data_5YVM # _model_server_result.job_id kGFOCfXMddps-CVPD_t7Mg _model_server_result.datetime_utc '2024-10-19 17:34:26' _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 5yvm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 5YVM # _exptl.entry_id 5YVM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 779.436 _entity.id 3 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description 5,6-DIHYDROXY-NADP _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 90 _cell.entry_id 5YVM _cell.length_a 57.19 _cell.length_b 103.72 _cell.length_c 128.51 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YVM _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 57.19 0 64.255 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 213 A ASP 204 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc2 A NE2 HIS 217 A HIS 208 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc3 A NE2 HIS 282 A HIS 273 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc4 A NE2 HIS 297 A HIS 288 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc5 B MN MN . A MN 501 1_555 C O5N NZQ . A NZQ 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? # _chem_comp.formula 'C21 H32 N7 O19 P3' _chem_comp.formula_weight 779.436 _chem_comp.id NZQ _chem_comp.mon_nstd_flag . _chem_comp.name 5,6-DIHYDROXY-NADP _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 O1X P2B NZQ doub 237 n n P2B O2X NZQ sing 238 n n P2B O3X NZQ sing 239 n n P2B O2B NZQ sing 240 n n O2X HAK NZQ sing 241 n n O3X HAJ NZQ sing 242 n n O2B C2B NZQ sing 243 n n C2B C3B NZQ sing 244 n n C2B C1B NZQ sing 245 n n C2B HA' NZQ sing 246 n n C3B O3B NZQ sing 247 n n C3B C4B NZQ sing 248 n n C3B HAA NZQ sing 249 n n O3B HAC NZQ sing 250 n n C1B N9A NZQ sing 251 n n C1B O4B NZQ sing 252 n n C1B HAB NZQ sing 253 n n N9A C8A NZQ sing 254 n y N9A C4A NZQ sing 255 n y C8A N7A NZQ doub 256 n y C8A HAE NZQ sing 257 n n N7A C5A NZQ sing 258 n y C5A C4A NZQ doub 259 n y C5A C6A NZQ sing 260 n y C4A N3A NZQ sing 261 n y N3A C2A NZQ doub 262 n y C2A N1A NZQ sing 263 n y C2A HAF NZQ sing 264 n n N1A C6A NZQ doub 265 n y C6A N6A NZQ sing 266 n n N6A "HA'1" NZQ sing 267 n n N6A "HA'2" NZQ sing 268 n n O4B C4B NZQ sing 269 n n C4B C5B NZQ sing 270 n n C4B HAD NZQ sing 271 n n C5B O5B NZQ sing 272 n n C5B HAA1 NZQ sing 273 n n C5B HAA2 NZQ sing 274 n n O5B PA NZQ sing 275 n n PA O1A NZQ doub 276 n n PA O2A NZQ sing 277 n n PA O3 NZQ sing 278 n n O2A HAL NZQ sing 279 n n O3 PN NZQ sing 280 n n PN O1N NZQ doub 281 n n PN O2N NZQ sing 282 n n PN O5D NZQ sing 283 n n O2N HNK NZQ sing 284 n n O5D C5D NZQ sing 285 n n C5D C4D NZQ sing 286 n n C5D "HN'1" NZQ sing 287 n n C5D "HN'2" NZQ sing 288 n n C4D O4D NZQ sing 289 n n C4D C3D NZQ sing 290 n n C4D HN' NZQ sing 291 n n O4D