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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALPHA-DEFENSIN 5, HD5 (LEU29NLE MUTANT)
 
Authors :  M. Pazgier
Date :  19 Mar 12  (Deposition) - 16 May 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Beta-Sheet Structure, Antimicrobial Peptide, Leu29Nle Mutant, Paneth Cells, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Rajabi, B. Ericksen, X. Wu, E. De Leeuw, L. Zhao, M. Pazgier, W. Lu
Functional Determinants Of Human Enteric {Alpha}-Defensin Hd5: Crucial Role For Hydrophobicity At Dimer Interface.
J. Biol. Chem. V. 287 21615 2012
PubMed-ID: 22573326  |  Reference-DOI: 10.1074/JBC.M112.367995

(-) Compounds

Molecule 1 - DEFENSIN-5
    Chains: A, B
    Engineered: YES
    Fragment: UNP RESIDUES 63-94
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-DEFENSIN 5, HD5, DEFENSIN, ALPHA 5
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NLE2Mod. Amino AcidNORLEUCINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NLE1Mod. Amino AcidNORLEUCINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NLE1Mod. Amino AcidNORLEUCINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NLE2Mod. Amino AcidNORLEUCINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:6 , THR B:7BINDING SITE FOR RESIDUE CL B 101

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:3 -A:31
2A:5 -A:20
3A:10 -A:30
4B:3 -B:31
5B:5 -B:20
6B:10 -B:30

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4E83)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E83)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E83)

(-) Exons   (0, 0)

(no "Exon" information available for 4E83)

(-) 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:32
                                                               
               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
                  4e83 A  1 ATCYCRTGRCATRESLSGVCEISGRLYRlCCR 32
                                    10        20        30  
                                                       29-NLE


Chain B from PDB  Type:PROTEIN  Length:32
                                                               
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author .eeeee........ee...eee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                  4e83 B  1 ATCYCRTGRCATRESLSGVCEISGRLYRlCCR 32
                                    10        20        30  
                                                       29-NLE
   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 4E83)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E83)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E83)

(-) Gene Ontology  (12, 12)

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  4e83
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  DEF5_HUMAN | Q01523
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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF5_HUMAN | Q01523: 1zmp 2lxz 2mit 3i5w 4e82 4e86 4rbw 4rbx 5cui 5cuj 5cum

(-) Related Entries Specified in the PDB File

1zmp CRYSTAL STRUCTURE OF WILD TYPE HD5
4e82 CRYSTAL STRUCTURE OF MONOMERIC FORM OF HUMAN ALPHA-DEFENSIN 5, HD5
4e86 CRYSTAL STRUCTURE OF HUMAN ALPHA-DEFENSIN 5, HD5 (LEU29ABA MUTANT)