data_4XF7 # _model_server_result.job_id x38p6_FnVmIHBJL5OsYyNQ _model_server_result.datetime_utc '2024-11-24 17:26:50' _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":"D","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 . . . D 3 12.196 79.665 -1.279 1 44.76 ? PG ACP 302 A 1 HETATM 2 O O1G ACP . . . D 3 11.765 78.641 -2.46 1 50.2 ? O1G ACP 302 A 1 HETATM 3 O O2G ACP . . . D 3 13.36 78.96 -0.416 1 45.29 ? O2G ACP 302 A 1 HETATM 4 O O3G ACP . . . D 3 12.722 80.918 -1.866 1 44.8 ? O3G ACP 302 A 1 HETATM 5 P PB ACP . . . D 3 10.948 80.966 1.098 1 35.91 ? PB ACP 302 A 1 HETATM 6 O O1B ACP . . . D 3 9.556 81.687 1.355 1 31.43 ? O1B ACP 302 A 1 HETATM 7 O O2B ACP . . . D 3 11.358 80.115 2.273 1 32.71 ? O2B ACP 302 A 1 HETATM 8 C C3B ACP . . . D 3 10.669 79.942 -0.359 1 38.44 ? C3B ACP 302 A 1 HETATM 9 P PA ACP . . . D 3 11.719 83.437 -0.007 1 35.4 ? PA ACP 302 A 1 HETATM 10 O O1A ACP . . . D 3 11.318 82.975 -1.394 1 37.86 ? O1A ACP 302 A 1 HETATM 11 O O2A ACP . . . D 3 10.803 84.401 0.696 1 33.67 ? O2A ACP 302 A 1 HETATM 12 O O3A ACP . . . D 3 12.034 82.111 0.877 1 32.04 ? O3A ACP 302 A 1 HETATM 13 O O5' ACP . . . D 3 13.174 84.08 -0.084 1 32.99 ? O5' ACP 302 A 1 HETATM 14 C C5' ACP . . . D 3 13.831 84.563 1.07 1 34.37 ? C5' ACP 302 A 1 HETATM 15 C C4' ACP . . . D 3 14.663 85.78 0.749 1 35.23 ? C4' ACP 302 A 1 HETATM 16 O O4' ACP . . . D 3 15.582 85.492 -0.315 1 36.81 ? O4' ACP 302 A 1 HETATM 17 C C3' ACP . . . D 3 13.866 86.999 0.297 1 34.71 ? C3' ACP 302 A 1 HETATM 18 O O3' ACP . . . D 3 13.393 87.761 1.413 1 34.83 ? O3' ACP 302 A 1 HETATM 19 C C2' ACP . . . D 3 14.878 87.75 -0.548 1 33.6 ? C2' ACP 302 A 1 HETATM 20 O O2' ACP . . . D 3 15.767 88.555 0.233 1 31.57 ? O2' ACP 302 A 1 HETATM 21 C C1' ACP . . . D 3 15.695 86.64 -1.173 1 37.05 ? C1' ACP 302 A 1 HETATM 22 N N9 ACP . . . D 3 15.085 86.359 -2.483 1 40.74 ? N9 ACP 302 A 1 HETATM 23 C C8 ACP . . . D 3 14.163 85.413 -2.765 1 41.36 ? C8 ACP 302 A 1 HETATM 24 N N7 ACP . . . D 3 13.8 85.46 -4.063 1 42.41 ? N7 ACP 302 A 1 HETATM 25 C C5 ACP . . . D 3 14.499 86.471 -4.608 1 46.09 ? C5 ACP 302 A 1 HETATM 26 C C6 ACP . . . D 3 14.599 87.061 -5.958 1 50.14 ? C6 ACP 302 A 1 HETATM 27 N N6 ACP . . . D 3 13.846 86.535 -6.944 1 45.13 ? N6 ACP 302 A 1 HETATM 28 N N1 ACP . . . D 3 15.448 88.107 -6.123 1 53.21 ? N1 ACP 302 A 1 HETATM 29 C C2 ACP . . . D 3 16.197 88.603 -5.106 1 54.07 ? C2 ACP 302 A 1 HETATM 30 N N3 ACP . . . D 3 16.157 88.116 -3.846 1 48.24 ? N3 ACP 302 A 1 HETATM 31 C C4 ACP . . . D 3 15.339 87.073 -3.563 1 45.7 ? C4 ACP 302 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #