data_4XF6 # _model_server_result.job_id oelLFQ2StKsO8G7p4Xsyfg _model_server_result.datetime_utc '2024-11-14 17:41:54' _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 4xf6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 4XF6 # _exptl.entry_id 4XF6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 4XF6 _cell.length_a 77.364 _cell.length_b 81.255 _cell.length_c 82.046 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XF6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,AA 1 1 B,S,T,U,V,W,X,Y,Z,BA 2 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 ? 3 D N N ? 3 T 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 G I IOD . A IOD 305 1_555 L I IOD . A IOD 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.098 ? metalc ? metalc1 A OE1 GLN 136 A GLN 136 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc2 C O8 LIP . A LIP 301 1_555 F MG MG . A MG 304 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc3 D O3B ADP . A ADP 302 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc4 F MG MG . A MG 304 1_555 AA O HOH . A HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc5 F MG MG . A MG 304 1_555 AA O HOH . A HOH 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc6 F MG MG . A MG 304 1_555 AA O HOH . A HOH 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc7 B OE1 GLN 136 B GLN 136 1_555 V MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc8 S O7 LIP . B LIP 301 1_555 V MG MG . B MG 304 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc9 T O1B ADP . B ADP 302 1_555 V MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc10 V MG MG . B MG 304 1_555 BA O HOH . B HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc11 V MG MG . B MG 304 1_555 BA O HOH . B HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc12 V MG MG . B MG 304 1_555 BA O HOH . B HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 4XF6 _atom_sites.fract_transf_matrix[1][1] 0.012926 _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] 0.012307 _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] 0.012188 _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 LIP A 1 301 301 LIP MIP . D 3 ADP A 1 302 302 ADP ADP . E 4 INS A 1 303 303 INS INS . F 5 MG A 1 304 401 MG MG . G 6 IOD A 1 305 502 IOD IOD . H 6 IOD A 1 306 503 IOD IOD . I 6 IOD A 1 307 504 IOD IOD . J 6 IOD A 1 308 505 IOD IOD . K 6 IOD A 1 309 506 IOD IOD . L 6 IOD A 1 310 507 IOD IOD . M 6 IOD A 1 311 509 IOD IOD . N 6 IOD A 1 312 510 IOD IOD . O 6 IOD A 1 313 511 IOD IOD . P 6 IOD A 1 314 513 IOD IOD . Q 6 IOD A 1 315 515 IOD IOD . R 7 EDO A 1 316 701 EDO EDO . S 2 LIP B 1 301 301 LIP MIP . T 3 ADP B 1 302 302 ADP ADP . U 4 INS B 1 303 303 INS INS . V 5 MG B 1 304 401 MG MG . W 6 IOD B 1 305 501 IOD IOD . X 6 IOD B 1 306 508 IOD IOD . Y 6 IOD B 1 307 512 IOD IOD . Z 6 IOD B 1 308 514 IOD IOD . AA 8 HOH A 1 401 649 HOH HOH . AA 8 HOH A 2 402 612 HOH HOH . AA 8 HOH A 3 403 628 HOH HOH . AA 8 HOH A 4 404 615 HOH HOH . AA 8 HOH A 5 405 625 HOH HOH . AA 8 HOH A 6 406 643 HOH HOH . AA 8 HOH A 7 407 630 HOH HOH . AA 8 HOH A 8 408 622 HOH HOH . AA 8 HOH A 9 409 651 HOH HOH . AA 8 HOH A 10 410 659 HOH HOH . AA 8 HOH A 11 411 627 HOH HOH . AA 8 HOH A 12 412 648 HOH HOH . AA 8 HOH A 13 413 604 HOH HOH . AA 8 HOH A 14 414 605 HOH HOH . AA 8 HOH A 15 415 606 HOH HOH . AA 8 HOH A 16 416 607 HOH HOH . AA 8 HOH A 17 417 609 HOH HOH . AA 8 HOH A 18 418 611 HOH HOH . AA 8 HOH A 19 419 614 HOH HOH . AA 8 HOH A 20 420 616 HOH HOH . AA 8 HOH A 21 421 618 HOH HOH . AA 8 HOH A 22 422 619 HOH HOH . AA 8 HOH A 23 423 621 HOH HOH . AA 8 HOH A 24 424 623 HOH HOH . AA 8 HOH A 25 425 626 HOH HOH . AA 8 HOH A 26 426 629 HOH HOH . AA 8 HOH A 27 427 631 HOH HOH . AA 8 HOH A 28 428 633 HOH HOH . AA 8 HOH A 29 429 634 HOH HOH . AA 8 HOH A 30 430 637 HOH HOH . AA 8 HOH A 31 431 639 HOH HOH . AA 8 HOH A 32 432 641 HOH HOH . AA 8 HOH A 33 433 644 HOH HOH . AA 8 HOH A 34 434 646 HOH HOH . AA 8 HOH A 35 435 647 HOH HOH . AA 8 HOH A 36 436 650 HOH HOH . AA 8 HOH A 37 437 652 HOH HOH . BA 8 HOH B 1 401 658 HOH HOH . BA 8 HOH B 2 402 624 HOH HOH . BA 8 HOH B 3 403 613 HOH HOH . BA 8 HOH B 4 404 645 HOH HOH . BA 8 HOH B 5 405 653 HOH HOH . BA 8 HOH B 6 406 601 HOH HOH . BA 8 HOH B 7 407 602 HOH HOH . BA 8 HOH B 8 408 603 HOH HOH . BA 8 HOH B 9 409 608 HOH HOH . BA 8 HOH B 10 410 610 HOH HOH . BA 8 HOH B 11 411 617 HOH HOH . BA 8 HOH B 12 412 620 HOH HOH . BA 8 HOH B 13 413 632 HOH HOH . BA 8 HOH B 14 414 635 HOH HOH . BA 8 HOH B 15 415 636 HOH HOH . BA 8 HOH B 16 416 638 HOH HOH . BA 8 HOH B 17 417 640 HOH HOH . BA 8 HOH B 18 418 642 HOH HOH . BA 8 HOH B 19 419 654 HOH HOH . BA 8 HOH B 20 420 655 HOH HOH . BA 8 HOH B 21 421 656 HOH HOH . BA 8 HOH B 22 422 657 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 P PB ADP . . . D 3 11.536 80.984 0.712 1 31.84 ? PB ADP 302 A 1 HETATM 2 O O1B ADP . . . D 3 12.632 80.482 -0.23 1 30.96 ? O1B ADP 302 A 1 HETATM 3 O O2B ADP . . . D 3 10.214 81.108 -0.037 1 35.89 ? O2B ADP 302 A 1 HETATM 4 O O3B ADP . . . D 3 11.461 80.333 2.057 1 29.74 ? O3B ADP 302 A 1 HETATM 5 P PA ADP . . . D 3 11.815 83.741 -0.169 1 35.05 ? PA ADP 302 A 1 HETATM 6 O O1A ADP . . . D 3 11.649 83.3 -1.623 1 37.12 ? O1A ADP 302 A 1 HETATM 7 O O2A ADP . . . D 3 11.093 84.939 0.382 1 36.57 ? O2A ADP 302 A 1 HETATM 8 O O3A ADP . . . D 3 11.815 82.553 0.945 1 32.53 ? O3A ADP 302 A 1 HETATM 9 O O5' ADP . . . D 3 13.383 84.198 -0.111 1 34.23 ? O5' ADP 302 A 1 HETATM 10 C C5' ADP . . . D 3 13.944 84.801 1.06 1 32.82 ? C5' ADP 302 A 1 HETATM 11 C C4' ADP . . . D 3 14.839 85.972 0.649 1 33.73 ? C4' ADP 302 A 1 HETATM 12 O O4' ADP . . . D 3 15.674 85.595 -0.459 1 33.47 ? O4' ADP 302 A 1 HETATM 13 C C3' ADP . . . D 3 14.041 87.181 0.187 1 35.93 ? C3' ADP 302 A 1 HETATM 14 O O3' ADP . . . D 3 13.613 88 1.249 1 36.38 ? O3' ADP 302 A 1 HETATM 15 C C2' ADP . . . D 3 15.055 87.876 -0.678 1 37.98 ? C2' ADP 302 A 1 HETATM 16 O O2' ADP . . . D 3 15.946 88.648 0.116 1 38.58 ? O2' ADP 302 A 1 HETATM 17 C C1' ADP . . . D 3 15.811 86.73 -1.317 1 36.47 ? C1' ADP 302 A 1 HETATM 18 N N9 ADP . . . D 3 15.209 86.435 -2.629 1 38.44 ? N9 ADP 302 A 1 HETATM 19 C C8 ADP . . . D 3 14.384 85.408 -2.877 1 37.43 ? C8 ADP 302 A 1 HETATM 20 N N7 ADP . . . D 3 14.027 85.383 -4.155 1 39.63 ? N7 ADP 302 A 1 HETATM 21 C C5 ADP . . . D 3 14.625 86.403 -4.761 1 42.09 ? C5 ADP 302 A 1 HETATM 22 C C6 ADP . . . D 3 14.618 86.928 -6.125 1 45.63 ? C6 ADP 302 A 1 HETATM 23 N N6 ADP . . . D 3 13.901 86.308 -7.078 1 47.38 ? N6 ADP 302 A 1 HETATM 24 N N1 ADP . . . D 3 15.362 88.03 -6.365 1 48.02 ? N1 ADP 302 A 1 HETATM 25 C C2 ADP . . . D 3 16.064 88.638 -5.394 1 46.18 ? C2 ADP 302 A 1 HETATM 26 N N3 ADP . . . D 3 16.103 88.207 -4.121 1 43.64 ? N3 ADP 302 A 1 HETATM 27 C C4 ADP . . . D 3 15.407 87.115 -3.753 1 40.97 ? C4 ADP 302 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #