data_6V3I # _model_server_result.job_id Zyu2oM4f1jI9pjViSCjeeA _model_server_result.datetime_utc '2024-11-06 22:46:38' _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 6v3i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 6V3I # _exptl.entry_id 6V3I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.525 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)' _entity.pdbx_number_of_molecules 1 _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 6V3I _cell.length_a 67.945 _cell.length_b 120.303 _cell.length_c 127.818 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6V3I _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,K,L,M,N,O,P,Q,R,S,T,U _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 74 A CYS 93 1_555 B SG CYS 74 B CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 B OD2 ASP 81 B ASP 100 1_555 Q C2 OCT . B OCT 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? metalc ? metalc1 A O THR 123 A THR 142 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc2 A O THR 123 A THR 142 1_555 O K K . B K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.147 ? metalc ? metalc3 A OG1 THR 123 A THR 142 1_555 O K K . B K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.403 ? metalc ? metalc4 A O ILE 124 A ILE 143 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? metalc ? metalc5 A O ILE 124 A ILE 143 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? metalc ? metalc6 A O GLY 125 A GLY 144 1_555 G K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.827 ? metalc ? metalc7 A O GLY 125 A GLY 144 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.847 ? metalc ? metalc8 A O PHE 126 A PHE 145 1_555 G K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? metalc ? metalc9 A O THR 232 A THR 251 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? metalc ? metalc10 A O THR 232 A THR 251 1_555 O K K . B K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.802 ? metalc ? metalc11 A OG1 THR 232 A THR 251 1_555 O K K . B K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.128 ? metalc ? metalc12 A O ILE 233 A ILE 252 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? metalc ? metalc13 A O ILE 233 A ILE 252 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? metalc ? metalc14 A O GLY 234 A GLY 253 1_555 G K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.128 ? metalc ? metalc15 A O GLY 234 A GLY 253 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc16 A O PHE 235 A PHE 254 1_555 G K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.84 ? metalc ? metalc17 A OE1 GLU 290 A GLU 309 1_555 L CD CD . A CD 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc18 G K K . A K 405 1_555 B O GLY 125 B GLY 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.085 ? metalc ? metalc19 G K K . A K 405 1_555 B O PHE 126 B PHE 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? metalc ? metalc20 G K K . A K 405 1_555 B O GLY 234 B GLY 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.984 ? metalc ? metalc21 G K K . A K 405 1_555 B O PHE 235 B PHE 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.076 ? metalc ? metalc22 H K K . A K 406 1_555 B O THR 123 B THR 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc23 H K K . A K 406 1_555 B O ILE 124 B ILE 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.876 ? metalc ? metalc24 H K K . A K 406 1_555 B O THR 232 B THR 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc25 H K K . A K 406 1_555 B O ILE 233 B ILE 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? metalc ? metalc26 L CD CD . A CD 410 2_554 B OE1 GLU 290 B GLU 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? metalc ? metalc27 B O THR 123 B THR 142 1_555 O K K . B K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc28 B OG1 THR 123 B THR 142 1_555 O K K . B K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.012 ? metalc ? metalc29 B O ILE 124 B ILE 143 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc30 B O GLY 125 B GLY 144 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? metalc ? metalc31 B O THR 232 B THR 251 1_555 O K K . B K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc32 B OG1 THR 232 B THR 251 1_555 O K K . B K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? metalc ? metalc33 B O ILE 233 B ILE 252 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? metalc ? metalc34 B O GLY 234 B GLY 253 1_555 N K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? # _chem_comp.formula 'H28 N14 O2 Ru3' _chem_comp.formula_weight 559.525 _chem_comp.id R2R _chem_comp.mon_nstd_flag . _chem_comp.name 'ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)' _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 N08 RU3 R2R sing 374 n n N11 RU3 R2R sing 375 n n N10 RU3 R2R sing 376 n n RU3 N09 R2R sing 377 n n RU3 N12 R2R sing 378 n n RU3 O06 R2R sing 379 n n O06 RU2 R2R sing 380 n n N01 RU2 R2R sing 381 n n N05 RU2 R2R sing 382 n n RU2 N04 R2R sing 383 n n RU2 N03 R2R sing 384 n n RU2 O13 R2R sing 385 n n O13 RU1 R2R sing 386 n n N18 RU1 R2R sing 387 n n N16 RU1 R2R sing 388 n n RU1 N17 R2R sing 389 n n RU1 N19 R2R sing 390 n n RU1 N15 R2R sing 391 n n N01 H1 R2R sing 392 n n N01 H2 R2R sing 393 n n N03 H3 R2R sing 394 n n N03 H4 R2R sing 395 n n N04 H5 R2R sing 396 n n N04 H6 R2R sing 397 n n N05 H7 R2R sing 398 n n N05 H8 R2R sing 399 n n N08 H9 R2R sing 400 n n N08 H10 R2R sing 401 n n N09 H11 R2R sing 402 n n N09 H12 R2R sing 403 n n N10 H13 R2R sing 404 n n N10 H14 R2R sing 405 n n N11 H15 R2R sing 406 n n N11 H16 R2R sing 407 n n N12 H17 R2R sing 408 n n N12 H18 R2R sing 409 n n N15 H19 R2R sing 410 n n N15 H20 R2R sing 411 n n N16 H21 R2R sing 412 n n N16 H22 R2R sing 413 n n N17 H23 R2R sing 414 n n N17 H24 R2R sing 415 n n N18 H25 R2R sing 416 n n N18 H26 R2R sing 417 n n N19 H27 R2R sing 418 n n N19 H28 R2R sing 419 n n # _atom_sites.entry_id 6V3I _atom_sites.fract_transf_matrix[1][1] 0.014718 _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] 0.008312 _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] 0.007824 _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 R2R A 1 401 401 R2R R2R . D 3 D12 A 1 402 801 D12 D12 . E 4 OCT A 1 403 901 OCT OCT . F 5 HEX A 1 404 1101 HEX HEX . G 6 K A 1 405 1 K K . H 6 K A 1 406 3 K K . I 6 K A 1 407 5 K K . J 3 D12 A 1 408 2 D12 D12 . K 7 LNK A 1 409 2 LNK LNK . L 8 CD A 1 410 2 CD CD . M 8 CD B 1 401 401 CD CD . N 6 K B 1 402 2 K K . O 6 K B 1 403 4 K K . P 4 OCT B 1 404 1 OCT OCT . Q 4 OCT B 1 405 2 OCT OCT . R 3 D12 B 1 406 6 D12 D12 . S 8 CD B 1 407 3 CD CD . T 9 HOH A 1 501 2 HOH HOH . U 9 HOH B 1 501 1 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 N N01 R2R . . . C 2 -3.337 -39.152 -25.196 1 267 ? N01 R2R 401 A 1 HETATM 2 N N03 R2R . . . C 2 -4.517 -39.469 -28.525 1 251.21 ? N03 R2R 401 A 1 HETATM 3 N N04 R2R . . . C 2 -2.388 -38.895 -27.506 1 264.79 ? N04 R2R 401 A 1 HETATM 4 N N05 R2R . . . C 2 -5.427 -39.939 -26.042 1 244.89 ? N05 R2R 401 A 1 HETATM 5 O O06 R2R . . . C 2 -4.441 -37.731 -26.729 1 281.74 ? O06 R2R 401 A 1 HETATM 6 N N08 R2R . . . C 2 -5.508 -35.652 -26.422 1 267.59 ? N08 R2R 401 A 1 HETATM 7 N N09 R2R . . . C 2 -7.711 -36.499 -27.35 1 229.43 ? N09 R2R 401 A 1 HETATM 8 N N10 R2R . . . C 2 -6.602 -37.703 -25.429 1 262.27 ? N10 R2R 401 A 1 HETATM 9 N N11 R2R . . . C 2 -5.563 -36.738 -28.707 1 246.7 ? N11 R2R 401 A 1 HETATM 10 N N12 R2R . . . C 2 -6.851 -38.671 -27.773 1 270.41 ? N12 R2R 401 A 1 HETATM 11 O O13 R2R . . . C 2 -3.561 -41.053 -27.185 1 250.64 ? O13 R2R 401 A 1 HETATM 12 N N15 R2R . . . C 2 -1.849 -42.768 -27.301 1 255.49 ? N15 R2R 401 A 1 HETATM 13 N N16 R2R . . . C 2 -3.968 -41.601 -24.685 1 272.1 ? N16 R2R 401 A 1 HETATM 14 N N17 R2R . . . C 2 -2.204 -43.314 -24.861 1 248.05 ? N17 R2R 401 A 1 HETATM 15 N N18 R2R . . . C 2 -4.167 -43.306 -26.446 1 274.35 ? N18 R2R 401 A 1 HETATM 16 N N19 R2R . . . C 2 -1.585 -40.999 -25.627 1 278.98 ? N19 R2R 401 A 1 HETATM 17 RU RU2 R2R . . . C 2 -3.954 -39.394 -26.846 1 362.87 ? RU2 R2R 401 A 1 HETATM 18 RU RU3 R2R . . . C 2 -6.093 -37.208 -27.071 1 311.87 ? RU3 R2R 401 A 1 HETATM 19 RU RU1 R2R . . . C 2 -2.9 -42.136 -26.008 1 307.5 ? RU1 R2R 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #