data_2ZI7 # _model_server_result.job_id CcHXzbRLcmhFt4CKHhTi1w _model_server_result.datetime_utc '2024-11-13 05:51:48' _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 2zi7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 2ZI7 # _exptl.entry_id 2ZI7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-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 2ZI7 _cell.length_a 43.8 _cell.length_b 107.5 _cell.length_c 110.4 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZI7 _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 _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 ? 3 D N N ? 3 F 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 OE2 GLU 72 B GLU 53 1_555 C O5' GNG . B GNG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? covale ? covale2 B OE2 GLU 72 A GLU 53 1_555 E O5' GNG . A GNG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 N1 C2 UDP sing 392 n n N1 C6 UDP sing 393 n n N1 C1' UDP sing 394 n n C2 N3 UDP sing 395 n n C2 O2 UDP doub 396 n n N3 C4 UDP sing 397 n n N3 HN3 UDP sing 398 n n C4 C5 UDP sing 399 n n C4 O4 UDP doub 400 n n C5 C6 UDP doub 401 n n C5 H5 UDP sing 402 n n C6 H6 UDP sing 403 n n C1' C2' UDP sing 404 n n C1' O4' UDP sing 405 n n C1' H1' UDP sing 406 n n C2' O2' UDP sing 407 n n C2' C3' UDP sing 408 n n C2' H2' UDP sing 409 n n O2' HO2' UDP sing 410 n n C3' C4' UDP sing 411 n n C3' O3' UDP sing 412 n n C3' H3' UDP sing 413 n n C4' O4' UDP sing 414 n n C4' C5' UDP sing 415 n n C4' H4' UDP sing 416 n n O3' HO3' UDP sing 417 n n C5' O5' UDP sing 418 n n C5' "H5'1" UDP sing 419 n n C5' "H5'2" UDP sing 420 n n O5' PA UDP sing 421 n n PA O1A UDP doub 422 n n PA O2A UDP sing 423 n n PA O3A UDP sing 424 n n O2A HOA2 UDP sing 425 n n O3A PB UDP sing 426 n n PB O1B UDP doub 427 n n PB O2B UDP sing 428 n n PB O3B UDP sing 429 n n O2B HOB2 UDP sing 430 n n O3B HOB3 UDP sing 431 n n # _atom_sites.entry_id 2ZI7 _atom_sites.fract_transf_matrix[1][1] 0.022831 _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] 0.009302 _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] 0.009058 _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 GNG B 1 503 503 GNG DGU . D 3 UDP B 1 301 301 UDP UDP . E 2 GNG A 1 502 502 GNG DGU . F 3 UDP A 1 301 301 UDP UDP . G 4 HOH B 1 504 3 HOH HOH . G 4 HOH B 2 505 4 HOH HOH . G 4 HOH B 3 506 5 HOH HOH . G 4 HOH B 4 507 7 HOH HOH . G 4 HOH B 5 508 8 HOH HOH . G 4 HOH B 6 509 12 HOH HOH . G 4 HOH B 7 510 14 HOH HOH . G 4 HOH B 8 511 15 HOH HOH . G 4 HOH B 9 512 16 HOH HOH . G 4 HOH B 10 513 26 HOH HOH . G 4 HOH B 11 514 27 HOH HOH . G 4 HOH B 12 515 28 HOH HOH . G 4 HOH B 13 516 37 HOH HOH . G 4 HOH B 14 517 38 HOH HOH . G 4 HOH B 15 518 39 HOH HOH . G 4 HOH B 16 519 41 HOH HOH . G 4 HOH B 17 520 42 HOH HOH . G 4 HOH B 18 521 46 HOH HOH . G 4 HOH B 19 522 49 HOH HOH . G 4 HOH B 20 523 50 HOH HOH . G 4 HOH B 21 524 52 HOH HOH . G 4 HOH B 22 525 53 HOH HOH . G 4 HOH B 23 526 57 HOH HOH . G 4 HOH B 24 527 58 HOH HOH . G 4 HOH B 25 528 59 HOH HOH . G 4 HOH B 26 529 61 HOH HOH . G 4 HOH B 27 530 62 HOH HOH . G 4 HOH B 28 531 65 HOH HOH . G 4 HOH B 29 532 67 HOH HOH . G 4 HOH B 30 533 68 HOH HOH . G 4 HOH B 31 534 69 HOH HOH . G 4 HOH B 32 535 71 HOH HOH . G 4 HOH B 33 536 73 HOH HOH . G 4 HOH B 34 537 76 HOH HOH . G 4 HOH B 35 538 79 HOH HOH . G 4 HOH B 36 539 86 HOH HOH . G 4 HOH B 37 540 87 HOH HOH . G 4 HOH B 38 541 88 HOH HOH . G 4 HOH B 39 542 92 HOH HOH . G 4 HOH B 40 543 93 HOH HOH . G 4 HOH B 41 544 94 HOH HOH . H 4 HOH A 1 503 1 HOH HOH . H 4 HOH A 2 504 2 HOH HOH . H 4 HOH A 3 505 6 HOH HOH . H 4 HOH A 4 506 9 HOH HOH . H 4 HOH A 5 507 10 HOH HOH . H 4 HOH A 6 508 11 HOH HOH . H 4 HOH A 7 509 13 HOH HOH . H 4 HOH A 8 510 17 HOH HOH . H 4 HOH A 9 511 18 HOH HOH . H 4 HOH A 10 512 19 HOH HOH . H 4 HOH A 11 513 20 HOH HOH . H 4 HOH A 12 514 21 HOH HOH . H 4 HOH A 13 515 22 HOH HOH . H 4 HOH A 14 516 23 HOH HOH . H 4 HOH A 15 517 24 HOH HOH . H 4 HOH A 16 518 25 HOH HOH . H 4 HOH A 17 519 29 HOH HOH . H 4 HOH A 18 520 30 HOH HOH . H 4 HOH A 19 521 31 HOH HOH . H 4 HOH A 20 522 32 HOH HOH . H 4 HOH A 21 523 33 HOH HOH . H 4 HOH A 22 524 35 HOH HOH . H 4 HOH A 23 525 36 HOH HOH . H 4 HOH A 24 526 40 HOH HOH . H 4 HOH A 25 527 43 HOH HOH . H 4 HOH A 26 528 44 HOH HOH . H 4 HOH A 27 529 45 HOH HOH . H 4 HOH A 28 530 47 HOH HOH . H 4 HOH A 29 531 48 HOH HOH . H 4 HOH A 30 532 51 HOH HOH . H 4 HOH A 31 533 54 HOH HOH . H 4 HOH A 32 534 55 HOH HOH . H 4 HOH A 33 535 56 HOH HOH . H 4 HOH A 34 536 63 HOH HOH . H 4 HOH A 35 537 64 HOH HOH . H 4 HOH A 36 538 66 HOH HOH . H 4 HOH A 37 539 70 HOH HOH . H 4 HOH A 38 540 74 HOH HOH . H 4 HOH A 39 541 75 HOH HOH . H 4 HOH A 40 542 84 HOH HOH . H 4 HOH A 41 543 85 HOH HOH . H 4 HOH A 42 544 89 HOH HOH . H 4 HOH A 43 545 90 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 UDP . . . F 3 -3.995 -4.903 -20.361 1 26.51 ? N1 UDP 301 A 1 HETATM 2 C C2 UDP . . . F 3 -4.142 -4.74 -21.756 1 29.02 ? C2 UDP 301 A 1 HETATM 3 N N3 UDP . . . F 3 -3.543 -5.591 -22.637 1 26.13 ? N3 UDP 301 A 1 HETATM 4 C C4 UDP . . . F 3 -2.777 -6.596 -22.106 1 28.81 ? C4 UDP 301 A 1 HETATM 5 C C5 UDP . . . F 3 -2.593 -6.798 -20.717 1 26.85 ? C5 UDP 301 A 1 HETATM 6 C C6 UDP . . . F 3 -3.23 -5.917 -19.854 1 28.49 ? C6 UDP 301 A 1 HETATM 7 O O2 UDP . . . F 3 -4.801 -3.823 -22.224 1 30.27 ? O2 UDP 301 A 1 HETATM 8 O O4 UDP . . . F 3 -2.226 -7.334 -22.894 1 30.39 ? O4 UDP 301 A 1 HETATM 9 C C1' UDP . . . F 3 -4.698 -3.986 -19.455 1 25.88 ? C1' UDP 301 A 1 HETATM 10 C C2' UDP . . . F 3 -5.735 -4.671 -18.582 1 20.78 ? C2' UDP 301 A 1 HETATM 11 O O2' UDP . . . F 3 -6.97 -4.695 -19.186 1 22.35 ? O2' UDP 301 A 1 HETATM 12 C C3' UDP . . . F 3 -5.836 -3.782 -17.371 1 20.03 ? C3' UDP 301 A 1 HETATM 13 C C4' UDP . . . F 3 -4.428 -3.259 -17.244 1 16.26 ? C4' UDP 301 A 1 HETATM 14 O O4' UDP . . . F 3 -3.829 -3.343 -18.543 1 21.87 ? O4' UDP 301 A 1 HETATM 15 O O3' UDP . . . F 3 -6.582 -2.683 -17.813 1 23 ? O3' UDP 301 A 1 HETATM 16 C C5' UDP . . . F 3 -3.534 -4.009 -16.24 1 12.72 ? C5' UDP 301 A 1 HETATM 17 O O5' UDP . . . F 3 -3.629 -5.488 -16.55 1 16.13 ? O5' UDP 301 A 1 HETATM 18 P PA UDP . . . F 3 -3.987 -6.353 -15.349 1 15.58 ? PA UDP 301 A 1 HETATM 19 O O1A UDP . . . F 3 -5.009 -5.943 -14.438 1 13.86 ? O1A UDP 301 A 1 HETATM 20 O O2A UDP . . . F 3 -4.1 -7.818 -15.777 1 11.06 ? O2A UDP 301 A 1 HETATM 21 O O3A UDP . . . F 3 -2.617 -6.299 -14.48 1 15.7 ? O3A UDP 301 A 1 HETATM 22 P PB UDP . . . F 3 -2.143 -6.778 -12.986 1 13.81 ? PB UDP 301 A 1 HETATM 23 O O1B UDP . . . F 3 -2.918 -7.939 -12.489 1 20.76 ? O1B UDP 301 A 1 HETATM 24 O O2B UDP . . . F 3 -2.05 -5.655 -12.04 1 22.78 ? O2B UDP 301 A 1 HETATM 25 O O3B UDP . . . F 3 -0.769 -7.105 -13.331 1 15.2 ? O3B UDP 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #