data_3TSD # _model_server_result.job_id 4O51fbWMyaidKiFWR_aX1A _model_server_result.datetime_utc '2024-11-25 04:38:44' _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 3tsd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 3TSD # _exptl.entry_id 3TSD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 365.213 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "XANTHOSINE-5'-MONOPHOSPHATE" _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 3TSD _cell.length_a 123.25 _cell.length_b 123.25 _cell.length_c 141.636 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TSD _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # 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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 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,G 1 1,2,3,4 B,D,E,F,H 2 1,2,3,4 # 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' 2_465 -x-1,-y+1,z -1 0 0 0 -1 0 0 0 1 -123.25 123.25 0 3 'crystal symmetry operation' 3_565 -y,x+1,z 0 -1 0 1 0 0 0 0 1 0 123.25 0 4 'crystal symmetry operation' 4_455 y-1,-x,z 0 1 0 -1 0 0 0 0 1 -123.25 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _chem_comp.formula 'C10 H14 N4 O9 P 1' _chem_comp.formula_weight 365.213 _chem_comp.id XMP _chem_comp.mon_nstd_flag . _chem_comp.name "XANTHOSINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE' # 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 P O1P XMP sing 395 n n P O2P XMP sing 396 n n P O5' XMP sing 397 n n P O3P XMP doub 398 n n O1P HOP1 XMP sing 399 n n O2P HOP2 XMP sing 400 n n O5' C5' XMP sing 401 n n C5' C4' XMP sing 402 n n C5' "H5'2" XMP sing 403 n n C5' "H5'1" XMP sing 404 n n C4' O4' XMP sing 405 n n C4' C3' XMP sing 406 n n C4' H4' XMP sing 407 n n O4' C1' XMP sing 408 n n C1' N9 XMP sing 409 n n C1' C2' XMP sing 410 n n C1' H1' XMP sing 411 n n N9 C4 XMP sing 412 n y N9 C8 XMP sing 413 n y C4 N3 XMP sing 414 n n C4 C5 XMP doub 415 n y N3 C2 XMP sing 416 n n N3 H3 XMP sing 417 n n N1 C2 XMP sing 418 n n N1 C6 XMP sing 419 n n N1 H1 XMP sing 420 n n C2 O2 XMP doub 421 n n C6 O6 XMP doub 422 n n C6 C5 XMP sing 423 n n C5 N7 XMP sing 424 n y N7 C8 XMP doub 425 n y N7 H7 XMP sing 426 n n C8 H8 XMP sing 427 n n C2' O2' XMP sing 428 n n C2' C3' XMP sing 429 n n C2' H2' XMP sing 430 n n O2' H2O1 XMP sing 431 n n C3' O3' XMP sing 432 n n C3' H3' XMP sing 433 n n O3' H3O1 XMP sing 434 n n # _atom_sites.entry_id 3TSD _atom_sites.fract_transf_matrix[1][1] 0.008114 _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] 0.008114 _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] 0.00706 _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 XMP A 1 500 500 XMP XMP . D 2 XMP B 1 500 500 XMP XMP . E 3 TAR B 1 501 501 TAR TAR . F 4 SO4 B 1 502 502 SO4 SO4 . G 5 HOH A 1 488 1 HOH HOH . G 5 HOH A 2 489 6 HOH HOH . G 5 HOH A 3 490 7 HOH HOH . G 5 HOH A 4 491 9 HOH HOH . G 5 HOH A 5 492 10 HOH HOH . G 5 HOH A 6 493 11 HOH HOH . G 5 HOH A 7 494 16 HOH HOH . G 5 HOH A 8 495 18 HOH HOH . G 5 HOH A 9 496 20 HOH HOH . G 5 HOH A 10 497 21 HOH HOH . G 5 HOH A 11 498 22 HOH HOH . G 5 HOH A 12 499 26 HOH HOH . G 5 HOH A 13 501 27 HOH HOH . G 5 HOH A 14 502 28 HOH HOH . G 5 HOH A 15 503 31 HOH HOH . G 5 HOH A 16 504 32 HOH HOH . G 5 HOH A 17 505 33 HOH HOH . G 5 HOH A 18 506 34 HOH HOH . G 5 HOH A 19 507 35 HOH HOH . G 5 HOH A 20 508 36 HOH HOH . G 5 HOH A 21 509 38 HOH HOH . G 5 HOH A 22 510 40 HOH HOH . G 5 HOH A 23 511 44 HOH HOH . G 5 HOH A 24 512 47 HOH HOH . G 5 HOH A 25 513 50 HOH HOH . G 5 HOH A 26 514 53 HOH HOH . G 5 HOH A 27 515 54 HOH HOH . G 5 HOH A 28 516 57 HOH HOH . G 5 HOH A 29 517 58 HOH HOH . G 5 HOH A 30 518 59 HOH HOH . G 5 HOH A 31 519 60 HOH HOH . G 5 HOH A 32 520 61 HOH HOH . G 5 HOH A 33 521 62 HOH HOH . G 5 HOH A 34 522 63 HOH HOH . G 5 HOH A 35 523 64 HOH HOH . G 5 HOH A 36 524 65 HOH HOH . G 5 HOH A 37 525 66 HOH HOH . G 5 HOH A 38 526 67 HOH HOH . G 5 HOH A 39 527 68 HOH HOH . G 5 HOH A 40 528 69 HOH HOH . G 5 HOH A 41 529 86 HOH HOH . G 5 HOH A 42 530 87 HOH HOH . G 5 HOH A 43 531 88 HOH HOH . G 5 HOH A 44 532 89 HOH HOH . G 5 HOH A 45 533 90 HOH HOH . G 5 HOH A 46 534 91 HOH HOH . G 5 HOH A 47 535 92 HOH HOH . G 5 HOH A 48 536 93 HOH HOH . G 5 HOH A 49 537 94 HOH HOH . H 5 HOH B 1 488 2 HOH HOH . H 5 HOH B 2 489 3 HOH HOH . H 5 HOH B 3 490 4 HOH HOH . H 5 HOH B 4 491 5 HOH HOH . H 5 HOH B 5 492 8 HOH HOH . H 5 HOH B 6 493 12 HOH HOH . H 5 HOH B 7 494 13 HOH HOH . H 5 HOH B 8 495 14 HOH HOH . H 5 HOH B 9 496 15 HOH HOH . H 5 HOH B 10 497 17 HOH HOH . H 5 HOH B 11 498 19 HOH HOH . H 5 HOH B 12 499 23 HOH HOH . H 5 HOH B 13 503 24 HOH HOH . H 5 HOH B 14 504 25 HOH HOH . H 5 HOH B 15 505 29 HOH HOH . H 5 HOH B 16 506 30 HOH HOH . H 5 HOH B 17 507 37 HOH HOH . H 5 HOH B 18 508 39 HOH HOH . H 5 HOH B 19 509 41 HOH HOH . H 5 HOH B 20 510 42 HOH HOH . H 5 HOH B 21 511 43 HOH HOH . H 5 HOH B 22 512 45 HOH HOH . H 5 HOH B 23 513 46 HOH HOH . H 5 HOH B 24 514 48 HOH HOH . H 5 HOH B 25 515 49 HOH HOH . H 5 HOH B 26 516 51 HOH HOH . H 5 HOH B 