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(-) Description

Title :  CRYSTAL STRUCTURE OF D-ENANTIOMER OF HUMAN ALPHA-DEFENSIN 1 (D-HNP1)
 
Authors :  M. Pazgier, W-Y. Lu
Date :  18 Mar 09  (Deposition) - 28 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Antimicrobial Peptide, D-Enantiomer Of Human Alpha Defensin 1, D- Enantiomer Of Human Neutrophil Peptide 1, D-Hnp1, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Wei, E. De Leeuw, M. Pazgier, W. Yuan, G. Zou, J. Wang, B. Ericksen, W. Y. Lu, R. I. Lehrer, W. Lu
Through The Looking Glass, Mechanistic Insights From Enantiomeric Human Defensins.
J. Biol. Chem. V. 284 29180 2009
PubMed-ID: 19640840  |  Reference-DOI: 10.1074/JBC.M109.018085

(-) Compounds

Molecule 1 - NEUTROPHIL DEFENSIN 1
    Chains: A, B
    Engineered: YES
    Other Details: D-ENANTIOMER
    Other Details - Source: THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
    Synonym: HNP-1, HP-1, HP1, DEFENSIN, ALPHA 1, HP 1-56, NEUTROPHIL DEFENSIN 2, HNP-2, HP-2, HP2
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (13, 57)

Asymmetric Unit (13, 57)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2DAL8Mod. Amino AcidD-ALANINE
3DAR8Mod. Amino AcidD-ARGININE
4DCY12Mod. Amino AcidD-CYSTEINE
5DGL2Mod. Amino AcidD-GLUTAMIC ACID
6DGN2Mod. Amino AcidD-GLUTAMINE
7DIL6Mod. Amino AcidD-ISOLEUCINE
8DLE2Mod. Amino AcidD-LEUCINE
9DPN2Mod. Amino AcidD-PHENYLALANINE
10DPR2Mod. Amino AcidD-PROLINE
11DTH2Mod. Amino AcidD-THREONINE
12DTR2Mod. Amino AcidD-TRYPTOPHAN
13DTY6Mod. Amino AcidD-TYROSINE
Biological Unit 1 (12, 108)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DAL16Mod. Amino AcidD-ALANINE
3DAR16Mod. Amino AcidD-ARGININE
4DCY24Mod. Amino AcidD-CYSTEINE
5DGL4Mod. Amino AcidD-GLUTAMIC ACID
6DGN4Mod. Amino AcidD-GLUTAMINE
7DIL12Mod. Amino AcidD-ISOLEUCINE
8DLE4Mod. Amino AcidD-LEUCINE
9DPN4Mod. Amino AcidD-PHENYLALANINE
10DPR4Mod. Amino AcidD-PROLINE
11DTH4Mod. Amino AcidD-THREONINE
12DTR4Mod. Amino AcidD-TRYPTOPHAN
13DTY12Mod. Amino AcidD-TYROSINE
Biological Unit 2 (12, 54)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DAL8Mod. Amino AcidD-ALANINE
3DAR8Mod. Amino AcidD-ARGININE
4DCY12Mod. Amino AcidD-CYSTEINE
5DGL2Mod. Amino AcidD-GLUTAMIC ACID
6DGN2Mod. Amino AcidD-GLUTAMINE
7DIL6Mod. Amino AcidD-ISOLEUCINE
8DLE2Mod. Amino AcidD-LEUCINE
9DPN2Mod. Amino AcidD-PHENYLALANINE
10DPR2Mod. Amino AcidD-PROLINE
11DTH2Mod. Amino AcidD-THREONINE
12DTR2Mod. Amino AcidD-TRYPTOPHAN
13DTY6Mod. Amino AcidD-TYROSINE

(-) Sites  (0, 0)

(no "Site" information available for 3GO0)

(-) SS Bonds  (6, 6)

Asymmetric 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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GO0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GO0)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 3GO0)

(-) 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: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
                  3go0 A  1 xxxxxxxxxxxGxxxxGxxxxxGxxxxxxx 30
                            ||||||||10| |||| |20|| |||||30
                            ||||||||9-DCY||| |20-DIL||||30-DCY
                            1-DAL|||10-DIL|| ||21-DTY|||| 
                             2-DCY|| 11-DAL| || 22-DGN||| 
                              3-DTY|   13-DGL||   24-DAR| 
                               4-DCY    14-DAR|    25-DLE 
                                5-DAR    15-DAR     26-DTR
                                 6-DIL    16-DTY     27-DAL
                                  7-DPR     18-DTH    28-DPN
                                   8-DAL     19-DCY    29-DCY


Chain B 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
                  3go0 B  1 xxxxxxxxxxxGxxxxGxxxxxGxxxxxxx 30
                            ||||||||10| |||| |20|| |||||30
                            ||||||||9-DCY||| |20-DIL||||30-DCY
                            1-DAL|||10-DIL|| ||21-DTY|||| 
                             2-DCY|| 11-DAL| || 22-DGN||| 
                              3-DTY|   13-DGL||   24-DAR| 
                               4-DCY    14-DAR|    25-DLE 
                                5-DAR    15-DAR     26-DTR
                                 6-DIL    16-DTY     27-DAL
                                  7-DPR     18-DTH    28-DPN
                                   8-DAL     19-DCY    29-DCY
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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(-) Related Entries Specified in the PDB File

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2pm1 DERIVATIVE OF HUMAN ALPHA-DEFENSIN 1
2pm4 HUMAN ALPHA-DEFENSIN 1 (MULTIPLE ARG TO LYS MUTANT)
2pm5 HUMAN ALPHA-DEFENSIN 1 DERIVATIVE
3gny CRYSTAL STRCTURE OF HUMAN ALPHA-DEFENSIN 1 (HNP1)