data_6425 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR strcutre of sst1-selective somatostatin (SRIF) analog 1 ; _BMRB_accession_number 6425 _BMRB_flat_file_name bmr6425.str _Entry_type original _Submission_date 2004-12-10 _Accession_date 2004-12-10 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Grace C. R.R. . 2 Durrer D. . . 3 Koerber S. C. . 4 Erchegyi J. . . 5 Reubi J. C. . 6 Rivier J. E. . 7 Riek R. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 70 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-16 update BMRB 'Updating non-standard residue' stop_ loop_ _Related_BMRB_accession_number _Relationship 6421 'sst1-selective somatostatin (SRIF) (analog 5)' 6422 'sst1-selective somatostatin (SRIF) (analog 1)' 6423 'sst1-selective somatostatin (SRIF) (analog 1)' 6424 'sst1-selective somatostatin (SRIF) (analog 1)' 6426 'sst1-selective somatostatin (SRIF) (analog 1)' stop_ _Original_release_date 2004-12-10 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Somatostatin receptor 1 selective analogues: 4. Three-dimensional consensus structure by NMR ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15658866 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Grace C. R.R. . 2 Durrer D. . . 3 Koerber S. C. . 4 Erchegyi J. . . 5 Reubi J. C. . 6 Rivier J. E. . 7 Riek R. . . stop_ _Journal_abbreviation 'J. Med. Chem.' _Journal_volume 48 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 523 _Page_last 533 _Year 2005 _Details . loop_ _Keyword 'Gamma turn' stop_ save_ ################################## # Molecular system description # ################################## save_system_somatostatin _Saveframe_category molecular_system _Mol_system_name 'sst1-selective somatostatin (analog 1)' _Abbreviation_common 'sst1-selective somatostatin (analog 1)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'SST1-selective somatostatin analog' $somatostatin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all disulfide bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_somatostatin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common somatostatin _Abbreviation_common somatostatin _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; YCKFEXXTFXSC ; loop_ _Residue_seq_code _Residue_label 1 TYR 2 CYS 3 LYS 4 PHE 5 GLU 6 DTR 7 IAM 8 THR 9 PHE 10 HHK 11 SER 12 CYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DTR _Saveframe_category polymer_residue _Mol_type 'D-peptide linking' _Name_common D-TRYPTOPHAN _BMRB_code . _PDB_code DTR _Standard_residue_derivative . _Molecular_mass 204.225 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Aug 2 10:33:24 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD1 CD1 C . 0 . ? NE1 NE1 N . 0 . ? CE2 CE2 C . 0 . ? CZ2 CZ2 C . 0 . ? CH2 CH2 C . 0 . ? CZ3 CZ3 C . 0 . ? CE3 CE3 C . 0 . ? CD2 CD2 C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HD1 HD1 H . 0 . ? HE1 HE1 H . 0 . ? HZ2 HZ2 H . 0 . ? HH2 HH2 H . 0 . ? HZ3 HZ3 H . 0 . ? HE3 HE3 H . 0 . ? HXT HXT H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N H ? ? SING N HN2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 NE1 ? ? SING CD1 HD1 ? ? SING NE1 CE2 ? ? SING NE1 HE1 ? ? DOUB CE2 CZ2 ? ? SING CE2 CD2 ? ? SING CZ2 CH2 ? ? SING CZ2 HZ2 ? ? DOUB CH2 CZ3 ? ? SING CH2 HH2 ? ? SING CZ3 CE3 ? ? SING CZ3 HZ3 ? ? DOUB CE3 CD2 ? ? SING CE3 HE3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_IAM _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common 4-[(ISOPROPYLAMINO)METHYL]PHENYLALANINE _BMRB_code . _PDB_code IAM _Standard_residue_derivative . _Molecular_mass 236.310 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Aug 2 10:35:05 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD1 CD1 C . 0 . ? CE1 CE1 C . 0 . ? CZ CZ C . 0 . ? CE2 CE2 C . 0 . ? CD2 CD2 C . 0 . ? CT CT C . 0 . ? NH NH N . 0 . ? CI CI C . 0 . ? CK1 CK1 C . 0 . ? CK2 CK2 C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? HN2 HN2 H . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB HB H . 0 . ? HB1 HB1 H . 0 . ? HD1 HD1 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 H . 0 . ? HD2 HD2 H . 0 . ? HT1 HT1 H . 0 . ? HT2 HT2 H . 0 . ? HH HH H . 0 . ? HI HI H . 0 . ? HK11 HK11 H . 0 . ? HK12 HK12 H . 0 . ? HK13 HK13 H . 0 . ? HK21 HK21 H . 0 . ? HK22 HK22 H . 0 . ? HK23 HK23 H . 0 . ? HXT HXT H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N HN2 ? ? SING N H ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB ? ? SING CB HB1 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 CE1 ? ? SING CD1 HD1 ? ? DOUB CE1 CZ ? ? SING CE1 HE1 ? ? SING CZ CE2 ? ? SING CZ CT ? ? DOUB CE2 CD2 ? ? SING CE2 HE2 ? ? SING CD2 HD2 ? ? SING CT NH ? ? SING CT HT1 ? ? SING CT HT2 ? ? SING NH CI ? ? SING NH HH ? ? SING CI CK1 ? ? SING CI CK2 ? ? SING CI HI ? ? SING CK1 HK11 ? ? SING CK1 HK12 ? ? SING CK1 HK13 ? ? SING CK2 HK21 ? ? SING CK2 HK22 ? ? SING CK2 HK23 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_HHK _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common '(2S)-2,8-DIAMINOOCTANOIC ACID' _BMRB_code . _PDB_code HHK _Standard_residue_derivative . _Molecular_mass 174.241 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Aug 2 10:54:18 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? CE CE C . 0 . ? CZ CZ C . 0 . ? CT CT C . 0 . ? NH NH N . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HE2 HE2 H . 0 . ? HE3 HE3 H . 0 . ? HZ2 HZ2 H . 0 . ? HZ3 HZ3 H . 0 . ? HT2 HT2 H . 0 . ? HT1 HT1 H . 0 . ? HH1 HH1 H . 0 . ? HH2 HH2 H . 0 . ? HXT HXT H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N H ? ? SING N H2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD CE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING CE CZ ? ? SING CE HE2 ? ? SING CE HE3 ? ? SING CZ CT ? ? SING CZ HZ2 ? ? SING CZ HZ3 ? ? SING CT NH ? ? SING CT HT2 ? ? SING CT HT1 ? ? SING NH HH1 ? ? SING NH HH2 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $somatostatin . . . . . . 'SYNTHESIZED IN THE LAB' stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $somatostatin 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $somatostatin 2.5 mM . DMSO-d6 100 % . stop_ save_ ############################ # Computer software used # ############################ save_DYANA _Saveframe_category software _Name DYANA _Version 1.0.6 loop_ _Task refinement 'structure solution' stop_ _Details 'Peter Guntert' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_2D_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DMSO H 1 'methyl protons' ppm . . . . . . 1.0 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label DQF-COSY '2D NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'SST1-selective somatostatin analog' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 TYR HA H 3.962 0.000 . 2 . 1 TYR HB2 H 3.065 0.001 . 3 . 1 TYR HB3 H 2.747 0.001 . 4 . 1 TYR HD1 H 7.021 0.002 . 5 . 1 TYR HE1 H 6.651 0.000 . 6 . 2 CYS H H 8.737 0.000 . 7 . 2 CYS HA H 4.738 0.000 . 8 . 2 CYS HB2 H 3.079 0.003 . 9 . 2 CYS HB3 H 2.882 0.001 . 10 . 3 LYS H H 8.382 0.002 . 11 . 3 LYS HA H 4.365 0.001 . 12 . 3 LYS HB2 H 1.568 0.008 . 13 . 3 LYS HG2 H 1.285 0.004 . 14 . 3 LYS HD2 H 1.500 0.008 . 15 . 3 LYS HE2 H 2.737 0.000 . 16 . 4 PHE H H 8.302 0.001 . 17 . 4 PHE HA H 4.712 0.000 . 18 . 4 PHE HB2 H 2.891 0.001 . 19 . 4 PHE HB3 H 2.722 0.003 . 20 . 4 PHE HD1 H 7.063 0.002 . 21 . 4 PHE HE1 H 7.136 0.002 . 22 . 5 GLU H H 8.189 0.001 . 23 . 5 GLU HA H 4.218 0.004 . 24 . 5 GLU HB2 H 1.788 0.000 . 25 . 5 GLU HB3 H 1.575 0.008 . 26 . 5 GLU HG2 H 1.895 0.000 . 27 . 6 DTR H H 8.301 0.001 . 28 . 6 DTR HA H 4.350 0.001 . 29 . 6 DTR HB2 H 2.659 0.000 . 30 . 6 DTR HZ2 H 7.325 0.000 . 31 . 6 DTR HE3 H 7.517 0.000 . 32 . 6 DTR HE1 H 10.792 0.001 . 33 . 6 DTR HZ3 H 7.147 0.000 . 34 . 6 DTR HD1 H 7.030 0.003 . 35 . 6 DTR HH2 H 7.018 0.000 . 36 . 7 IAM H H 8.708 0.005 . 37 . 7 IAM HA H 4.415 0.002 . 38 . 7 IAM HB2 H 3.138 0.000 . 39 . 7 IAM HB3 H 2.660 0.006 . 40 . 7 IAM HD1 H 7.270 0.003 . 41 . 7 IAM HE1 H 7.322 0.001 . 42 . 7 IAM HH H 8.545 0.000 . 43 . 7 IAM HT H 4.031 0.001 . 44 . 7 IAM HI H 3.144 0.001 . 45 . 7 IAM HK H 1.144 0.001 . 46 . 8 THR H H 7.503 0.005 . 47 . 8 THR HA H 4.368 0.001 . 48 . 8 THR HB H 3.933 0.001 . 49 . 8 THR HG2 H 1.001 0.002 . 50 . 9 PHE H H 8.300 0.001 . 51 . 9 PHE HA H 4.516 0.001 . 52 . 9 PHE HB2 H 2.882 0.003 . 53 . 9 PHE HB3 H 2.726 0.003 . 54 . 9 PHE HD1 H 7.063 0.003 . 55 . 9 PHE HE1 H 7.135 0.001 . 56 . 10 HHK H H 7.911 0.003 . 57 . 10 HHK HA H 4.269 0.001 . 58 . 10 HHK HB2 H 1.454 0.000 . 59 . 10 HHK HG2 H 1.191 0.002 . 60 . 10 HHK HD1 H 1.342 0.002 . 61 . 10 HHK HE1 H 2.994 0.004 . 62 . 10 HHK HZ1 H 1.161 0.000 . 63 . 10 HHK HT1 H 3.032 0.000 . 64 . 10 HHK HH1 H 7.611 0.002 . 65 . 11 SER H H 7.917 0.003 . 66 . 11 SER HA H 4.292 0.000 . 67 . 11 SER HB2 H 3.588 0.003 . 68 . 12 CYS H H 8.484 0.000 . 69 . 12 CYS HA H 4.366 0.001 . 70 . 12 CYS HB2 H 2.716 0.000 . stop_ save_