data_4DL6 # _model_server_result.job_id JcivDAAJpki8IrSDFl7IAg _model_server_result.datetime_utc '2024-10-18 17:18:43' _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 4dl6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":503}' # _entry.id 4DL6 # _exptl.entry_id 4DL6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine" _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 120 _cell.entry_id 4DL6 _cell.length_a 98.78 _cell.length_b 98.78 _cell.length_c 81.51 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DL6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _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 metalc ? metalc1 A OD1 ASP 16 A ASP 13 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc2 A OD2 ASP 16 A ASP 13 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc4 A OD1 ASP 118 A ASP 115 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc5 A OD2 ASP 118 A ASP 115 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc6 A OE2 GLU 119 A GLU 116 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? metalc ? metalc7 D MG MG . A MG 501 1_555 F O1B XG4 . A XG4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc8 D MG MG . A MG 501 1_555 F O1G XG4 . A XG4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc9 D MG MG . A MG 501 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc10 E MG MG . A MG 502 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc11 E MG MG . A MG 502 1_555 H O HOH . A HOH 631 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc12 E MG MG . A MG 502 1_555 C O3' DC 9 P DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc13 B N7 DG 5 T DG 5 1_555 G PT1 CPT . T CPT 101 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.068 ? metalc ? metalc14 B N7 DG 5 T DG 5 1_555 G PT1 CPT . T CPT 101 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.079 ? metalc ? metalc15 B N7 DG 6 T DG 6 1_555 G PT1 CPT . T CPT 101 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.046 ? metalc ? metalc16 B N7 DG 6 T DG 6 1_555 G PT1 CPT . T CPT 101 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.123 ? hydrog WATSON-CRICK hydrog1 B N1 DG 5 T DG 5 1_555 C N3 DC 9 P DC 9 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 5 T DG 5 1_555 C O2 DC 9 P DC 9 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 5 T DG 5 1_555 C N4 DC 9 P DC 9 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DG 6 T DG 6 1_555 C N3 DC 8 P DC 8 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 DG 6 T DG 6 1_555 C O2 DC 8 P DC 8 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 6 T DG 6 1_555 C N4 DC 8 P DC 8 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 DC 7 T DC 7 1_555 C N1 DG 7 P DG 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N4 DC 7 T DC 7 1_555 C O6 DG 7 P DG 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O2 DC 7 T DC 7 1_555 C N2 DG 7 P DG 7 1_555 ? A ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DA 8 T DA 8 1_555 C N3 DT 6 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N6 DA 8 T DA 8 1_555 C O4 DT 6 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N3 DC 9 T DC 9 1_555 C N1 DG 5 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N4 DC 9 T DC 9 1_555 C O6 DG 5 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O2 DC 9 T DC 9 1_555 C N2 DG 5 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N1 DA 10 T DA 10 1_555 C N3 DT 4 P DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N6 DA 10 T DA 10 1_555 C O4 DT 4 P DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DC 11 T DC 11 1_555 C N1 DG 3 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N4 DC 11 T DC 11 1_555 C O6 DG 3 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O2 DC 11 T DC 11 1_555 C N2 DG 3 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N3 DT 12 T DT 12 1_555 C N1 DA 2 P DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O4 DT 12 T DT 12 1_555 C N6 DA 2 P DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id XG4 _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine" _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 C2 N1 XG4 sing 535 n n N1 C6 XG4 sing 536 n n N1 HN1 XG4 sing 537 n n N3 C2 XG4 doub 538 n n N2 C2 XG4 sing 539 n n N2 HN2 XG4 sing 540 n n N2 HN2A XG4 sing 541 n n N3 C4 XG4 sing 542 n n N9 C4 XG4 sing 543 n y C4 C5 XG4 doub 544 n y C5 N7 XG4 sing 545 n y C5 C6 XG4 sing 546 n n C6 O6 XG4 doub 547 n n C8 N7 XG4 doub 548 n y N9 C8 XG4 sing 549 n y C8 H8 XG4 sing 550 n n C1' N9 XG4 sing 551 n n O5' PA XG4 sing 552 n n O1A PA XG4 doub 553 n n PA O2A XG4 sing 554 n n PA N3A XG4 sing 555 n n O1B PB XG4 doub 556 n n N3A PB XG4 sing 557 n n PB O2B XG4 sing 558 n n PB O3B XG4 sing 559 n n O1G PG XG4 doub 560 n n PG O3B XG4 sing 561 n n PG O2G XG4 sing 562 n n PG O3G XG4 sing 563 n n O4' C1' XG4 sing 564 n n C1' C2' XG4 sing 565 n n C1' H1' XG4 sing 566 n n C2' C3' XG4 sing 567 n n C2' H2' XG4 sing 568 n n C2' "H2'A" XG4 sing 569 n n O2A HO2A XG4 sing 570 n n O2B HO2B XG4 sing 571 n n O2G HO2G XG4 sing 572 n n C4' C3' XG4 sing 573 n n C3' O3' XG4 sing 574 n n C3' H3' XG4 sing 575 n n O3' HO3' XG4 sing 576 n n N3A HN3A XG4 sing 577 n n O3G HO3G XG4 sing 578 n n O4' C4' XG4 sing 579 n n C4' C5' XG4 sing 580 n n C4' H4' XG4 sing 581 n n C5' O5' XG4 sing 582 n n C5' H5' XG4 sing 583 n n C5' "H5'A" XG4 sing 584 n n # _atom_sites.entry_id 4DL6 _atom_sites.fract_transf_matrix[1][1] 0.010124 _atom_sites.fract_transf_matrix[1][2] 0.005845 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01169 _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] 0.012268 _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 D 4 MG A 1 501 501 MG MG . E 4 MG A 1 502 502 MG MG . F 5 XG4 A 1 503 10 XG4 XG4 . G 6 CPT T 1 101 13 CPT CTP . H 7 HOH A 1 601 601 HOH HOH . H 7 HOH A 2 602 602 HOH HOH . H 7 HOH A 3 603 603 HOH HOH . H 7 HOH A 4 604 604 HOH HOH . H 7 HOH A 5 605 605 HOH HOH . H 7 HOH A 6 606 606 HOH HOH . H 7 HOH A 7 607 607 HOH HOH . H 7 HOH A 8 608 608 HOH HOH . H 7 HOH A 9 609 609 HOH HOH . H 7 HOH A 10 610 610 HOH HOH . H 7 HOH A 11 611 611 HOH HOH . H 7 HOH A 12 612 612 HOH HOH . H 7 HOH A 13 613 613 HOH HOH . H 7 HOH A 14 614 614 HOH HOH . H 7 HOH A 15 615 615 HOH HOH . H 7 HOH A 16 616 616 HOH HOH . H 7 HOH A 17 617 617 HOH HOH . H 7 HOH A 18 618 618 HOH HOH . H 7 HOH A 19 619 619 HOH HOH . H 7 HOH A 20 620 620 HOH HOH . H 7 HOH A 21 621 621 HOH HOH . H 7 HOH A 22 622 622 HOH HOH . H 7 HOH A 23 623 623 HOH HOH . H 7 HOH A 24 624 624 HOH HOH . H 7 HOH A 25 625 625 HOH HOH . H 7 HOH A 26 626 626 HOH HOH . H 7 HOH A 27 627 627 HOH HOH . H 7 HOH A 28 628 628 HOH HOH . H 7 HOH A 29 629 629 HOH HOH . H 7 HOH A 30 630 630 HOH HOH . H 7 HOH A 31 631 631 HOH HOH . H 7 HOH A 32 632 632 HOH HOH . H 7 HOH A 33 633 633 HOH HOH . H 7 HOH A 34 634 634 HOH HOH . H 7 HOH A 35 635 635 HOH HOH . H 7 HOH A 36 636 636 HOH HOH . H 7 HOH A 37 637 637 HOH HOH . H 7 HOH A 38 638 638 HOH HOH . H 7 HOH A 39 639 639 HOH HOH . H 7 HOH A 40 640 640 HOH HOH . H 7 HOH A 41 641 641 HOH HOH . H 7 HOH A 42 642 642 HOH HOH . H 7 HOH A 43 643 643 HOH HOH . H 7 HOH A 44 644 644 HOH HOH . H 7 HOH A 45 645 645 HOH HOH . H 7 HOH A 46 646 646 HOH HOH . H 7 HOH A 47 647 647 HOH HOH . H 7 HOH A 48 648 648 HOH HOH . H 7 HOH A 49 649 649 HOH HOH . H 7 HOH A 50 650 650 HOH HOH . H 7 HOH A 51 651 651 HOH HOH . H 7 HOH A 52 652 652 HOH HOH . H 7 HOH A 53 653 653 HOH HOH . H 7 HOH A 54 654 654 HOH HOH . H 7 HOH A 55 655 655 HOH HOH . I 7 HOH T 1 201 201 HOH HOH . I 7 HOH T 2 202 202 HOH HOH . I 7 HOH T 3 203 203 HOH HOH . J 7 HOH P 1 101 101 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 N1 XG4 . . . F 5 43.242 4.576 4.754 1 46.78 ? N1 XG4 503 A 1 HETATM 2 C C2 XG4 . . . F 5 43.701 5.595 3.906 1 46.76 ? C2 XG4 503 A 1 HETATM 3 N N2 XG4 . . . F 5 42.739 6.512 3.542 1 45.53 ? N2 XG4 503 A 1 HETATM 4 N N3 XG4 . . . F 5 44.983 5.779 3.399 1 44.52 ? N3 XG4 503 A 1 HETATM 5 C C4 XG4 . . . F 5 45.867 4.819 3.82 1 39.22 ? C4 XG4 503 A 1 HETATM 6 C C5 XG4 . . . F 5 45.507 3.74 4.68 1 38.91 ? C5 XG4 503 A 1 HETATM 7 C C6 XG4 . . . F 5 44.175 3.665 5.122 1 43.62 ? C6 XG4 503 A 1 HETATM 8 O O6 XG4 . . . F 5 43.817 2.655 5.933 1 47.17 ? O6 XG4 503 A 1 HETATM 9 N N7 XG4 . . . F 5 46.613 2.92 4.935 1 41.78 ? N7 XG4 503 A 1 HETATM 10 C C8 XG4 . . . F 5 47.615 3.477 4.252 1 42.41 ? C8 XG4 503 A 1 HETATM 11 N N9 XG4 . . . F 5 47.24 4.646 3.53 1 38.83 ? N9 XG4 503 A 1 HETATM 12 P PA XG4 . . . F 5 51.795 2.133 3.981 1 35.16 ? PA XG4 503 A 1 HETATM 13 P PB XG4 . . . F 5 53.358 4.32 5.26 1 37.8 ? PB XG4 503 A 1 HETATM 14 P PG XG4 . . . F 5 55.498 2.666 6.342 1 33.87 ? PG XG4 503 A 1 HETATM 15 C C1' XG4 . . . F 5 48.092 5.534 2.669 1 32.06 ? C1' XG4 503 A 1 HETATM 16 O O1A XG4 . . . F 5 53.064 1.789 3.111 1 31.6 ? O1A XG4 503 A 1 HETATM 17 O O1B XG4 . . . F 5 54.153 4.431 3.901 1 35.69 ? O1B XG4 503 A 1 HETATM 18 O O1G XG4 . . . F 5 55.421 2.03 4.915 1 37.85 ? O1G XG4 503 A 1 HETATM 19 C C2' XG4 . . . F 5 48.783 6.653 3.481 1 33.57 ? C2' XG4 503 A 1 HETATM 20 O O2A XG4 . . . F 5 51.029 0.912 4.28 1 37.36 ? O2A XG4 503 A 1 HETATM 21 O O2B XG4 . . . F 5 52.575 5.519 5.711 1 40.31 ? O2B XG4 503 A 1 HETATM 22 O O2G XG4 . . . F 5 56.98 3.212 6.393 1 34.46 ? O2G XG4 503 A 1 HETATM 23 C C3' XG4 . . . F 5 50.203 6.088 3.666 1 29.67 ? C3' XG4 503 A 1 HETATM 24 O O3' XG4 . . . F 5 51.172 7.04 3.96 1 34.4 ? O3' XG4 503 A 1 HETATM 25 N N3A XG4 . . . F 5 52.283 3.063 5.269 1 37.29 ? N3A XG4 503 A 1 HETATM 26 O O3B XG4 . . . F 5 54.47 3.86 6.287 1 34.46 ? O3B XG4 503 A 1 HETATM 27 O O3G XG4 . . . F 5 55.046 1.867 7.491 1 35.08 ? O3G XG4 503 A 1 HETATM 28 C C4' XG4 . . . F 5 50.413 5.333 2.348 1 32.79 ? C4' XG4 503 A 1 HETATM 29 O O4' XG4 . . . F 5 49.127 4.841 1.994 1 29.39 ? O4' XG4 503 A 1 HETATM 30 C C5' XG4 . . . F 5 51.448 4.179 2.254 1 33.32 ? C5' XG4 503 A 1 HETATM 31 O O5' XG4 . . . F 5 50.933 3.019 2.848 1 35.6 ? O5' XG4 503 A 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 31 #