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

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALPHA-DEFENSIN 1 (HNP1) Y16A/I20A/L25A/F28A MUTANT.
 
Authors :  W. D. Tolbert, X. Wu, M. Pazgier
Date :  20 Jun 13  (Deposition) - 27 Nov 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,D,E
Keywords :  Antimicrobial Peptide, Human Alpha Defensin 1, Human Neutrophil Peptide 1, Hnp1, Antibiotic, Antiviral Defense, Defensin, Disulfide Bond, Fungicide, Phosphoprotein, Secreted, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Zhao, W. D. Tolbert, B. Ericksen, C. Zhan, X. Wu, W. Yuan, X. Li, M. Pazgier, W. Lu
Single, Double And Quadruple Alanine Substitutions At Oligomeric Interfaces Identify Hydrophobicity As The Key Determinant Of Human Neutrophil Alpha Defensin Hnp1 Function.
Plos One V. 8 78937 2013
PubMed-ID: 24236072  |  Reference-DOI: 10.1371/JOURNAL.PONE.0078937

(-) Compounds

Molecule 1 - NEUTROPHIL DEFENSIN 1
    ChainsD, E, A, B
    EngineeredYES
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDEFENSIN, ALPHA 1, HNP-1, HP-1, HP1, HP 1-56, NEUTROPHIL DEFENSIN 2, HNP-2, HP-2, HP2
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4LB7)

(-) Sites  (0, 0)

(no "Site" information available for 4LB7)

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:2 -A:30
2A:4 -A:19
3A:9 -A:29
4B:2 -B:30
5B:4 -B:19
6B:9 -B:29
7D:2 -D:30
8D:4 -D:19
9D:9 -D:29
10E:2 -E:30
11E:4 -E:19
12E:9 -E:29

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ile D:6 -Pro D:7
2Ile E:6 -Pro E:7
3Ile A:6 -Pro A:7
4Ile B:6 -Pro B:7

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LB7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LB7)

(-) Exons   (0, 0)

(no "Exon" information available for 4LB7)

(-) 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:30
                                                             
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..eee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  4lb7 A  1 ACYCRIPACIAGERRAGTCAYQGRAWAACC 30
                                    10        20        30

Chain B from PDB  Type:PROTEIN  Length:30
                                                             
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .eeee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  4lb7 B  1 ACYCRIPACIAGERRAGTCAYQGRAWAACC 30
                                    10        20        30

Chain D from PDB  Type:PROTEIN  Length:30
                                                             
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .eeee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  4lb7 D  1 ACYCRIPACIAGERRAGTCAYQGRAWAACC 30
                                    10        20        30

Chain E from PDB  Type:PROTEIN  Length:30
                                                             
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .eeee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  4lb7 E  1 ACYCRIPACIAGERRAGTCAYQGRAWAACC 30
                                    10        20        30

   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 4LB7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LB7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LB7)

(-) Gene Ontology  (18, 18)

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
(no "Ligands, Modified Residues, Ions" information available for 4lb7)
 
  Sites
(no "Sites" information available for 4lb7)
 
  Cis Peptide Bonds
    Ile A:6 - Pro A:7   [ RasMol ]  
    Ile B:6 - Pro B:7   [ RasMol ]  
    Ile D:6 - Pro D:7   [ RasMol ]  
    Ile E:6 - Pro E:7   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4lb7
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DEF1_HUMAN | P59665
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  DEF1_HUMAN | P59665
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DEF1_HUMAN | P596651dfn 2kht 2pm1 2pm4 2pm5 3gny 3h6c 3hj2 3hjd 3lo1 3lo2 3lo4 3lo6 3lo9 3loe 3lvx 4du0 4lb1 4lbb 4lbf

(-) Related Entries Specified in the PDB File

3gny WILD TYPE HNP1
4lb1
4lbb
4lbf