data_1NFS # _model_server_result.job_id 10uJtVvm01YvEh5gipsR-w _model_server_result.datetime_utc '2024-10-19 00:47:58' _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 1nfs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 1NFS # _exptl.entry_id 1NFS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 249.096 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-DIMETHYLAMINO-ETHYL-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 1NFS _cell.length_a 68.982 _cell.length_b 71.493 _cell.length_c 91.441 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NFS _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 ? 4 E N N ? 4 H 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 metalc ? metalc1 A NE2 HIS 25 A HIS 25 1_555 C MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc2 A NE2 HIS 32 A HIS 32 1_555 C MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc3 A O CYS 67 A CYS 67 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc4 A NE2 HIS 69 A HIS 69 1_555 C MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc5 A OE2 GLU 87 A GLU 87 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc6 A OE1 GLU 87 A GLU 87 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.111 ? metalc ? metalc7 A OE2 GLU 114 A GLU 114 1_555 C MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc8 A OE1 GLU 114 A GLU 114 1_555 C MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc9 A OE2 GLU 116 A GLU 116 1_555 C MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.845 ? metalc ? metalc10 E O7 DED . A DED 301 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.792 ? metalc ? metalc11 E O2 DED . A DED 301 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc12 D MG MG . A MG 401 1_555 I O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc13 D MG MG . A MG 401 1_555 I O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc14 B NE2 HIS 25 B HIS 25 1_555 F MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc15 B NE2 HIS 32 B HIS 32 1_555 F MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc16 B O CYS 67 B CYS 67 1_555 G MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc17 B NE2 HIS 69 B HIS 69 1_555 F MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc18 B OE2 GLU 87 B GLU 87 1_555 G MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? metalc ? metalc19 B OE1 GLU 87 B GLU 87 1_555 G MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.087 ? metalc ? metalc20 B OE2 GLU 114 B GLU 114 1_555 F MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc21 B OE1 GLU 114 B GLU 114 1_555 F MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc22 B OE2 GLU 116 B GLU 116 1_555 F MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc23 H O7 DED . B DED 302 1_555 G MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.71 ? metalc ? metalc24 H O2 DED . B DED 302 1_555 G MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc25 G MG MG . B MG 401 1_555 J O HOH . B HOH 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc26 G MG MG . B MG 401 1_555 J O HOH . B HOH 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? # _chem_comp.formula 'C4 H13 N O7 P2' _chem_comp.formula_weight 249.096 _chem_comp.id DED _chem_comp.mon_nstd_flag . _chem_comp.name 2-DIMETHYLAMINO-ETHYL-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 O1 P4 DED sing 83 n n O1 HO1 DED sing 84 n n O2 P4 DED doub 85 n n O3 P4 DED sing 86 n n O3 HO3 DED sing 87 n n P4 O5 DED sing 88 n n O5 P8 DED sing 89 n n O6 P8 DED doub 90 n n O7 P8 DED sing 91 n n O7 HO7 DED sing 92 n n P8 O9 DED sing 93 n n O9 C10 DED sing 94 n n C10 C11 DED sing 95 n n C10 H101 DED sing 96 n n C10 H102 DED sing 97 n n C11 N12 DED sing 98 n n C11 H111 DED sing 99 n n C11 H112 DED sing 100 n n N12 C13 DED sing 101 n n N12 C14 DED sing 102 n n C13 H131 DED sing 103 n n C13 H132 DED sing 104 n n C13 H133 DED sing 105 n n C14 H141 DED sing 106 n n C14 H142 DED sing 107 n n C14 H143 DED sing 108 n n # _atom_sites.entry_id 1NFS _atom_sites.fract_transf_matrix[1][1] 0.014497 _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] 0.013987 _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] 0.010936 _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 MN A 1 201 201 MN MN . D 3 MG A 1 401 401 MG MG . E 4 DED A 1 301 301 DED NIP . F 2 MN B 1 201 201 MN MN . G 3 MG B 1 401 401 MG MG . H 4 DED B 1 302 302 DED NIP . I 5 HOH A 1 501 501 HOH HOH . I 5 HOH A 2 502 502 HOH HOH . I 5 HOH A 3 503 503 HOH HOH . I 5 HOH A 4 504 504 HOH HOH . I 5 HOH A 5 505 505 HOH HOH . I 5 HOH A 6 506 506 HOH HOH . I 5 HOH A 7 507 507 HOH HOH . I 5 HOH A 8 508 508 HOH HOH . I 5 HOH A 9 509 509 HOH HOH . I 5 HOH A 10 510 510 HOH HOH . I 5 HOH A 11 511 511 HOH HOH . I 5 HOH A 12 512 512 HOH HOH . I 5 HOH A 13 513 513 HOH HOH . I 5 HOH A 14 524 524 HOH HOH . I 5 HOH A 15 526 526 HOH HOH . I 5 HOH A 16 527 527 HOH HOH . I 5 HOH A 17 528 528 HOH HOH . I 5 HOH A 18 529 529 HOH HOH . I 5 HOH A 19 530 530 HOH HOH . I 5 HOH A 20 531 531 HOH HOH . I 5 HOH A 21 532 532 HOH HOH . I 5 HOH A 22 533 533 HOH HOH . I 5 HOH A 23 535 535 HOH HOH . I 5 HOH A 24 538 538 HOH HOH . I 5 HOH A 25 541 541 HOH HOH . I 5 HOH A 26 543 543 HOH HOH . I 5 HOH A 27 548 548 HOH HOH . I 5 HOH A 28 552 552 HOH HOH . I 5 HOH A 29 556 556 HOH HOH . I 5 HOH A 30 558 558 HOH HOH . I 5 HOH A 31 559 559 HOH HOH . I 5 HOH A 32 560 560 HOH HOH . I 5 HOH A 33 563 563 HOH HOH . I 5 HOH A 34 564 564 HOH HOH . I 5 HOH A 35 569 569 HOH HOH . I 5 HOH A 36 570 570 HOH HOH . I 5 HOH A 37 571 571 HOH HOH . I 5 HOH A 38 572 572 HOH HOH . I 5 HOH A 39 576 576 HOH HOH . I 5 HOH A 40 577 577 HOH HOH . I 5 HOH A 41 578 578 HOH HOH . I 5 HOH A 42 579 579 HOH HOH . I 5 HOH A 43 581 581 HOH HOH . I 5 HOH A 44 582 582 HOH HOH . I 5 HOH A 45 586 586 HOH HOH . I 5 HOH A 46 589 589 HOH HOH . I 5 HOH A 47 592 592 HOH HOH . I 5 HOH A 48 596 596 HOH HOH . I 5 HOH A 49 597 597 HOH HOH . I 5 HOH A 50 599 599 HOH HOH . I 5 HOH A 51 600 600 HOH HOH . I 5 HOH A 52 601 601 HOH HOH . I 5 HOH A 53 603 603 HOH HOH . I 5 HOH A 54 604 604 HOH HOH . I 5 HOH A 55 605 605 HOH HOH . I 5 HOH A 56 606 606 HOH HOH . I 5 HOH A 57 607 607 HOH HOH . I 5 HOH A 58 608 608 HOH HOH . I 5 HOH A 59 609 609 HOH HOH . I 5 HOH A 60 612 612 HOH HOH . I 5 HOH A 61 613 613 HOH HOH . I 5 HOH A 62 615 615 HOH HOH . I 5 HOH A 63 617 617 HOH HOH . J 5 HOH B 1 514 514 HOH HOH . J 5 HOH B 2 515 515 HOH HOH . J 5 HOH B 3 516 516 HOH HOH . J 5 HOH B 4 517 517 HOH HOH . J 5 HOH B 5 518 518 HOH HOH . J 5 HOH B 6 519 519 HOH HOH . J 5 HOH B 7 520 520 HOH HOH . J 5 HOH B 8 521 521 HOH HOH . J 5 HOH B 9 522 522 HOH HOH . J 5 HOH B 10 523 523 HOH HOH . J 5 HOH B 11 525 525 HOH HOH . J 5 HOH B 12 534 534 HOH HOH . J 5 HOH B 13 536 536 HOH HOH . J 5 HOH B 14 537 537 HOH HOH . J 5 HOH B 15 539 539 HOH HOH . J 5 HOH B 16 540 540 HOH HOH . J 5 HOH B 17 542 542 HOH HOH . J 5 HOH B 18 544 544 HOH HOH . J 5 HOH B 19 545 545 HOH HOH . J 5 HOH B 20 546 546 HOH HOH . J 5 HOH B 21 547 547 HOH HOH . J 5 HOH B 22 549 549 HOH HOH . J 5 HOH B 23 550 550 HOH HOH . J 5 HOH B 24 551 551 HOH HOH . J 5 HOH B 25 553 553 HOH HOH . J 5 HOH B 26 554 554 HOH HOH . J 5 HOH B 27 555 555 HOH HOH . J 5 HOH B 28 557 557 HOH HOH . J 5 HOH B 29 561 561 HOH HOH . J 5 HOH B 30 562 562 HOH HOH . J 5 HOH B 31 565 565 HOH HOH . J 5 HOH B 32 566 566 HOH HOH . J 5 HOH B 33 567 567 HOH HOH . J 5 HOH B 34 568 568 HOH HOH . J 5 HOH B 35 573 573 HOH HOH . J 5 HOH B 36 574 574 HOH HOH . J 5 HOH B 37 575 575 HOH HOH . J 5 HOH B 38 580 580 HOH HOH . J 5 HOH B 39 583 583 HOH HOH . J 5 HOH B 40 584 584 HOH HOH . J 5 HOH B 41 585 585 HOH HOH . J 5 HOH B 42 587 587 HOH HOH . J 5 HOH B 43 588 588 HOH HOH . J 5 HOH B 44 590 590 HOH HOH . J 5 HOH B 45 591 591 HOH HOH . J 5 HOH B 46 593 593 HOH HOH . J 5 HOH B 47 594 594 HOH HOH . J 5 HOH B 48 595 595 HOH HOH . J 5 HOH B 49 598 598 HOH HOH . J 5 HOH B 50 602 602 HOH HOH . J 5 HOH B 51 610 610 HOH HOH . J 5 HOH B 52 611 611 HOH HOH . J 5 HOH B 53 614 614 HOH HOH . J 5 HOH B 54 616 616 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 O O1 DED . . . E 4 11.084 2.494 10.328 1 30.95 ? O1 DED 301 A 1 HETATM 2 O O2 DED . . . E 4 10.723 2.289 12.621 1 23.24 ? O2 DED 301 A 1 HETATM 3 O O3 DED . . . E 4 8.857 2.093 11.106 1 37.32 ? O3 DED 301 A 1 HETATM 4 P P4 DED . . . E 4 10.196 2.764 11.282 1 29.96 ? P4 DED 301 A 1 HETATM 5 O O5 DED . . . E 4 9.923 4.267 11.444 1 28.75 ? O5 DED 301 A 1 HETATM 6 O O6 DED . . . E 4 11.608 5.916 11.815 1 31.72 ? O6 DED 301 A 1 HETATM 7 O O7 DED . . . E 4 11.547 3.889 13.184 1 41.74 ? O7 DED 301 A 1 HETATM 8 P P8 DED . . . E 4 10.844 4.996 12.435 1 37 ? P8 DED 301 A 1 HETATM 9 O O9 DED . . . E 4 9.93 5.696 13.422 1 37.84 ? O9 DED 301 A 1 HETATM 10 C C10 DED . . . E 4 9.793 7.097 13.188 1 39.62 ? C10 DED 301 A 1 HETATM 11 C C11 DED . . . E 4 8.641 7.654 14.059 1 42.01 ? C11 DED 301 A 1 HETATM 12 N N12 DED . . . E 4 8.885 9.093 14.248 1 42.44 ? N12 DED 301 A 1 HETATM 13 C C13 DED . . . E 4 9.149 9.388 15.66 1 29.38 ? C13 DED 301 A 1 HETATM 14 C C14 DED . . . E 4 10.047 9.456 13.413 1 36.92 ? C14 DED 301 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #