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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALPHA-DEFENSIN 1 (HNP1) I20A/L25A 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 :  1.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Antimicrobial Peptide, Human Alpha Defensin 1, Human Neutrophil Peptide 1, 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
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEFENSIN, ALPHA 1, HNP-1, HP-1, HP1, HP 1-56, NEUTROPHIL DEFENSIN 2, HNP-2, HP-2, HP2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:23 , ARG A:24 , ALA A:25 , HOH A:108 , HOH A:130 , ARG D:5 , PRO D:7 , HOH D:205 , HOH D:207 , HOH D:221 , HOH D:223BINDING SITE FOR RESIDUE GOL D 101

(-) SS Bonds  (24, 24)

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
7C:2 -C:30
8C:4 -C:19
9C:9 -C:29
10D:2 -D:30
11D:4 -D:19
12D:9 -D:29
13E:2 -E:30
14E:4 -E:19
15E:9 -E:29
16F:2 -F:30
17F:4 -F:19
18F:9 -F:29
19G:2 -G:30
20G:4 -G:19
21G:9 -G:29
22H:2 -H:30
23H:4 -H:19
24H:9 -H:29

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ile A:6 -Pro A:7
2Ile B:6 -Pro B:7
3Ile C:6 -Pro C:7
4Ile D:6 -Pro D:7
5Ile E:6 -Pro E:7
6Ile F:6 -Pro F:7
7Ile G:6 -Pro G:7
8Ile H:6 -Pro H:7

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LBF)

(-) 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
                  4lbf A  1 ACYCRIPACIAGERRYGTCAYQGRAWAFCC 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
                  4lbf B  1 ACYCRIPACIAGERRYGTCAYQGRAWAFCC 30
                                    10        20        30


Chain C 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
                  4lbf C  1 ACYCRIPACIAGERRYGTCAYQGRAWAFCC 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 ..eee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  4lbf D  1 ACYCRIPACIAGERRYGTCAYQGRAWAFCC 30
                                    10        20        30


Chain E from PDB  Type:PROTEIN  Length:25
                                                        
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ..eee........eeeee...eeee Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  4lbf E  1 ACYCRIPACIAGERRYGTCAWAFCC 30
                                    10        25     
                                             19|     
                                              25     


Chain F 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
                  4lbf F  1 ACYCRIPACIAGERRYGTCAYQGRAWAFCC 30
                                    10        20        30


Chain G 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
                  4lbf G  1 ACYCRIPACIAGERRYGTCAYQGRAWAFCC 30
                                    10        20        30


Chain H 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
                  4lbf H  1 ACYCRIPACIAGERRYGTCAYQGRAWAFCC 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 4LBF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)

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  DEF1_HUMAN | P59665
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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF1_HUMAN | P59665: 1dfn 2kht 2pm1 2pm4 2pm5 3gny 3h6c 3hj2 3hjd 3lo1 3lo2 3lo4 3lo6 3lo9 3loe 3lvx 4du0 4lb1 4lb7 4lbb

(-) Related Entries Specified in the PDB File

3gny WILD TYPE HNP1
4lb1
4lb7
4lbb