data_5GMG # _model_server_result.job_id xYOocQowLgk9c-B8ZiVawA _model_server_result.datetime_utc '2024-11-25 00:25:38' _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 5gmg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":901}' # _entry.id 5GMG # _exptl.entry_id 5GMG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 339.304 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-7-prop-2-enyl-1~{H}-purine-6,8-dione _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 98.58 _cell.angle_gamma 90 _cell.entry_id 5GMG _cell.length_a 98.277 _cell.length_b 99.41 _cell.length_c 112.096 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GMG _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 K N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n E NAG 1 E 1 NAG A 904 NAG 3 n E NAG 2 E 2 NAG A 905 NAG 3 n F NAG 1 F 1 NAG B 903 NAG 3 n F NAG 2 F 2 NAG B 904 NAG # 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 14 A CYS 36 1_555 A SG CYS 29 A CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf2 A SG CYS 76 A CYS 98 1_555 A SG CYS 453 A CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? disulf ? disulf3 A SG CYS 78 A CYS 100 1_555 A SG CYS 90 A CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 A SG CYS 161 A CYS 183 1_555 A SG CYS 167 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 A SG CYS 238 A CYS 260 1_555 A SG CYS 251 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf6 A SG CYS 241 A CYS 263 1_555 A SG CYS 248 A CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf7 A SG CYS 469 A CYS 491 1_555 A SG CYS 499 A CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? disulf ? disulf8 A SG CYS 765 A CYS 787 1_555 A SG CYS 792 A CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf9 A SG CYS 767 A CYS 789 1_555 A SG CYS 811 A CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? disulf ? disulf10 B SG CYS 14 B CYS 36 1_555 B SG CYS 29 B CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf11 B SG CYS 76 B CYS 98 1_555 B SG CYS 453 B CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf12 B SG CYS 78 B CYS 100 1_555 B SG CYS 90 B CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf13 B SG CYS 161 B CYS 183 1_555 B SG CYS 167 B CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf14 B SG CYS 238 B CYS 260 1_555 B SG CYS 251 B CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf15 B SG CYS 241 B CYS 263 1_555 B SG CYS 248 B CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf16 B SG CYS 469 B CYS 491 1_555 B SG CYS 499 B CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf17 B SG CYS 765 B CYS 787 1_555 B SG CYS 792 B CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf18 B SG CYS 767 B CYS 789 1_555 B SG CYS 811 B CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? covale ? covale1 A ND2 ASN 47 A ASN 69 1_555 G C1 NAG . A NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale2 A ND2 ASN 193 A ASN 215 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 A ND2 ASN 501 A ASN 523 1_555 I C1 NAG . A NAG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale4 A ND2 ASN 657 A ASN 679 1_555 H C1 NAG . A NAG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 B ND2 ASN 47 B ASN 69 1_555 N C1 NAG . B NAG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale6 B ND2 ASN 193 B ASN 215 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale7 B ND2 ASN 501 B ASN 523 1_555 M C1 NAG . B NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale8 B ND2 ASN 568 B ASN 590 1_555 L C1 NAG . B NAG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale10 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _chem_comp.formula 'C13 H17 N5 O6' _chem_comp.formula_weight 339.304 _chem_comp.id SDL _chem_comp.mon_nstd_flag . _chem_comp.name 2-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-7-prop-2-enyl-1~{H}-purine-6,8-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Loxoribine # 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 O1 C2 SDL sing 311 n n C2 C3 SDL sing 312 n n C2 C1 SDL sing 313 n n O2 C3 SDL sing 314 n n O C SDL sing 315 n n C C1 SDL sing 316 n n C3 C4 SDL sing 317 n n C1 O3 SDL sing 318 n n N3 C8 SDL sing 319 n n C4 O3 SDL sing 320 n n C4 N SDL sing 321 n n N4 C8 SDL doub 322 n n N4 C9 SDL sing 323 n n C8 N2 SDL sing 324 n n C9 N SDL sing 325 n n C9 C6 SDL doub 326 n n N C5 SDL sing 327 n n N2 C7 SDL sing 328 n n C5 O5 SDL doub 329 n n C5 N1 SDL sing 330 n n C6 C7 SDL sing 331 n n C6 N1 SDL sing 332 n n C7 O4 SDL doub 333 n n N1 C10 SDL sing 334 n n C12 C11 SDL doub 335 n n C11 C10 SDL sing 336 n n C10 H1 SDL sing 337 n n C10 H2 SDL sing 338 n n C11 H3 SDL sing 339 n n C12 H4 SDL sing 340 n n C12 H5 SDL sing 341 n n N3 H7 SDL sing 342 n n N3 H8 SDL sing 343 n n C4 H9 SDL sing 344 n n C3 H10 SDL sing 345 n n O2 H11 SDL sing 346 n n C2 H12 SDL sing 347 n n O1 H13 SDL sing 348 n n C1 H14 SDL sing 349 n n C H15 SDL sing 350 n n C H16 SDL sing 351 n n O H17 SDL sing 352 n n N2 H6 SDL sing 353 n n # _atom_sites.entry_id 5GMG _atom_sites.fract_transf_matrix[1][1] 0.010175 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001535 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010059 _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] 0.009022 _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 4 NAG A 1 901 902 NAG NAG . H 4 NAG A 1 904 906 NAG NAG . I 4 NAG A 1 905 907 NAG NAG . J 5 SDL B 1 901 901 SDL SDL . K 5 SDL B 1 902 901 SDL SDL . L 4 NAG B 1 903 902 NAG NAG . M 4 NAG B 1 906 905 NAG NAG . N 4 NAG B 1 907 906 NAG NAG . O 6 PO4 B 1 908 907 PO4 PO4 . P 7 HOH A 1 1001 1001 HOH HOH . P 7 HOH A 2 1002 1003 HOH HOH . P 7 HOH A 3 1003 1002 HOH HOH . P 7 HOH A 4 1004 1004 HOH HOH . P 7 HOH A 5 1005 1005 HOH HOH . P 7 HOH A 6 1006 1006 HOH HOH . P 7 HOH A 7 1007 1007 HOH HOH . P 7 HOH A 8 1008 1008 HOH HOH . P 7 HOH A 9 1009 1009 HOH HOH . P 7 HOH A 10 1010 1010 HOH HOH . P 7 HOH A 11 1011 1011 HOH HOH . P 7 HOH A 12 1012 1012 HOH HOH . P 7 HOH A 13 1013 1013 HOH HOH . P 7 HOH A 14 1014 1014 HOH HOH . P 7 HOH A 15 1015 1015 HOH HOH . P 7 HOH A 16 1016 1016 HOH HOH . Q 7 HOH B 1 1001 1001 HOH HOH . Q 7 HOH B 2 1002 1002 HOH HOH . Q 7 HOH B 3 1003 1003 HOH HOH . Q 7 HOH B 4 1004 1004 HOH HOH . Q 7 HOH B 5 1005 1005 HOH HOH . Q 7 HOH B 6 1006 1006 HOH HOH . Q 7 HOH B 7 1007 1008 HOH HOH . Q 7 HOH B 8 1008 1007 HOH HOH . Q 7 HOH B 9 1009 1009 HOH HOH . Q 7 HOH B 10 1010 1010 HOH HOH . Q 7 HOH B 11 1011 1011 HOH HOH . Q 7 HOH B 12 1012 1012 HOH HOH . Q 7 HOH B 13 1013 1013 HOH HOH . Q 7 HOH B 14 1014 1014 HOH HOH . Q 7 HOH B 15 1015 1015 HOH HOH . Q 7 HOH B 16 1016 1016 HOH HOH . Q 7 HOH B 17 1017 1017 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 SDL . . . J 5 -8.966 -32.706 34.522 1 80.07 ? O5 SDL 901 B 1 HETATM 2 C C5 SDL . . . J 5 -7.969 -31.995 34.133 1 77.07 ? C5 SDL 901 B 1 HETATM 3 N N1 SDL . . . J 5 -7.469 -31.039 34.911 1 75.91 ? N1 SDL 901 B 1 HETATM 4 C C10 SDL . . . J 5 -7.931 -30.668 36.236 1 67.13 ? C10 SDL 901 B 1 HETATM 5 C C11 SDL . . . J 5 -8.958 -29.56 36.185 1 61.09 ? C11 SDL 901 B 1 HETATM 6 C C12 SDL . . . J 5 -9.415 -29.037 35.057 1 56.1 ? C12 SDL 901 B 1 HETATM 7 C C6 SDL . . . J 5 -6.471 -30.531 34.176 1 80 ? C6 SDL 901 B 1 HETATM 8 C C9 SDL . . . J 5 -6.403 -31.255 32.894 1 78.98 ? C9 SDL 901 B 1 HETATM 9 N N4 SDL . . . J 5 -5.455 -30.877 32.003 1 78.79 ? N4 SDL 901 B 1 HETATM 10 C C8 SDL . . . J 5 -4.6 -29.869 32.272 1 71.08 ? C8 SDL 901 B 1 HETATM 11 N N3 SDL . . . J 5 -3.691 -29.561 31.325 1 62.32 ? N3 SDL 901 B 1 HETATM 12 N N2 SDL . . . J 5 -4.622 -29.191 33.44 1 80.68 ? N2 SDL 901 B 1 HETATM 13 C C7 SDL . . . J 5 -5.507 -29.43 34.427 1 79.94 ? C7 SDL 901 B 1 HETATM 14 O O4 SDL . . . J 5 -5.499 -28.752 35.494 1 75.44 ? O4 SDL 901 B 1 HETATM 15 N N SDL . . . J 5 -7.392 -32.154 32.932 1 69.64 ? N SDL 901 B 1 HETATM 16 C C4 SDL . . . J 5 -7.757 -33.171 31.933 1 63.81 ? C4 SDL 901 B 1 HETATM 17 C C3 SDL . . . J 5 -7.835 -32.766 30.472 1 63.11 ? C3 SDL 901 B 1 HETATM 18 O O2 SDL . . . J 5 -9.087 -32.221 30.035 1 62.28 ? O2 SDL 901 B 1 HETATM 19 C C2 SDL . . . J 5 -7.533 -34.108 29.84 1 64.34 ? C2 SDL 901 B 1 HETATM 20 O O1 SDL . . . J 5 -8.675 -34.983 29.894 1 75.33 ? O1 SDL 901 B 1 HETATM 21 O O3 SDL . . . J 5 -6.707 -34.129 32.027 1 62.86 ? O3 SDL 901 B 1 HETATM 22 C C1 SDL . . . J 5 -6.462 -34.685 30.741 1 63.24 ? C1 SDL 901 B 1 HETATM 23 C C SDL . . . J 5 -5.054 -34.349 30.276 1 64.63 ? C SDL 901 B 1 HETATM 24 O O SDL . . . J 5 -4.858 -32.933 30.199 1 65.79 ? O SDL 901 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 24 #