Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NEUTROPHIL ELASTASE IN COMPLEX WITH A DIHYDROPYRIMIDONE INHIBITOR
 
Authors :  F. Vonnussbaum, V. M. Li, D. Meibom, S. Anlauf, M. Bechem, M. Delbeck, M. A. Harrenga, D. Karthaus, D. Lang, K. Lustig, J. Mittendorf, M. Schaef S. Schaefer, J. Schamberger
Date :  17 Jul 15  (Deposition) - 03 Aug 16  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Trypsin Family Fold, Protease, Hydrolase, Hydrolase- Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Von Nussbaum, V. M. Li, D. Meibom, S. Anlauf, M. Bechem, M. Delbeck, M. Gerisch, A. Harrenga, D. Karthaus, D. Lang, K. Lustig, J. Mittendorf, M. Schafer, S. Schafer, J. Schamberger
Potent And Selective Human Neutrophil Elastase Inhibitors With Novel Equatorial Ring Topology: In Vivo Efficacy Of Th Polar Pyrimidopyridazine Bay-8040 In A Pulmonary Arterial Hypertension Rat Model.
Chemmedchem V. 11 199 2016
PubMed-ID: 26333652  |  Reference-DOI: 10.1002/CMDC.201500269

(-) Compounds

Molecule 1 - NEUTROPHIL ELASTASE
    Chains: A
    EC Number: 3.4.21.37
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BONE MARROW SERINE PROTEASE, ELASTASE-2, HUMAN LEUKOCYTE ELASTASE, HLE, MEDULLASIN, PMN ELASTASE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2IUL1Ligand/Ion4-[(4R)-7-METHYL-2,5-BIS(OXIDANYLIDENE)-1-[3-(TRIFLUOROMETHYL)PHENYL]-3,4,6,8-TETRAHYDROPYRIMIDO[4,5-D]PYRIDAZIN-4-YL]BENZENECARBONITRILE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARENAG A:401 , FUC A:402BINDING SITE FOR RESIDUE NAG A 403
2AC2SOFTWAREHIS A:57 , TYR A:94 , LEU A:99 , ASP A:102 , VAL A:190 , CYS A:191 , PHE A:192 , ASP A:194 , SER A:195 , ALA A:213 , SER A:214 , PHE A:215 , VAL A:216 , TYR A:224 , HOH A:2077BINDING SITE FOR RESIDUE IUL A 1001
3AC3SOFTWAREARG A:63B , VAL A:64 , ARG A:65 , ALA A:84 , ASN A:109Binding site for Poly-Saccharide residues NAG A 411 through FUC A 412 bound to ASN A 109
4AC4SOFTWARETRP A:27 , GLN A:135 , ASN A:159 , VAL A:200 , CYS A:201 , ASN A:202 , GLY A:207 , NAG A:403 , HOH A:2055 , HOH A:2056 , HOH A:2091Binding site for Poly-Saccharide residues NAG A 401 through FUC A 402 bound to ASN A 159

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:136 -A:201
3A:168 -A:182
4A:191 -A:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A8Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A8Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A8Z)

(-) Exons   (0, 0)

(no "Exon" information available for 5A8Z)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhhh.......eeee............eeeeeeeeee............eeeee..........................eeeeee...........eeeeeeee........eeee...............eeee..eeeeeeee...........eeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5a8z A   16 IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGVQCLAMGWGLLGGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ  243
                                    25        35||      46        56       63C        73        83      ||94       104       114       124       134       144||     158       177      186A|      195      |209       219 |     228       238     
                                               36|                       63A||                         90|                                                  145|             166||      186A|             202|          220A                       
                                                38                        63B|                          92                                                   150              168|       186B              207                                     
                                                                           63C                                                                                                 177
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5A8Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A8Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A8Z)

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IUL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5a8z)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5a8z
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ELNE_HUMAN | P08246
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.37
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ELNE_HUMAN | P08246
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ELNE_HUMAN | P08246: 1b0f 1h1b 1hne 1ppf 1ppg 2rg3 2z7f 3q76 3q77 4nzl 4wvp 5a09 5a0a 5a0b 5a0c 5a8x 5a8y 5abw

(-) Related Entries Specified in the PDB File

5a8x CRYSTAL STRUCTURE OF HUMAN NEUTROPHIL ELASTASE IN COMPLEX WITH A DIHYDROPYRIMIDONE INHIBITOR
5a8y CRYSTAL STRUCTURE OF HUMAN NEUTROPHIL ELASTASE IN COMPLEX WITH A DIHYDROPYRIMIDONE INHIBITOR