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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALPHA_DEFENSIN-2 (VARIANT GLY16->D-ALA), P 32 2 1 SPACE GROUP )
 
Authors :  J. Lubkowski, A. Prahl, W. Lu
Date :  10 May 05  (Deposition) - 16 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (2x),B (2x),C (2x),D (2x)
Biol. Unit 4:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 5:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 6:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Alpha-Defensin, Antimicrobial, D-Amino Acid Substitution, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Xie, A. Prahl, B. Ericksen, Z. Wu, P. Zeng, X. Li, W. Y. Lu, J. Lubkowski, W. Lu
Reconstruction Of The Conserved Beta-Bulge In Mammalian Defensins Using D-Amino Acids.
J. Biol. Chem. V. 280 32921 2005
PubMed-ID: 15894545  |  Reference-DOI: 10.1074/JBC.M503084200

(-) Compounds

Molecule 1 - NEUTROPHIL DEFENSIN 2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DEFA3, DEF3
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (2x): A (2x)B (2x)C (2x)D (2x)
Biological Unit 4 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 5 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 6 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1DAL4Mod. Amino AcidD-ALANINE
2GOL4Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1DAL2Mod. Amino AcidD-ALANINE
2GOL4Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1DAL2Mod. Amino AcidD-ALANINE
2GOL-1Ligand/IonGLYCEROL
3SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (3, 18)
No.NameCountTypeFull Name
1DAL4Mod. Amino AcidD-ALANINE
2GOL8Ligand/IonGLYCEROL
3SO46Ligand/IonSULFATE ION
Biological Unit 4 (3, 9)
No.NameCountTypeFull Name
1DAL2Mod. Amino AcidD-ALANINE
2GOL4Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
Biological Unit 5 (3, 9)
No.NameCountTypeFull Name
1DAL2Mod. Amino AcidD-ALANINE
2GOL4Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
Biological Unit 6 (3, 9)
No.NameCountTypeFull Name
1DAL2Mod. Amino AcidD-ALANINE
2GOL4Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:13 , CYS B:29 , HOH B:137 , HOH B:167 , ARG C:14BINDING SITE FOR RESIDUE SO4 B 401
2AC2SOFTWAREGLY B:11 , HOH B:138 , HOH B:219 , ARG C:14 , THR C:17BINDING SITE FOR RESIDUE SO4 B 402
3AC3SOFTWAREILE B:5 , ARG B:23 , HOH B:112 , HOH B:114 , HOH B:128 , HOH B:140 , HOH B:227 , HOH B:228BINDING SITE FOR RESIDUE SO4 B 403
4AC4SOFTWARECYS A:3 , TRP A:25 , HOH A:102 , HOH A:106 , HOH A:186 , HOH A:203 , GOL A:507 , PHE B:27 , ILE C:5 , HOH C:150BINDING SITE FOR RESIDUE GOL A 501
5AC5SOFTWARECYS A:1 , TYR B:2 , CYS B:3 , HOH B:153 , HOH B:178BINDING SITE FOR RESIDUE GOL B 502
6AC6SOFTWAREPRO B:6 , ARG B:14 , LEU B:24 , ALA B:26 , HOH B:206 , HOH C:113BINDING SITE FOR RESIDUE GOL B 503
7AC7SOFTWAREPRO A:6 , ALA A:7 , GOL A:501 , ILE C:5 , ARG C:23 , TRP C:25BINDING SITE FOR RESIDUE GOL A 507

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:1 -A:29
2A:3 -A:18
3A:8 -A:28
4B:1 -B:29
5B:3 -B:18
6B:8 -B:28
7C:1 -C:29
8C:3 -C:18
9C:8 -C:28
10D:1 -D:29
11D:3 -D:18
12D:8 -D:28

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ile A:5 -Pro A:6
2Ile B:5 -Pro B:6
3Ile C:5 -Pro C:6
4Ile D:5 -Pro D:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZMI)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEFENSINPS00269 Mammalian defensins signature.DEF3_HUMAN66-94
 
 
 		  4A:1-29
B:1-29
C:1-29
D:1-29
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEFENSINPS00269 Mammalian defensins signature.DEF3_HUMAN66-94
 
 
 		  2A:1-29
B:1-29
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEFENSINPS00269 Mammalian defensins signature.DEF3_HUMAN66-94
 
 
 		  2-
-
C:1-29
D:1-29
Biological Unit 3 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEFENSINPS00269 Mammalian defensins signature.DEF3_HUMAN66-94
 
 
 		  8A:1-29
B:1-29
C:1-29
D:1-29
Biological Unit 4 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEFENSINPS00269 Mammalian defensins signature.DEF3_HUMAN66-94
 
 
 		  4A:1-29
B:1-29
C:1-29
D:1-29
Biological Unit 5 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEFENSINPS00269 Mammalian defensins signature.DEF3_HUMAN66-94
 
