Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NEUTROPHIL ELASTASE IN COMPLEX WITH A DIHYDROPYRIMIDONE INHIBITOR
 
Authors :  F. Vonnussbaum, V. M. -J. Li, S. Allerheiligen, S. Anlauf, L. Baerfacke M. Bechem, M. Delbeck, M. F. Fitzgerald, M. Gerisch, H. Gielen-Haertw H. Haning, D. Karthaus, D. Lang, K. Lustig, D. Meibom, J. Mittendorf, U. Rosentreter, M. Schaefer, S. Schaefer, J. Schamberger, L. A. Telan A. Tersteegen
Date :  17 Apr 15  (Deposition) - 19 Aug 15  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Trypsin Family Fold, Protease, Hydrolase, Hydrolase- Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Von Nussbaum, V. M. Li, S. Allerheiligen, S. Anlauf, L. Barfacker, M. Bechem, M. Delbeck, M. F. Fitzgerald, M. Gerisch, H. Gielen-Haertwig, H. Haning, D. Karthaus, D. Lang, K. Lustig, D. Meibom, J. Mittendorf, U. Rosentreter, M. Schafer, S. Schafer, J. Schamberger, L. A. Telan, A. Tersteegen
Freezing The Bioactive Conformation To Boost Potency: The Identification Of Bay 85-8501, A Selective And Potent Inhibitor Of Human Neutrophil Elastase For Pulmonary Diseases.
Chemmedchem V. 10 1163 2015
PubMed-ID: 26083237  |  Reference-DOI: 10.1002/CMDC.201500131

(-) Compounds

Molecule 1 - NEUTROPHIL ELASTASE
    Chains: A, B
    EC Number: 3.4.21.37
    Fragment: UNP RESIDUES 30-247
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BONE MARROW SERINE PROTEASE, ELASTASE-2, HUMAN LEUKOCYTE EL ASTASE, HLE, MEDULLASIN, PMN ELASTASE, ELASTASE, HLE, MEDULIASIN, PMN ELASTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
1FUC4Ligand/IonALPHA-L-FUCOSE
2JJV2Ligand/Ion(6S)-6-(4-CYANO-2-METHYLSULFONYL-PHENYL)-4-METHYL-2-OXIDANYLIDENE-3-[3-(TRIFLUOROMETHYL)PHENYL]-1,6-DIHYDROPYRIMIDINE-5-CARBONITRILE
3MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
5XPE1Ligand/Ion3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
Biological Unit 1 (5, 8)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2JJV1Ligand/Ion(6S)-6-(4-CYANO-2-METHYLSULFONYL-PHENYL)-4-METHYL-2-OXIDANYLIDENE-3-[3-(TRIFLUOROMETHYL)PHENYL]-1,6-DIHYDROPYRIMIDINE-5-CARBONITRILE
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5XPE1Ligand/Ion3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2JJV1Ligand/Ion(6S)-6-(4-CYANO-2-METHYLSULFONYL-PHENYL)-4-METHYL-2-OXIDANYLIDENE-3-[3-(TRIFLUOROMETHYL)PHENYL]-1,6-DIHYDROPYRIMIDINE-5-CARBONITRILE
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5XPE-1Ligand/Ion3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:57 , TYR A:98 , PRO A:100 , LEU A:103 , ASP A:106 , VAL A:197 , CYS A:198 , PHE A:199 , ASP A:201 , SER A:202 , ALA A:220 , SER A:221 , PHE A:222 , VAL A:223 , MES A:1002 , XPE A:1003 , HOH A:2035 , HOH A:2069 , HOH A:2169 , LEU B:147 , PHE B:199BINDING SITE FOR RESIDUE JJV A 1001
2AC2SOFTWARELEU A:147 , PHE A:199 , XPE A:1003 , HIS B:57 , TYR B:98 , PRO B:100 , LEU B:103 , ASP B:106 , VAL B:197 , CYS B:198 , PHE B:199 , ASP B:201 , SER B:202 , ALA B:220 , SER B:221 , PHE B:222 , VAL B:223 , MES B:1002 , HOH B:2029 , HOH B:2055BINDING SITE FOR RESIDUE JJV B 1001
3AC3SOFTWARELEU A:103 , ARG A:181 , PHE A:222 , VAL A:223 , ARG A:224 , JJV A:1001 , HOH A:3001 , ARG B:151 , PHE B:199 , HOH B:2104 , HOH B:2133BINDING SITE FOR RESIDUE MES A 1002
4AC4SOFTWARELEU A:147 , ARG A:150 , PHE A:199 , HOH A:2114 , HOH A:2144 , HOH A:3002 , LEU B:103 , ARG B:181 , PHE B:222 , VAL B:223 , ARG B:224 , JJV B:1001 , HOH B:3003BINDING SITE FOR RESIDUE MES B 1002
5AC5SOFTWAREPHE A:41 , HIS A:57 , CYS A:58 , ILE A:155 , JJV A:1001 , HOH A:2036 , HOH A:2039 , HOH A:2145 , PHE B:41 , HIS B:57 , CYS B:58 , ALA B:60 , GLY B:200 , JJV B:1001 , HOH B:2020 , HOH B:2134BINDING SITE FOR RESIDUE XPE A 1003
6AC6SOFTWAREARG A:65 , VAL A:68 , ARG A:69 , ASN A:113Binding site for Poly-Saccharide residues NAG A 411 through FUC A 412 bound to ASN A 113
7AC7SOFTWARETRP A:27 , GLN A:139 , CYS A:140 , ASN A:163 , VAL A:207 , CYS A:208 , ASN A:209 , GLY A:214 , HOH A:2167 , HOH A:2168Binding site for Poly-Saccharide residues NAG A 401 through NAG A 403 bound to ASN A 163
8AC8SOFTWAREALA B:66 , VAL B:68 , ARG B:69 , ASN B:113Binding site for Poly-Saccharide residues NAG B 411 through FUC B 412 bound to ASN B 113
9AC9SOFTWARETRP B:27 , GLN B:139 , CYS B:140 , ASN B:163 , VAL B:207 , CYS B:208 , ASN B:209 , GLY B:214 , HOH B:2096 , HOH B:2137 , HOH B:2157 , HOH B:2158Binding site for Poly-Saccharide residues NAG B 401 through NAG B 403 bound to ASN B 163

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:42 -A:58
2A:140 -A:208
3A:172 -A:186
4A:198 -A:227
5B:42 -B:58
6B:140 -B:208
7B:172 -B:186
8B:198 -B:227

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A0C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A0C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A0C)

(-) Exons   (0, 0)

(no "Exon" information available for 5A0C)

(-) Sequences/Alignments

Asymmetric 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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhhh..hhhh.eeee............eeeeeeeeee............eeeee..........................eeeeee..............eeeeeeee........eeee...............eeee..eeeeeeee...........eeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a0c A  16 IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGVQCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ 252
                                    25        35||      46        56        66|       77        87      ||98       108       118       128       138       148   ||  159       169|||    188   ||  199       209|      223    || 234       244        
                                               36|                          66|                        94|                                                     152|             170||        192|            209|           228|                      
                                                38                           68                         96                                                      154              172|         194             214            230                      
                                                                                                                                                                                  181                                                                 


Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhhh..hhhh.eeee............eeeeeeeeee............eeeee..........................eeeeee..............eeeeeeee........eeee...............eeee..eeeeeeee...........eeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a0c B  16 IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGVQCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ 252
                                    25        35||      46        56        66|       77        87      ||98       108       118       128       138       148||     159       169|||    188   ||  199       209|      223    || 234       244        
                                               36|                          66|                        94|                                                  149|                170||        192|            209|           228|                      
                                                38                           68                         96                                                   151                 172|         194             214            230                      
                                                                                                                                                                                  181
   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 5A0C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A0C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A0C)

(-) Gene Ontology  (40, 40)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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 ]
    JJV  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    XPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5a0c)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  5a0c
    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 5a8x 5a8y 5a8z 5abw

(-) Related Entries Specified in the PDB File

5a09 CRYSTAL STRUCTURE OF HUMAN NEUTROPHIL ELASTASE IN COMPLEX WITH A DIHYDROPYRIMIDONE INHIBITOR
5a0a CRYSTAL STRUCTURE OF HUMAN NEUTROPHIL ELASTASE IN COMPLEX WITH A DIHYDROPYRIMIDONE INHIBITOR
5a0b CRYSTAL STRUCTURE OF HUMAN NEUTROPHIL ELASTASE IN COMPLEX WITH A DIHYDROPYRIMIDONE INHIBITOR