C1D NZQ sing 292 n n C1D C2D NZQ sing 293 n n C1D N1N NZQ sing 294 n n C1D HNB NZQ sing 295 n n C2D O2D NZQ sing 296 n n C2D C3D NZQ sing 297 n n C2D HNC NZQ sing 298 n n O2D HND NZQ sing 299 n n C3D O3D NZQ sing 300 n n C3D HNA NZQ sing 301 n n O3D HNE NZQ sing 302 n n N1N C2N NZQ sing 303 n n N1N C6N NZQ sing 304 n n C2N C3N NZQ doub 305 n n C2N HNF NZQ sing 306 n n C3N C7N NZQ sing 307 n n C3N C4N NZQ sing 308 n n C7N N7N NZQ sing 309 n n C7N O7N NZQ doub 310 n n N7N HNB1 NZQ sing 311 n n N7N HNB2 NZQ sing 312 n n C4N C5N NZQ sing 313 n n C4N HNA1 NZQ sing 314 n n C4N HNA2 NZQ sing 315 n n C5N O5N NZQ sing 316 n n C5N C6N NZQ sing 317 n n C5N HNG NZQ sing 318 n n O5N HNH NZQ sing 319 n n C6N O6N NZQ sing 320 n n C6N HC6 NZQ sing 321 n n O6N HO6 NZQ sing 322 n n # _atom_sites.entry_id 5YVM _atom_sites.fract_transf_matrix[1][1] 0.017486 _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] 0.009641 _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] 0.007781 _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 B 2 MN A 1 501 1 MN MN . C 3 NZQ A 1 502 1 NZQ NZQ . D 4 HOH A 1 601 46 HOH HOH . D 4 HOH A 2 602 36 HOH HOH . D 4 HOH A 3 603 100 HOH HOH . D 4 HOH A 4 604 95 HOH HOH . D 4 HOH A 5 605 61 HOH HOH . D 4 HOH A 6 606 3 HOH HOH . D 4 HOH A 7 607 34 HOH HOH . D 4 HOH A 8 608 90 HOH HOH . D 4 HOH A 9 609 42 HOH HOH . D 4 HOH A 10 610 29 HOH HOH . D 4 HOH A 11 611 24 HOH HOH . D 4 HOH A 12 612 35 HOH HOH . D 4 HOH A 13 613 20 HOH HOH . D 4 HOH A 14 614 5 HOH HOH . D 4 HOH A 15 615 76 HOH HOH . D 4 HOH A 16 616 45 HOH HOH . D 4 HOH A 17 617 43 HOH HOH . D 4 HOH A 18 618 67 HOH HOH . D 4 HOH A 19 619 1 HOH HOH . D 4 HOH A 20 620 104 HOH HOH . D 4 HOH A 21 621 65 HOH HOH . D 4 HOH A 22 622 23 HOH HOH . D 4 HOH A 23 623 16 HOH HOH . D 4 HOH A 24 624 75 HOH HOH . D 4 HOH A 25 625 14 HOH HOH . D 4 HOH A 26 626 41 HOH HOH . D 4 HOH A 27 627 6 HOH HOH . D 4 HOH A 28 628 33 HOH HOH . D 4 HOH A 29 629 91 HOH HOH . D 4 HOH A 30 630 57 HOH HOH . D 4 HOH A 31 631 66 HOH HOH . D 4 HOH A 32 632 12 HOH HOH . D 4 HOH A 33 633 94 HOH HOH . D 4 HOH A 34 634 102 HOH HOH . D 4 HOH A 35 635 55 HOH HOH . D 4 HOH A 36 636 27 HOH HOH . D 4 HOH A 37 637 53 HOH HOH . D 4 HOH A 38 638 83 HOH HOH . D 4 HOH A 39 639 15 HOH HOH . D 4 HOH A 40 640 28 HOH HOH . D 4 HOH A 41 641 31 HOH HOH . D 4 HOH A 42 642 101 HOH HOH . D 4 HOH A 43 643 19 HOH HOH . D 4 HOH A 44 644 60 HOH HOH . D 4 HOH A 45 645 17 HOH HOH . D 4 HOH A 46 646 9 HOH HOH . D 4 HOH A 47 647 32 HOH HOH . D 4 HOH A 48 648 40 HOH HOH . D 4 HOH A 49 649 54 HOH HOH . D 4 HOH A 50 650 64 HOH HOH . D 4 HOH A 51 651 72 HOH HOH . D 4 HOH A 52 652 11 HOH HOH . D 4 HOH A 53 653 13 HOH HOH . D 4 HOH A 54 654 68 HOH HOH . D 4 HOH A 55 655 26 HOH HOH . D 4 HOH A 56 656 92 HOH HOH . D 4 HOH A 57 657 4 HOH HOH . D 4 HOH A 58 658 73 HOH HOH . D 4 HOH A 59 659 7 HOH HOH . D 4 HOH A 60 660 69 HOH HOH . D 4 HOH A 61 661 71 HOH HOH . D 4 HOH A 62 662 8 HOH HOH . D 4 HOH A 63 663 47 HOH HOH . D 4 HOH A 64 664 38 HOH HOH . D 4 HOH A 65 665 37 HOH HOH . D 4 HOH A 66 666 59 HOH HOH . D 4 HOH A 67 667 18 HOH HOH . D 4 HOH A 68 668 25 HOH HOH . D 4 HOH A 69 669 48 HOH HOH . D 4 HOH A 70 670 87 HOH HOH . D 4 HOH A 71 671 84 HOH HOH . D 4 HOH A 72 672 2 HOH HOH . D 4 HOH A 73 673 89 HOH HOH . D 4 HOH A 74 674 10 HOH HOH . D 4 HOH A 75 675 49 HOH HOH . D 4 HOH A 76 676 22 HOH HOH . D 4 HOH A 77 677 62 HOH HOH . D 4 HOH A 78 678 58 HOH HOH . D 4 HOH A 79 679 44 HOH HOH . D 4 HOH A 80 680 81 HOH HOH . D 4 HOH A 81 681 79 HOH HOH . D 4 HOH A 82 682 70 HOH HOH . D 4 HOH A 83 683 21 HOH HOH . D 4 HOH A 84 684 85 HOH HOH . D 4 HOH A 85 685 52 HOH HOH . D 4 HOH A 86 686 82 HOH HOH . D 4 HOH A 87 687 78 HOH HOH . D 4 HOH A 88 688 39 HOH HOH . D 4 HOH A 89 689 63 HOH HOH . D 4 HOH A 90 690 98 HOH HOH . D 4 HOH A 91 691 96 HOH HOH . D 4 HOH A 92 692 103 HOH HOH . D 4 HOH A 93 693 30 HOH HOH . D 4 HOH A 94 694 99 HOH HOH . D 4 HOH A 95 695 56 HOH HOH . D 4 HOH A 96 696 51 HOH HOH . D 4 HOH A 97 697 97 HOH HOH . D 4 HOH A 98 698 74 HOH HOH . D 4 HOH A 99 699 106 HOH HOH . D 4 HOH A 100 700 80 HOH HOH . D 4 HOH A 101 701 88 HOH HOH . D 4 HOH A 102 702 50 HOH HOH . D 4 HOH A 103 703 93 HOH HOH . D 4 HOH A 104 704 77 HOH HOH . D 4 HOH A 105 705 86 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 O1X NZQ . . . C 3 23.764 16.276 62.131 1 55.76 ? O1X NZQ 502 A 1 HETATM 2 P P2B NZQ . . . C 3 25.078 16.32 61.403 1 54.61 ? P2B NZQ 502 A 1 HETATM 3 O O2X NZQ . . . C 3 26.11 17.09 62.196 1 63.7 ? O2X NZQ 502 A 1 HETATM 4 O O3X NZQ . . . C 3 24.869 17.033 60.096 1 55.91 ? O3X NZQ 502 A 1 HETATM 5 O O2B NZQ . . . C 3 25.598 14.768 61.094 1 55.68 ? O2B NZQ 502 A 1 HETATM 6 C C2B NZQ . . . C 3 24.93 13.996 59.995 1 53.11 ? C2B NZQ 502 A 1 HETATM 7 C C3B NZQ . . . C 3 23.405 13.764 60.305 1 50.7 ? C3B NZQ 502 A 1 HETATM 8 O O3B NZQ . . . C 3 23.203 13.708 61.623 1 51.98 ? O3B NZQ 502 A 1 HETATM 9 C C1B NZQ . . . C 3 25.4 12.803 59.899 1 55.34 ? C1B NZQ 502 A 1 HETATM 10 N N9A NZQ . . . C 3 26.496 12.689 58.946 1 51.03 ? N9A NZQ 502 A 1 HETATM 11 C C8A NZQ . . . C 3 26.664 13.049 57.665 1 49.75 ? C8A NZQ 502 A 1 HETATM 12 N N7A NZQ . . . C 3 27.889 12.685 57.285 1 47.24 ? N7A NZQ 502 A 1 HETATM 13 C C5A NZQ . . . C 3 28.47 12.08 58.332 1 50.18 ? C5A NZQ 502 A 1 HETATM 14 C C4A NZQ . . . C 3 27.627 12.083 59.365 1 50.09 ? C4A NZQ 502 A 1 HETATM 15 N N3A NZQ . . . C 3 27.997 11.529 60.531 1 52.53 ? N3A NZQ 502 A 1 HETATM 16 C C2A NZQ . . . C 3 29.228 10.98 60.644 1 52.96 ? C2A NZQ 502 A 1 HETATM 17 N N1A NZQ . . . C 3 30.077 10.982 59.589 1 52.63 ? N1A NZQ 502 A 1 HETATM 18 C C6A NZQ . . . C 3 29.707 11.528 58.439 1 49.99 ? C6A NZQ 502 A 1 HETATM 19 N N6A NZQ . . . C 3 30.813 11.397 57.468 1 49.27 ? N6A NZQ 502 A 1 HETATM 20 O O4B NZQ . . . C 3 24.185 11.884 59.255 1 55.06 ? O4B NZQ 502 A 1 HETATM 21 C C4B NZQ . . . C 3 23.056 12.395 59.64 1 52.64 ? C4B NZQ 502 A 1 HETATM 22 C C5B NZQ . . . C 3 22.211 12.688 58.369 1 49.54 ? C5B NZQ 502 A 1 HETATM 23 O O5B NZQ . . . C 3 22.808 13.712 57.607 1 49.25 ? O5B NZQ 502 A 1 HETATM 24 P PA NZQ . . . C 3 22.007 14.011 56.173 1 44.33 ? PA NZQ 502 A 1 HETATM 25 O O1A NZQ . . . C 3 22.587 15.132 55.338 1 45.56 ? O1A NZQ 502 A 1 HETATM 26 O O2A NZQ . . . C 3 20.529 14.232 56.415 1 42.68 ? O2A NZQ 502 A 1 HETATM 27 O O3 NZQ . . . C 3 22.197 12.581 55.408 1 46 ? O3 NZQ 502 A 1 HETATM 28 P PN NZQ . . . C 3 21.949 12.365 53.804 1 45.29 ? PN NZQ 502 A 1 HETATM 29 O O1N NZQ . . . C 3 23.275 12.639 53.181 1 41.06 ? O1N NZQ 502 A 1 HETATM 30 O O2N NZQ . . . C 3 21.465 10.957 53.513 1 42.54 ? O2N NZQ 502 A 1 HETATM 31 O O5D NZQ . . . C 3 20.888 13.457 53.207 1 46.9 ? O5D NZQ 502 A 1 HETATM 32 C C5D NZQ . . . C 3 19.518 13.207 53.247 1 44.33 ? C5D NZQ 502 A 1 HETATM 33 C C4D NZQ . . . C 3 18.898 14.413 52.533 1 46.03 ? C4D NZQ 502 A 1 HETATM 34 O O4D NZQ . . . C 3 19.243 14.455 51.254 1 45.78 ? O4D NZQ 502 A 1 HETATM 35 C C1D NZQ . . . C 3 17.87 14.602 50.458 1 43.67 ? C1D NZQ 502 A 1 HETATM 36 C C2D NZQ . . . C 3 17.044 13.793 51.146 1 43.71 ? C2D NZQ 502 A 1 HETATM 37 O O2D NZQ . . . C 3 15.626 14.071 50.87 1 44 ? O2D NZQ 502 A 1 HETATM 38 C C3D NZQ . . . C 3 17.358 14.184 52.577 1 48.6 ? C3D NZQ 502 A 1 HETATM 39 O O3D NZQ . . . C 3 16.733 15.325 52.923 1 47.28 ? O3D NZQ 502 A 1 HETATM 40 N N1N NZQ . . . C 3 18.079 14.184 49.104 1 48.42 ? N1N NZQ 502 A 1 HETATM 41 C C2N NZQ . . . C 3 18.913 14.934 48.222 1 48.51 ? C2N NZQ 502 A 1 HETATM 42 C C3N NZQ . . . C 3 18.848 14.728 46.639 1 55.37 ? C3N NZQ 502 A 1 HETATM 43 C C7N NZQ . . . C 3 19.417 15.795 45.698 1 54.26 ? C7N NZQ 502 A 1 HETATM 44 N N7N NZQ . . . C 3 19.586 17.158 46.173 1 52.84 ? N7N NZQ 502 A 1 HETATM 45 O O7N NZQ . . . C 3 19.708 15.49 44.59 1 53.84 ? O7N NZQ 502 A 1 HETATM 46 C C4N NZQ . . . C 3 18.099 13.687 46.107 1 53.71 ? C4N NZQ 502 A 1 HETATM 47 C C5N NZQ . . . C 3 18.005 12.492 47.175 1 50.77 ? C5N NZQ 502 A 1 HETATM 48 O O5N NZQ . . . C 3 17.314 11.425 46.479 1 49.18 ? O5N NZQ 502 A 1 HETATM 49 C C6N NZQ . . . C 3 17.383 12.867 48.392 1 50.5 ? C6N NZQ 502 A 1 HETATM 50 O O6N NZQ . . . C 3 15.997 13.124 48.259 1 46.96 ? O6N NZQ 502 A 1 # _model_server_stats.io_time_ms 77 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 221 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 50 #