data_5XOO # _model_server_result.job_id ApFAYfzLLoG4wsd4E8-vzw _model_server_result.datetime_utc '2024-11-27 03:01:18' _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 5xoo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":503}' # _entry.id 5XOO # _exptl.entry_id 5XOO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 267.241 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 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 5XOO _cell.length_a 80.601 _cell.length_b 123.58 _cell.length_c 143.936 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XOO _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,G,H,I,J _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 G N N ? 5 J N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 GAL _pdbx_entity_branch_link.comp_id_2 XYP _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 2 n C XYP 1 C 1 XYP A 501 XYP 2 n C GAL 2 C 2 GAL A 502 GAL # 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 185 A CYS 207 1_555 A SG CYS 200 A CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 190 A CYS 212 1_555 A SG CYS 193 A CYS 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 245 A CYS 267 1_555 A SG CYS 318 A CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 319 A CYS 341 1_555 A SG CYS 378 A CYS 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 B SG CYS 185 B CYS 207 1_555 B SG CYS 200 B CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 B SG CYS 190 B CYS 212 1_555 B SG CYS 193 B CYS 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 B SG CYS 245 B CYS 267 1_555 B SG CYS 318 B CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 B SG CYS 319 B CYS 341 1_555 B SG CYS 378 B CYS 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 203 A ASN 225 1_555 D C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? covale ? covale2 A ND2 ASN 288 A ASN 310 1_555 E C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale3 F C MBN . A MBN 503 1_555 C O1 XYP . C XYP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale4 B ND2 ASN 203 B ASN 225 1_555 H C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? covale ? covale5 B ND2 ASN 288 B ASN 310 1_555 I C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale6 C O4 XYP . C XYP 1 1_555 C C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 sing # _chem_comp.formula 'C10 H13 N5 O4' _chem_comp.formula_weight 267.241 _chem_comp.id ADN _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE _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 O5' C5' ADN sing 1 n n O5' HO5' ADN sing 2 n n C5' C4' ADN sing 3 n n C5' "H5'1" ADN sing 4 n n C5' "H5'2" ADN sing 5 n n C4' O4' ADN sing 6 n n C4' C3' ADN sing 7 n n C4' H4' ADN sing 8 n n O4' C1' ADN sing 9 n n C3' O3' ADN sing 10 n n C3' C2' ADN sing 11 n n C3' H3' ADN sing 12 n n O3' HO3' ADN sing 13 n n C2' O2' ADN sing 14 n n C2' C1' ADN sing 15 n n C2' H2' ADN sing 16 n n O2' HO2' ADN sing 17 n n C1' N9 ADN sing 18 n n C1' H1' ADN sing 19 n n N9 C8 ADN sing 20 n y N9 C4 ADN sing 21 n y C8 N7 ADN doub 22 n y C8 H8 ADN sing 23 n n N7 C5 ADN sing 24 n y C5 C6 ADN sing 25 n y C5 C4 ADN doub 26 n y C6 N6 ADN sing 27 n n C6 N1 ADN doub 28 n y N6 HN61 ADN sing 29 n n N6 HN62 ADN sing 30 n n N1 C2 ADN sing 31 n y C2 N3 ADN doub 32 n y C2 H2 ADN sing 33 n n N3 C4 ADN sing 34 n y # _atom_sites.entry_id 5XOO _atom_sites.fract_transf_matrix[1][1] 0.012407 _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] 0.008092 _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] 0.006948 _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 3 NAG A 1 501 451 NAG NAG . E 3 NAG A 1 502 453 NAG NAG . F 4 MBN A 1 503 500 MBN MBN . G 5 ADN A 1 506 601 ADN ADN . H 3 NAG B 1 501 451 NAG NAG . I 3 NAG B 1 502 453 NAG NAG . J 5 ADN B 1 503 601 ADN ADN . # 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' ADN . . . J 5 73.271 125.743 151.148 1 86.36 ? O5' ADN 503 B 1 HETATM 2 C C5' ADN . . . J 5 73.62 126.456 152.33 1 81.34 ? C5' ADN 503 B 1 HETATM 3 C C4' ADN . . . J 5 72.612 127.53 152.662 1 90.73 ? C4' ADN 503 B 1 HETATM 4 O O4' ADN . . . J 5 72.85 127.995 154.01 1 85.11 ? O4' ADN 503 B 1 HETATM 5 C C3' ADN . . . J 5 72.687 128.772 151.798 1 106 ? C3' ADN 503 B 1 HETATM 6 O O3' ADN . . . J 5 71.439 129.463 151.841 1 123.33 ? O3' ADN 503 B 1 HETATM 7 C C2' ADN . . . J 5 73.764 129.595 152.505 1 92.98 ? C2' ADN 503 B 1 HETATM 8 O O2' ADN . . . J 5 73.668 130.991 152.312 1 93.63 ? O2' ADN 503 B 1 HETATM 9 C C1' ADN . . . J 5 73.58 129.213 153.981 1 84.87 ? C1' ADN 503 B 1 HETATM 10 N N9 ADN . . . J 5 74.844 128.985 154.684 1 65.53 ? N9 ADN 503 B 1 HETATM 11 C C8 ADN . . . J 5 75.748 128.052 154.375 1 60.16 ? C8 ADN 503 B 1 HETATM 12 N N7 ADN . . . J 5 76.758 128.143 155.234 1 59.74 ? N7 ADN 503 B 1 HETATM 13 C C5 ADN . . . J 5 76.475 129.141 156.079 1 58.14 ? C5 ADN 503 B 1 HETATM 14 C C6 ADN . . . J 5 77.173 129.646 157.141 1 48.28 ? C6 ADN 503 B 1 HETATM 15 N N6 ADN . . . J 5 78.445 129.318 157.753 1 43.37 ? N6 ADN 503 B 1 HETATM 16 N N1 ADN . . . J 5 76.688 130.657 157.845 1 42.12 ? N1 ADN 503 B 1 HETATM 17 C C2 ADN . . . J 5 75.491 131.192 157.512 1 47.13 ? C2 ADN 503 B 1 HETATM 18 N N3 ADN . . . J 5 74.798 130.695 156.462 1 55.8 ? N3 ADN 503 B 1 HETATM 19 C C4 ADN . . . J 5 75.294 129.666 155.745 1 62.98 ? C4 ADN 503 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 457 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 19 #