27 517 52 HOH HOH . H 5 HOH B 28 518 55 HOH HOH . H 5 HOH B 29 519 56 HOH HOH . H 5 HOH B 30 520 70 HOH HOH . H 5 HOH B 31 521 71 HOH HOH . H 5 HOH B 32 522 72 HOH HOH . H 5 HOH B 33 523 73 HOH HOH . H 5 HOH B 34 524 74 HOH HOH . H 5 HOH B 35 525 75 HOH HOH . H 5 HOH B 36 526 76 HOH HOH . H 5 HOH B 37 527 77 HOH HOH . H 5 HOH B 38 528 78 HOH HOH . H 5 HOH B 39 529 79 HOH HOH . H 5 HOH B 40 530 80 HOH HOH . H 5 HOH B 41 531 81 HOH HOH . H 5 HOH B 42 532 82 HOH HOH . H 5 HOH B 43 533 83 HOH HOH . H 5 HOH B 44 534 84 HOH HOH . H 5 HOH B 45 535 85 HOH HOH . H 5 HOH B 46 536 95 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 P XMP . . . C 2 -44.387 46.752 1.413 1 90.19 ? P XMP 500 A 1 HETATM 2 O O1P XMP . . . C 2 -44.473 45.277 1.631 1 90.33 ? O1P XMP 500 A 1 HETATM 3 O O2P XMP . . . C 2 -45.664 47.544 1.02 1 71.5 ? O2P XMP 500 A 1 HETATM 4 O O5' XMP . . . C 2 -43.178 47.106 0.43 1 91.09 ? O5' XMP 500 A 1 HETATM 5 O O3P XMP . . . C 2 -43.953 47.313 2.745 1 80.55 ? O3P XMP 500 A 1 HETATM 6 C C5' XMP . . . C 2 -41.876 46.586 0.662 1 78.59 ? C5' XMP 500 A 1 HETATM 7 C C4' XMP . . . C 2 -40.881 47.095 -0.35 1 82.37 ? C4' XMP 500 A 1 HETATM 8 O O4' XMP . . . C 2 -40.672 48.514 -0.162 1 96.05 ? O4' XMP 500 A 1 HETATM 9 C C1' XMP . . . C 2 -39.359 48.865 -0.562 1 102.88 ? C1' XMP 500 A 1 HETATM 10 N N9 XMP . . . C 2 -38.71 49.597 0.542 1 113 ? N9 XMP 500 A 1 HETATM 11 C C4 XMP . . . C 2 -38.039 50.755 0.399 1 122.42 ? C4 XMP 500 A 1 HETATM 12 N N3 XMP . . . C 2 -37.74 51.56 -0.636 1 134 ? N3 XMP 500 A 1 HETATM 13 N N1 XMP . . . C 2 -36.588 53.051 0.756 1 131.7 ? N1 XMP 500 A 1 HETATM 14 C C2 XMP . . . C 2 -37.024 52.684 -0.458 1 135.82 ? C2 XMP 500 A 1 HETATM 15 O O2 XMP . . . C 2 -36.741 53.466 -1.539 1 134.54 ? O2 XMP 500 A 1 HETATM 16 C C6 XMP . . . C 2 -36.856 52.288 1.833 1 123.21 ? C6 XMP 500 A 1 HETATM 17 O O6 XMP . . . C 2 -36.389 52.675 3.118 1 120.17 ? O6 XMP 500 A 1 HETATM 18 C C5 XMP . . . C 2 -37.594 51.111 1.676 1 122 ? C5 XMP 500 A 1 HETATM 19 N N7 XMP . . . C 2 -38.013 50.159 2.533 1 121.32 ? N7 XMP 500 A 1 HETATM 20 C C8 XMP . . . C 2 -38.696 49.236 1.835 1 117.5 ? C8 XMP 500 A 1 HETATM 21 C C2' XMP . . . C 2 -38.608 47.576 -0.916 1 87.7 ? C2' XMP 500 A 1 HETATM 22 O O2' XMP . . . C 2 -38.607 47.428 -2.329 1 69.9 ? O2' XMP 500 A 1 HETATM 23 C C3' XMP . . . C 2 -39.481 46.508 -0.253 1 86.05 ? C3' XMP 500 A 1 HETATM 24 O O3' XMP . . . C 2 -39.374 45.226 -0.849 1 78.61 ? O3' XMP 500 A 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 24 #