8 O O2' 6MD . . . J 5 19.128 54.268 -19.803 1 81.14 ? O2' 6MD 301 C 1 HETATM 9 C C1' 6MD . . . J 5 19.724 53.137 -21.875 1 77.43 ? C1' 6MD 301 C 1 HETATM 10 N N9 6MD . . . J 5 20.355 51.836 -21.645 1 74.46 ? N9 6MD 301 C 1 HETATM 11 C C8 6MD . . . J 5 21.063 51.11 -22.562 1 74.16 ? C8 6MD 301 C 1 HETATM 12 N N7 6MD . . . J 5 21.513 49.987 -22.088 1 73.48 ? N7 6MD 301 C 1 HETATM 13 C C5 6MD . . . J 5 21.085 49.973 -20.785 1 72.75 ? C5 6MD 301 C 1 HETATM 14 C C6 6MD . . . J 5 21.243 49.037 -19.743 1 70.59 ? C6 6MD 301 C 1 HETATM 15 N N6 6MD . . . J 5 21.908 47.893 -19.91 1 68.98 ? N6 6MD 301 C 1 HETATM 16 N N1 6MD . . . J 5 20.694 49.324 -18.558 1 71.25 ? N1 6MD 301 C 1 HETATM 17 C C2 6MD . . . J 5 20.024 50.47 -18.414 1 72.78 ? C2 6MD 301 C 1 HETATM 18 N N3 6MD . . . J 5 19.806 51.418 -19.308 1 72.63 ? N3 6MD 301 C 1 HETATM 19 C C4 6MD . . . J 5 20.362 51.118 -20.483 1 73.1 ? C4 6MD 301 C 1 HETATM 20 C CZ 6MD . . . J 5 21.759 46.727 -19.046 1 67.88 ? CZ 6MD 301 C 1 HETATM 21 H H1 6MD . . . J 5 23.741 55.766 -23.59 1 101.96 ? H1 6MD 301 C 1 HETATM 22 H H2 6MD . . . J 5 22.6 54.514 -22.116 1 98.42 ? H2 6MD 301 C 1 HETATM 23 H H3 6MD . . . J 5 22.528 54.027 -23.591 1 98.42 ? H3 6MD 301 C 1 HETATM 24 H H4 6MD . . . J 5 20.528 55.454 -23.741 1 98.72 ? H4 6MD 301 C 1 HETATM 25 H H5 6MD . . . J 5 20.802 56.122 -21.283 1 98.74 ? H5 6MD 301 C 1 HETATM 26 H H6 6MD . . . J 5 18.974 56.834 -21.974 1 100 ? H6 6MD 301 C 1 HETATM 27 H H7 6MD . . . J 5 20.982 54.004 -20.488 1 96.94 ? H7 6MD 301 C 1 HETATM 28 H H8 6MD . . . J 5 19.384 54.82 -19.212 1 97 ? H8 6MD 301 C 1 HETATM 29 H H9 6MD . . . J 5 18.764 52.999 -21.873 1 92.55 ? H9 6MD 301 C 1 HETATM 30 H H10 6MD . . . J 5 21.194 51.412 -23.432 1 88.62 ? H10 6MD 301 C 1 HETATM 31 H H11 6MD . . . J 5 22.457 47.845 -20.569 1 82.4 ? H11 6MD 301 C 1 HETATM 32 H H12 6MD . . . J 5 19.663 50.615 -17.569 1 86.97 ? H12 6MD 301 C 1 HETATM 33 H H13 6MD . . . J 5 22.394 46.029 -19.272 1 81.09 ? H13 6MD 301 C 1 HETATM 34 H H14 6MD . . . J 5 21.902 46.951 -18.113 1 81.09 ? H14 6MD 301 C 1 HETATM 35 H H15 6MD . . . J 5 20.873 46.34 -19.114 1 81.09 ? H15 6MD 301 C 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 35 #