data_4XF7 # _model_server_result.job_id 7paXqBGe5tAsjKpwJuinww _model_server_result.datetime_utc '2025-02-16 13:27:45' _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 4xf7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":302}' # _entry.id 4XF7 # _exptl.entry_id 4XF7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 4XF7 _cell.length_a 77.134 _cell.length_b 81.176 _cell.length_c 81.109 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XF7 _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,EA 1 1 B,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,FA 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 S 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 A O SER 123 A SER 123 1_555 N I IOD . A IOD 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? covale ? covale2 Z I IOD . B IOD 309 1_555 DA I IOD . B IOD 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc1 A OE1 GLN 136 A GLN 136 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc2 D O2B ACP . A ACP 302 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc3 E MG MG . A MG 303 1_555 EA O HOH . A HOH 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc4 E MG MG . A MG 303 1_555 EA O HOH . A HOH 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc5 E MG MG . A MG 303 1_555 EA O HOH . A HOH 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc6 E MG MG . A MG 303 1_555 EA O HOH . A HOH 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc7 B OE1 GLN 136 B GLN 136 1_555 T MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc8 S O1B ACP . B ACP 302 1_555 T MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc9 T MG MG . B MG 303 1_555 FA O HOH . B HOH 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc10 T MG MG . B MG 303 1_555 FA O HOH . B HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc11 T MG MG . B MG 303 1_555 FA O HOH . B HOH 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc12 T MG MG . B MG 303 1_555 FA O HOH . B HOH 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 PG O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 4XF7 _atom_sites.fract_transf_matrix[1][1] 0.012964 _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] 0.012319 _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] 0.012329 _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 INS A 1 301 301 INS INS . D 3 ACP A 1 302 302 ACP ACP . E 4 MG A 1 303 401 MG MG . F 5 IOD A 1 304 501 IOD IOD . G 5 IOD A 1 305 503 IOD IOD . H 5 IOD A 1 306 505 IOD IOD . I 5 IOD A 1 307 507 IOD IOD . J 5 IOD A 1 308 508 IOD IOD . K 5 IOD A 1 309 509 IOD IOD . L 5 IOD A 1 310 510 IOD IOD . M 5 IOD A 1 311 512 IOD IOD . N 5 IOD A 1 312 513 IOD IOD . O 5 IOD A 1 313 519 IOD IOD . P 5 IOD A 1 314 521 IOD IOD . Q 5 IOD A 1 315 522 IOD IOD . R 2 INS B 1 301 301 INS INS . S 3 ACP B 1 302 302 ACP ACP . T 4 MG B 1 303 401 MG MG . U 5 IOD B 1 304 502 IOD IOD . V 5 IOD B 1 305 504 IOD IOD . W 5 IOD B 1 306 506 IOD IOD . X 5 IOD B 1 307 511 IOD IOD . Y 5 IOD B 1 308 514 IOD IOD . Z 5 IOD B 1 309 515 IOD IOD . AA 5 IOD B 1 310 516 IOD IOD . BA 5 IOD B 1 311 517 IOD IOD . CA 5 IOD B 1 312 518 IOD IOD . DA 5 IOD B 1 313 520 IOD IOD . EA 6 HOH A 1 401 635 HOH HOH . EA 6 HOH A 2 402 669 HOH HOH . EA 6 HOH A 3 403 654 HOH HOH . EA 6 HOH A 4 404 659 HOH HOH . EA 6 HOH A 5 405 648 HOH HOH . EA 6 HOH A 6 406 670 HOH HOH . EA 6 HOH A 7 407 664 HOH HOH . EA 6 HOH A 8 408 624 HOH HOH . EA 6 HOH A 9 409 637 HOH HOH . EA 6 HOH A 10 410 672 HOH HOH . EA 6 HOH A 11 411 650 HOH HOH . EA 6 HOH A 12 412 684 HOH HOH . EA 6 HOH A 13 413 691 HOH HOH . EA 6 HOH A 14 414 623 HOH HOH . EA 6 HOH A 15 415 630 HOH HOH . EA 6 HOH A 16 416 629 HOH HOH . EA 6 HOH A 17 417 688 HOH HOH . EA 6 HOH A 18 418 705 HOH HOH . EA 6 HOH A 19 419 700 HOH HOH . EA 6 HOH A 20 420 662 HOH HOH . EA 6 HOH A 21 421 693 HOH HOH . EA 6 HOH A 22 422 680 HOH HOH . EA 6 HOH A 23 423 692 HOH HOH . EA 6 HOH A 24 424 603 HOH HOH . EA 6 HOH A 25 425 604 HOH HOH . EA 6 HOH A 26 426 605 HOH HOH . EA 6 HOH A 27 427 606 HOH HOH . EA 6 HOH A 28 428 608 HOH HOH . EA 6 HOH A 29 429 609 HOH HOH . EA 6 HOH A 30 430 610 HOH HOH . EA 6 HOH A 31 431 616 HOH HOH . EA 6 HOH A 32 432 618 HOH HOH . EA 6 HOH A 33 433 620 HOH HOH . EA 6 HOH A 34 434 621 HOH HOH . EA 6 HOH A 35 435 622 HOH HOH . EA 6 HOH A 36 436 627 HOH HOH . EA 6 HOH A 37 437 628 HOH HOH . EA 6 HOH A 38 438 631 HOH HOH . EA 6 HOH A 39 439 634 HOH HOH . EA 6 HOH A 40 440 636 HOH HOH . EA 6 HOH A 41 441 644 HOH HOH . EA 6 HOH A 42 442 655 HOH HOH . EA 6 HOH A 43 443 657 HOH HOH . EA 6 HOH A 44 444 663 HOH HOH . EA 6 HOH A 45 445 673 HOH HOH . EA 6 HOH A 46 446 676 HOH HOH . EA 6 HOH A 47 447 681 HOH HOH . EA 6 HOH A 48 448 682 HOH HOH . EA 6 HOH A 49 449 683 HOH HOH . EA 6 HOH A 50 450 685 HOH HOH . EA 6 HOH A 51 451 686 HOH HOH . EA 6 HOH A 52 452 689 HOH HOH . EA 6 HOH A 53 453 696 HOH HOH . EA 6 HOH A 54 454 697 HOH HOH . EA 6 HOH A 55 455 698 HOH HOH . EA 6 HOH A 56 456 699 HOH HOH . FA 6 HOH B 1 401 632 HOH HOH . FA 6 HOH B 2 402 671 HOH HOH . FA 6 HOH B 3 403 702 HOH HOH . FA 6 HOH B 4 404 665 HOH HOH . FA 6 HOH B 5 405 656 HOH HOH . FA 6 HOH B 6 406 660 HOH HOH . FA 6 HOH B 7 407 639 HOH HOH . FA 6 HOH B 8 408 666 HOH HOH . FA 6 HOH B 9 409 658 HOH HOH . FA 6 HOH B 10 410 646 HOH HOH . FA 6 HOH B 11 411 694 HOH HOH . FA 6 HOH B 12 412 678 HOH HOH . FA 6 HOH B 13 413 703 HOH HOH . FA 6 HOH B 14 414 695 HOH HOH . FA 6 HOH B 15 415 704 HOH HOH . FA 6 HOH B 16 416 687 HOH HOH . FA 6 HOH B 17 417 601 HOH HOH . FA 6 HOH B 18 418 602 HOH HOH . FA 6 HOH B 19 419 607 HOH HOH . FA 6 HOH B 20 420 611 HOH HOH . FA 6 HOH B 21 421 612 HOH HOH . FA 6 HOH B 22 422 613 HOH HOH . FA 6 HOH B 23 423 614 HOH HOH . FA 6 HOH B 24 424 615 HOH HOH . FA 6 HOH B 25 425 617 HOH HOH . FA 6 HOH B 26 426 619 HOH HOH . FA 6 HOH B 27 427 625 HOH HOH . FA 6 HOH B 28 428 626 HOH HOH . FA 6 HOH B 29 429 633 HOH HOH . FA 6 HOH B 30 430 638 HOH HOH . FA 6 HOH B 31 431 640 HOH HOH . FA 6 HOH B 32 432 641 HOH HOH . FA 6 HOH B 33 433 642 HOH HOH . FA 6 HOH B 34 434 643 HOH HOH . FA 6 HOH B 35 435 645 HOH HOH . FA 6 HOH B 36 436 647 HOH HOH . FA 6 HOH B 37 437 649 HOH HOH . FA 6 HOH B 38 438 651 HOH HOH . FA 6 HOH B 39 439 652 HOH HOH . FA 6 HOH B 40 440 653 HOH HOH . FA 6 HOH B 41 441 661 HOH HOH . FA 6 HOH B 42 442 667 HOH HOH . FA 6 HOH B 43 443 668 HOH HOH . FA 6 HOH B 44 444 674 HOH HOH . FA 6 HOH B 45 445 675 HOH HOH . FA 6 HOH B 46 446 677 HOH HOH . FA 6 HOH B 47 447 679 HOH HOH . FA 6 HOH B 48 448 690 HOH HOH . FA 6 HOH B 49 449 701 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 PG ACP . . . S 3 6.102 41.328 -13.167 1 44.64 ? PG ACP 302 B 1 HETATM 2 O O1G ACP . . . S 3 7.658 41.31 -13.512 1 39.05 ? O1G ACP 302 B 1 HETATM 3 O O2G ACP . . . S 3 5.661 39.973 -12.417 1 46.83 ? O2G ACP 302 B 1 HETATM 4 O O3G ACP . . . S 3 5.892 42.435 -12.188 1 47.64 ? O3G ACP 302 B 1 HETATM 5 P PB ACP . . . S 3 5.451 40.494 -16.015 1 30.9 ? PB ACP 302 B 1 HETATM 6 O O1B ACP . . . S 3 6.553 41.138 -16.787 1 30.14 ? O1B ACP 302 B 1 HETATM 7 O O2B ACP . . . S 3 4.084 40.401 -16.772 1 31.52 ? O2B ACP 302 B 1 HETATM 8 C C3B ACP . . . S 3 5.055 41.602 -14.619 1 35.73 ? C3B ACP 302 B 1 HETATM 9 P PA ACP . . . S 3 4.886 37.959 -14.965 1 30.38 ? PA ACP 302 B 1 HETATM 10 O O1A ACP . . . S 3 3.871 37.413 -15.949 1 30.27 ? O1A ACP 302 B 1 HETATM 11 O O2A ACP . . . S 3 4.322 38.556 -13.692 1 33.68 ? O2A ACP 302 B 1 HETATM 12 O O3A ACP . . . S 3 5.882 39.053 -15.539 1 29.75 ? O3A ACP 302 B 1 HETATM 13 O O5' ACP . . . S 3 5.901 36.839 -14.554 1 27.77 ? O5' ACP 302 B 1 HETATM 14 C C5' ACP . . . S 3 6.665 36.051 -15.434 1 29.42 ? C5' ACP 302 B 1 HETATM 15 C C4' ACP . . . S 3 6.707 34.639 -14.92 1 29.31 ? C4' ACP 302 B 1 HETATM 16 O O4' ACP . . . S 3 7.237 34.595 -13.583 1 30.74 ? O4' ACP 302 B 1 HETATM 17 C C3' ACP . . . S 3 5.379 33.909 -14.891 1 30.15 ? C3' ACP 302 B 1 HETATM 18 O O3' ACP . . . S 3 4.97 33.368 -16.167 1 27.19 ? O3' ACP 302 B 1 HETATM 19 C C2' ACP . . . S 3 5.65 32.821 -13.851 1 29.64 ? C2' ACP 302 B 1 HETATM 20 O O2' ACP . . . S 3 6.327 31.678 -14.407 1 27.75 ? O2' ACP 302 B 1 HETATM 21 C C1' ACP . . . S 3 6.571 33.539 -12.889 1 30.77 ? C1' ACP 302 B 1 HETATM 22 N N9 ACP . . . S 3 5.769 34.137 -11.805 1 33.39 ? N9 ACP 302 B 1 HETATM 23 C C8 ACP . . . S 3 5.289 35.392 -11.756 1 35.84 ? C8 ACP 302 B 1 HETATM 24 N N7 ACP . . . S 3 4.592 35.597 -10.605 1 34.42 ? N7 ACP 302 B 1 HETATM 25 C C5 ACP . . . S 3 4.623 34.446 -9.914 1 34.58 ? C5 ACP 302 B 1 HETATM 26 C C6 ACP . . . S 3 4.091 33.975 -8.615 1 36.98 ? C6 ACP 302 B 1 HETATM 27 N N6 ACP . . . S 3 3.374 34.825 -7.827 1 37.35 ? N6 ACP 302 B 1 HETATM 28 N N1 ACP . . . S 3 4.352 32.697 -8.255 1 35.32 ? N1 ACP 302 B 1 HETATM 29 C C2 ACP . . . S 3 5.069 31.861 -9.026 1 37.52 ? C2 ACP 302 B 1 HETATM 30 N N3 ACP . . . S 3 5.575 32.231 -10.228 1 35.39 ? N3 ACP 302 B 1 HETATM 31 C C4 ACP . . . S 3 5.398 33.487 -10.703 1 34.38 ? C4 ACP 302 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #