data_4630 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR STRUCTURE OF THROMBOMODULIN EGF(4-5) ; _BMRB_accession_number 4630 _BMRB_flat_file_name bmr4630.str _Entry_type original _Submission_date 2000-01-03 _Accession_date 2001-03-10 _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 Wood M. J. . 2 Sampoli-Benitez B. A. . 3 Komives E. A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count coupling_constants 2 stop_ loop_ _Data_type _Data_type_count "coupling constants" 43 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2001-05-07 original author . stop_ _Original_release_date 2001-05-07 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structure of the smallest cofactor-active fragment of thrombomodulin' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 10700277 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wood M. J. . 2 Sampoli-Benitez B. A. . 3 Komives E. A. . stop_ _Journal_abbreviation 'Nat. Struct. Biol.' _Journal_volume 7 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 200 _Page_last 204 _Year 2000 _Details . loop_ _Keyword NMR THROMBIN 'EGF MODULE' ANTICOAGULANT GLYCOSYLATION stop_ save_ ################################## # Molecular system description # ################################## save_system_THROMBOMODULIN _Saveframe_category molecular_system _Mol_system_name THROMBOMODULIN _Abbreviation_common THROMBOMODULIN _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label THROMBOMODULIN $THROMBOMODULIN N-ACETYL-D-GLUCOSAMINE-1 $NAG N-ACETYL-D-GLUCOSAMINE-2 $NAG 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_THROMBOMODULIN _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common THROMBOMODULIN _Abbreviation_common THROMBOMODULIN _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 83 _Mol_residue_sequence ; HMEPVDPCFRANCEYQCQPL NQTSYLCVCAEGFAPIPHEP HRCQMFCNQTACPADCDPNT QASCECPEGYILDDGFICTD IDE ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 HIS 2 2 MET 3 3 GLU 4 4 PRO 5 5 VAL 6 6 ASP 7 7 PRO 8 8 CYS 9 9 PHE 10 10 ARG 11 11 ALA 12 12 ASN 13 13 CYS 14 14 GLU 15 15 TYR 16 16 GLN 17 17 CYS 18 18 GLN 19 19 PRO 20 20 LEU 21 21 ASN 22 22 GLN 23 23 THR 24 24 SER 25 25 TYR 26 26 LEU 27 27 CYS 28 28 VAL 29 29 CYS 30 30 ALA 31 31 GLU 32 32 GLY 33 33 PHE 34 34 ALA 35 35 PRO 36 36 ILE 37 37 PRO 38 38 HIS 39 39 GLU 40 40 PRO 41 41 HIS 42 42 ARG 43 43 CYS 44 44 GLN 45 45 MET 46 46 PHE 47 47 CYS 48 48 ASN 49 49 GLN 50 50 THR 51 51 ALA 52 52 CYS 53 53 PRO 54 54 ALA 55 55 ASP 56 56 CYS 57 57 ASP 58 58 PRO 59 59 ASN 60 60 THR 61 61 GLN 62 62 ALA 63 63 SER 64 64 CYS 65 65 GLU 66 66 CYS 67 67 PRO 68 68 GLU 69 69 GLY 70 70 TYR 71 71 ILE 72 72 LEU 73 73 ASP 74 74 ASP 75 75 GLY 76 76 PHE 77 77 ILE 78 78 CYS 79 79 THR 80 80 ASP 81 81 ILE 82 82 ASP 83 83 GLU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-13 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 1DQB "Nmr Structure Of Thrombomodulin Egf(4-5)" 100.00 83 100.00 100.00 3.52e-52 PDB 1DX5 "Crystal Structure Of The Thrombin-Thrombomodulin Complex" 98.80 118 97.56 100.00 1.88e-49 PDB 1ZAQ "Fourth Egf-Like Domain Of Thrombomodulin, Nmr, 12 Structures" 53.01 44 100.00 100.00 1.62e-22 PDB 3GIS "Crystal Structure Of Na-Free Thrombin In Complex With Thrombomodulin" 98.80 121 97.56 100.00 9.80e-50 DBJ BAA00149 "thrombomodulin precursor [Homo sapiens]" 98.80 575 98.78 100.00 3.02e-48 DBJ BAG53913 "unnamed protein product [Homo sapiens]" 98.80 557 97.56 98.78 1.18e-47 DBJ BAJ17754 "thrombomodulin [synthetic construct]" 98.80 575 98.78 100.00 3.21e-48 EMBL CAA29045 "thrombomodulin [Homo sapiens]" 98.80 575 98.78 100.00 3.02e-48 GB AAA61175 "thrombomodulin precursor [Homo sapiens]" 98.80 575 98.78 100.00 3.21e-48 GB AAB27209 "thrombomodulin [human, urine, Peptide, 468 aa]" 98.80 468 98.78 100.00 4.44e-48 GB AAB59508 "thrombomodulin [Homo sapiens]" 98.80 575 98.78 100.00 3.21e-48 GB AAD49735 "thrombomodulin precursor [Saimiri sciureus]" 98.80 575 98.78 100.00 3.21e-48 GB AAH35602 "Thrombomodulin [Homo sapiens]" 98.80 575 98.78 100.00 3.02e-48 PRF 1403353A thrombomodulin 98.80 575 98.78 100.00 3.02e-48 REF NP_000352 "thrombomodulin precursor [Homo sapiens]" 98.80 575 98.78 100.00 3.21e-48 REF XP_003829427 "PREDICTED: thrombomodulin [Pan paniscus]" 98.80 631 98.78 100.00 2.83e-48 REF XP_525283 "PREDICTED: thrombomodulin [Pan troglodytes]" 98.80 631 98.78 100.00 2.97e-48 SP P07204 "RecName: Full=Thrombomodulin; Short=TM; AltName: Full=Fetomodulin; AltName: CD_antigen=CD141; Flags: Precursor" 98.80 575 98.78 100.00 3.21e-48 SP Q71U07 "RecName: Full=Thrombomodulin; Short=TM; AltName: CD_antigen=CD141; Flags: Precursor" 98.80 575 98.78 100.00 3.21e-48 stop_ save_ ############# # Ligands # ############# save_NAG _Saveframe_category ligand _Mol_type "non-polymer (D-SACCHARIDE)" _Name_common "NAG (N-ACETYL-D-GLUCOSAMINE)" _BMRB_code . _PDB_code NAG _Molecular_mass 221.208 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Aug 1 11:20:45 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? N2 N2 N . 0 . ? O1 O1 O . 0 . ? O3 O3 O . 0 . ? O4 O4 O . 0 . ? O5 O5 O . 0 . ? O6 O6 O . 0 . ? O7 O7 O . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H81 H81 H . 0 . ? H82 H82 H . 0 . ? H83 H83 H . 0 . ? HN2 HN2 H . 0 . ? HO1 HO1 H . 0 . ? HO3 HO3 H . 0 . ? HO4 HO4 H . 0 . ? HO6 HO6 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 C1 C2 ? ? SING C1 O1 ? ? SING C1 O5 ? ? SING C1 H1 ? ? SING C2 C3 ? ? SING C2 N2 ? ? SING C2 H2 ? ? SING C3 C4 ? ? SING C3 O3 ? ? SING C3 H3 ? ? SING C4 C5 ? ? SING C4 O4 ? ? SING C4 H4 ? ? SING C5 C6 ? ? SING C5 O5 ? ? SING C5 H5 ? ? SING C6 O6 ? ? SING C6 H61 ? ? SING C6 H62 ? ? SING C7 C8 ? ? SING C7 N2 ? ? DOUB C7 O7 ? ? SING C8 H81 ? ? SING C8 H82 ? ? SING C8 H83 ? ? SING N2 HN2 ? ? SING O1 HO1 ? ? SING O3 HO3 ? ? SING O4 HO4 ? ? SING O6 HO6 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $THROMBOMODULIN Human 9606 Eukaryota Metazoa Homo sapiens 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 $THROMBOMODULIN 'recombinant technology' Yeast Pichia pastoris . . 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 $THROMBOMODULIN 1 mM [U-15N] $NAG 2 mM . H2O 90 % . D2O 10 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $THROMBOMODULIN 1 mM . $NAG 2 mM . D2O 100 % . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name XWINNMR _Version 3.0 loop_ _Task collection stop_ _Details Bruker save_ save_FELIX _Saveframe_category software _Name FELIX _Version 97.0 loop_ _Task 'data analysis' stop_ _Details 'Molecular Simulations Inc.' save_ save_DGII _Saveframe_category software _Name DGII _Version 97.0 loop_ _Task 'structure solution' stop_ _Details 'Molecular Simulations Inc.' save_ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version 3.5 loop_ _Task refinement stop_ _Details Brunger save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_15N-separated_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 15N-separated NOESY' _Sample_label . save_ save_HNHA_2 _Saveframe_category NMR_applied_experiment _Experiment_name HNHA _Sample_label . save_ save_2D_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.5 . pH temperature 310 . K 'ionic strength' 0 . M pressure 1 . atm stop_ save_ ######################## # Coupling constants # ######################## save_JHNHA _Saveframe_category coupling_constants _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Spectrometer_frequency_1H 600 _Mol_system_component_name THROMBOMODULIN _Text_data_format . _Text_data . loop_ _Coupling_constant_ID _Coupling_constant_code _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_name _Coupling_constant_value _Coupling_constant_min_value _Coupling_constant_max_value _Coupling_constant_value_error 1 3JHNHA 6 ASP H 6 ASP HA 5.70 . . . 2 3JHNHA 9 PHE H 9 PHE HA 2.90 . . . 3 3JHNHA 11 ALA H 11 ALA HA 4.90 . . . 4 3JHNHA 13 CYS H 13 CYS HA 3.90 . . . 5 3JHNHA 14 GLU H 14 GLU HA 3.10 . . . 6 3JHNHA 15 TYR H 15 TYR HA 9.50 . . . 7 3JHNHA 17 CYS H 17 CYS HA 8.20 . . . 8 3JHNHA 18 GLN H 18 GLN HA 8.90 . . . 9 3JHNHA 21 ASN H 21 ASN HA 4.30 . . . 10 3JHNHA 23 THR H 23 THR HA 8.60 . . . 11 3JHNHA 26 LEU H 26 LEU HA 8.40 . . . 12 3JHNHA 28 VAL H 28 VAL HA 8.90 . . . 13 3JHNHA 29 CYS H 29 CYS HA 8.10 . . . 14 3JHNHA 30 ALA H 30 ALA HA 4.90 . . . 15 3JHNHA 31 GLU H 31 GLU HA 2.30 . . . 16 3JHNHA 36 ILE H 36 ILE HA 4.70 . . . 17 3JHNHA 43 CYS H 43 CYS HA 8.10 . . . 18 3JHNHA 45 MET H 45 MET HA 3.60 . . . 19 3JHNHA 52 CYS H 52 CYS HA 8.10 . . . 20 3JHNHA 54 ALA H 54 ALA HA 4.10 . . . 21 3JHNHA 56 CYS H 56 CYS HA 4.10 . . . 22 3JHNHA 60 THR H 60 THR HA 8.60 . . . 23 3JHNHA 62 ALA H 62 ALA HA 4.60 . . . 24 3JHNHA 68 GLU H 68 GLU HA 4.40 . . . 25 3JHNHA 70 TYR H 70 TYR HA 4.70 . . . 26 3JHNHA 72 LEU H 72 LEU HA 4.60 . . . 27 3JHNHA 74 ASP H 74 ASP HA 4.60 . . . 28 3JHNHA 77 ILE H 77 ILE HA 5.40 . . . 29 3JHNHA 81 ILE H 81 ILE HA 5.50 . . . stop_ save_ save_JHAHB _Saveframe_category coupling_constants _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Spectrometer_frequency_1H 600 _Mol_system_component_name THROMBOMODULIN _Text_data_format . _Text_data . loop_ _Coupling_constant_ID _Coupling_constant_code _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_name _Coupling_constant_value _Coupling_constant_min_value _Coupling_constant_max_value _Coupling_constant_value_error 1 3JHAHB 8 CYS HA 8 CYS HB2 12.00 . . . 2 3JHAHB 8 CYS HA 8 CYS HB3 4.00 . . . 3 3JHAHB 10 ARG HA 10 ARG HB2 12.00 . . . 4 3JHAHB 10 ARG HA 10 ARG HB3 4.00 . . . 5 3JHAHB 15 TYR HA 15 TYR HB2 12.00 . . . 6 3JHAHB 15 TYR HA 15 TYR HB3 4.00 . . . 7 3JHAHB 27 CYS HA 27 CYS HB2 12.00 . . . 8 3JHAHB 27 CYS HA 27 CYS HB3 4.00 . . . 9 3JHAHB 29 CYS HA 29 CYS HB2 12.00 . . . 10 3JHAHB 29 CYS HA 29 CYS HB3 4.00 . . . 11 3JHAHB 33 PHE HA 33 PHE HB2 4.00 . . . 12 3JHAHB 33 PHE HA 33 PHE HB3 12.00 . . . 13 3JHAHB 66 CYS HA 66 CYS HB2 12.00 . . . 14 3JHAHB 66 CYS HA 66 CYS HB3 4.00 . . . stop_ save_