 
 		  4A:1-29
B:1-29
C:1-29
D:1-29
Biological Unit 6 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEFENSINPS00269 Mammalian defensins signature.DEF3_HUMAN66-94
 
 
 		  4A:1-29
B:1-29
C:1-29
D:1-29

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003278571ENSE00001493010chr8:6875823-687574480DEF3_HUMAN-00--
1.2ENST000003278572ENSE00001719742chr8:6874384-6874198187DEF3_HUMAN1-59590--
1.3ENST000003278573ENSE00001306731chr8:6873621-6873391231DEF3_HUMAN59-94364A:1-29
B:1-29
C:1-29
D:1-29		29
29
29
29

(-) 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:29
 aligned with DEF3_HUMAN | P59666 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:29
                                    75        85         
            DEF3_HUMAN   66 CYCRIPACIAGERRYGTCIYQGRLWAFCC 94
               SCOP domains d1zmia_ A: automated matches  SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author .eee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE DEFENSIN  PDB: A:1-29         PROSITE
               Transcript 1 Exon 1.3  PDB: A:1-29         Transcript 1
                  1zmi A  1 CYCRIPACIAGERRYaTCIYQGRLWAFCC 29
                                    10     |  20         
                                          16-DAL         


Chain B from PDB  Type:PROTEIN  Length:29
 aligned with DEF3_HUMAN | P59666 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:29
                                    75        85         
            DEF3_HUMAN   66 CYCRIPACIAGERRYGTCIYQGRLWAFCC 94
               SCOP domains d1zmib_ B: automated matches  SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author .eee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE DEFENSIN  PDB: B:1-29         PROSITE
               Transcript 1 Exon 1.3  PDB: B:1-29         Transcript 1
                  1zmi B  1 CYCRIPACIAGERRYaTCIYQGRLWAFCC 29
                                    10     |  20         
                                          16-DAL         


Chain C from PDB  Type:PROTEIN  Length:29
 aligned with DEF3_HUMAN | P59666 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:29
                                    75        85         
            DEF3_HUMAN   66 CYCRIPACIAGERRYGTCIYQGRLWAFCC 94
               SCOP domains d1zmic_ C: automated matches  SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author .eee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE DEFENSIN  PDB: C:1-29         PROSITE
               Transcript 1 Exon 1.3  PDB: C:1-29         Transcript 1
                  1zmi C  1 CYCRIPACIAGERRYaTCIYQGRLWAFCC 29
                                    10     |  20         
                                          16-DAL         


Chain D from PDB  Type:PROTEIN  Length:29
 aligned with DEF3_HUMAN | P59666 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:29
                                    75        85         
            DEF3_HUMAN   66 CYCRIPACIAGERRYGTCIYQGRLWAFCC 94
               SCOP domains d1zmid_ D: automated matches  SCOP domains
               CATH domains ----------------------------- CATH domains
           Pfam domains (1) Defensin_1-1zmiD01 D:1-29     Pfam domains (1)
           Pfam domains (2) Defensin_1-1zmiD02 D:1-29     Pfam domains (2)
           Pfam domains (3) Defensin_1-1zmiD03 D:1-29     Pfam domains (3)
           Pfam domains (4) Defensin_1-1zmiD04 D:1-29     Pfam domains (4)
         Sec.struct. author .eee........eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE DEFENSIN  PDB: D:1-29         PROSITE
               Transcript 1 Exon 1.3  PDB: D:1-29         Transcript 1
                  1zmi D  1 CYCRIPACIAGERRYaTCIYQGRLWAFCC 29
                                    10     |  20         
                                          16-DAL
   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  (1, 4)

Asymmetric Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZMI)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Defensin (30)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DEF3_HUMAN | P59666)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0019731    antibacterial humoral response    An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0002227    innate immune response in mucosa    Any process of the innate immune response that takes place in the mucosal tissues.
    GO:0030520    intracellular estrogen receptor signaling pathway    Any series of molecular signals generated as a consequence of an intracellular estrogen receptor binding to one of its physiological ligands. The pathway begins with receptor-ligand binding, and ends with regulation of a downstream cellular process (e.g. transcription).
    GO:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
cellular component
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0035578    azurophil granule lumen    The volume enclosed by the membrane of an azurophil granule, a primary lysosomal granule found in neutrophil granulocytes that contains a wide range of hydrolytic enzymes and is released into the extracellular fluid.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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  1zmi
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  DEF3_HUMAN | P59666
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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF3_HUMAN | P59666: 1dfn 1zmh 1zmk 2pm4 2pm5

(-) Related Entries Specified in the PDB File

1dfn CRYSTAL STRUCTURE OF RELATED ALPHA-DEFENSIN
1zmh
1zmk
1zmm
1zmp
1zmq