3QTE - JenaLib

Title :   CRYSTAL STRUCTURE OF HUMAN ALPHA-DEFENSIN 6 (H27W MUTANT)

Authors :   M. Pazgier, W. Lu

Date :   22 Feb 11 (Deposition) - 11 Jan 12 (Release) - 12 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: A,B  (1x)
Biol. Unit 6: C (1x),D (1x)

Keywords :   Antimicrobial Protein, Paneth Cells Defensin, Hd6, Human Alpha Defensin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Chu, M. Pazgier, G. Jung, S. P. Nuccio, P. A. Castillo, M. F. De Jong, M. G. Winter, S. E. Winter, J. Wehkamp, B. Shen, N. H. Salzman, M. A. Underwood, R. M. Tsolis, G. M. Young, W. Lu, R. I. Lehrer, A. J. Baumler, C. L. Bevins
Human Alpha-Defensin 6 Promotes Mucosal Innate Immunity Through Self-Assembled Peptide Nanonets.
Science V. 337 477 2012
PubMed-ID: 22722251 | Reference-DOI: 10.1126/SCIENCE.1218831

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 6 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL

Sites (2, 2)

SS Bonds (12, 12)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF6_HUMAN	72-99	4	A:4-31 B:4-31 C:4-31 D:4-31

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF6_HUMAN	72-99	1	A:4-31 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF6_HUMAN	72-99	1	- B:4-31 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF6_HUMAN	72-99	1	- - C:4-31 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF6_HUMAN	72-99	1	- - - D:4-31

Biological Unit 5 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF6_HUMAN	72-99	2	A:4-31 B:4-31 - -

Biological Unit 6 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF6_HUMAN	72-99	2	- - C:4-31 D:4-31

Exons (1, 4)

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
 aligned with DEF6_HUMAN | Q01524 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:32
                                    78        88        98  
           DEF6_HUMAN    69 AFTCHCRRSCYSTEYSYGTCTVMGINHRFCCL 100
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......eeeeeeee..eeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE ---DEFENSIN  PDB: A:4-31       - PROSITE
               Transcript 1 Exon 1.2  PDB: A:1-32            Transcript 1
                 3qte A   1 AFTCHCRRSCYSTEYSYGTCTVMGINWRFCCL  32
                                    10        20        30

Chain B from PDB  Type:PROTEIN  Length:32
 aligned with DEF6_HUMAN | Q01524 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:32
                                    78        88        98  
           DEF6_HUMAN    69 AFTCHCRRSCYSTEYSYGTCTVMGINHRFCCL 100
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE ---DEFENSIN  PDB: B:4-31       - PROSITE
               Transcript 1 Exon 1.2  PDB: B:1-32            Transcript 1
                 3qte B   1 AFTCHCRRSCYSTEYSYGTCTVMGINWRFCCL  32
                                    10        20        30

Chain C from PDB  Type:PROTEIN  Length:32
 aligned with DEF6_HUMAN | Q01524 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:32
                                    78        88        98  
           DEF6_HUMAN    69 AFTCHCRRSCYSTEYSYGTCTVMGINHRFCCL 100
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeee..eeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE ---DEFENSIN  PDB: C:4-31       - PROSITE
               Transcript 1 Exon 1.2  PDB: C:1-32            Transcript 1
                 3qte C   1 AFTCHCRRSCYSTEYSYGTCTVMGINWRFCCL  32
                                    10        20        30

Chain D from PDB  Type:PROTEIN  Length:32
 aligned with DEF6_HUMAN | Q01524 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:32
                                    78        88        98  
           DEF6_HUMAN    69 AFTCHCRRSCYSTEYSYGTCTVMGINHRFCCL 100
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......eeeeeeee..eeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE ---DEFENSIN  PDB: D:4-31       - PROSITE
               Transcript 1 Exon 1.2  PDB: D:1-32            Transcript 1
                 3qte D   1 AFTCHCRRSCYSTEYSYGTCTVMGINWRFCCL  32
                                    10        20        30

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DEF6_HUMAN | Q01524)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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: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:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	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: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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