1ZMP - JenaLib

Title :   CRYSTAL STRUCTURE OF HUMAN DEFENSIN-5

Authors :   J. Lubkowski, A. Szyk, W. Lu

Date :   10 May 05 (Deposition) - 30 May 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: C  (1x)
Biol. Unit 3: B  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: A (2x),B (2x),C (2x),D (2x)
Biol. Unit 6: A (2x),B (2x),C (2x),D (2x)
Biol. Unit 7: A (2x),B (2x),C (2x),D (2x)

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

Reference :   A. Szyk, Z. Wu, K. Tucker, D. Yang, W. Lu, J. Lubkowski
Crystal Structures Of Human {Alpha}-Defensins Hnp4, Hd5, An Hd6.
Protein Sci. V. 15 2749 2006
PubMed-ID: 17088326 | Reference-DOI: 10.1110/PS.062336606

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 6 (2, 14)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	8	Ligand/Ion	GLYCEROL
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 7 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	SO4	-1	Ligand/Ion	SULFATE ION

Sites (11, 11)

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:6 , THR A:7 , GLY A:8 , HOH A:503 , HOH A:555 , ARG B:9 , HOH D:658	BINDING SITE FOR RESIDUE SO4 B 101
02	AC2	SOFTWARE	ARG A:9 , HOH A:535 , HOH A:546 , ARG B:6 , THR B:7 , GLY B:8 , HOH B:601 , HOH C:540	BINDING SITE FOR RESIDUE SO4 A 102
03	AC3	SOFTWARE	ARG C:13 , ARG C:32 , HOH C:591 , HOH C:594 , ARG D:6 , THR D:7 , GLY D:8 , HOH D:593	BINDING SITE FOR RESIDUE SO4 D 103
04	AC4	SOFTWARE	ALA B:1 , HOH B:528 , HOH B:598 , ARG C:9 , CYS C:10 , ARG C:28 , HOH C:529	BINDING SITE FOR RESIDUE SO4 C 104
05	AC5	SOFTWARE	ARG C:6 , THR C:7 , GLY C:8 , GOL C:204	BINDING SITE FOR RESIDUE SO4 C 105
06	AC6	SOFTWARE	ARG B:13 , ARG B:32	BINDING SITE FOR RESIDUE SO4 B 106
07	AC7	SOFTWARE	ARG A:9 , HOH A:558 , ARG B:9 , HOH B:635	BINDING SITE FOR RESIDUE CL B 151
08	AC8	SOFTWARE	TYR B:4 , ARG B:6 , LEU C:26 , TYR C:27 , ARG C:28 , HOH C:540 , HOH C:627	BINDING SITE FOR RESIDUE GOL C 201
09	AC9	SOFTWARE	SER A:15 , HOH A:538 , ARG B:13 , HOH B:519 , HOH B:539 , SER C:23	BINDING SITE FOR RESIDUE GOL A 202
10	BC1	SOFTWARE	CYS A:3 , CYS A:31 , TYR C:4 , CYS C:5 , ILE C:22 , GOL C:204 , HOH C:580 , HOH C:661	BINDING SITE FOR RESIDUE GOL C 203
11	BC2	SOFTWARE	CYS C:5 , SO4 C:105 , GOL C:203	BINDING SITE FOR RESIDUE GOL C 204

SS Bonds (11, 11)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 4)

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_059245	R	71	H	DEF5_HUMAN	Polymorphism	7839771	A/B/C/D	R	9	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_059245	R	71	H	DEF5_HUMAN	Polymorphism	7839771	A	R	9	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_059245	R	71	H	DEF5_HUMAN	Polymorphism	7839771	C	R	9	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_059245	R	71	H	DEF5_HUMAN	Polymorphism	7839771	B	R	9	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_059245	R	71	H	DEF5_HUMAN	Polymorphism	7839771	D	R	9	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 5 (1, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_059245	R	71	H	DEF5_HUMAN	Polymorphism	7839771	A/B/C/D	R	9	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 6 (1, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_059245	R	71	H	DEF5_HUMAN	Polymorphism	7839771	A/B/C/D	R	9	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 7 (1, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_059245	R	71	H	DEF5_HUMAN	Polymorphism	7839771	A/B/C/D	R	9	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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.	DEF5_HUMAN	65-93	4	A:3-31 B:3-31 C:3-31 D:3-31

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF5_HUMAN	65-93	1	A:3-31 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF5_HUMAN	65-93	1	- - C:3-31 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF5_HUMAN	65-93	1	- B:3-31 - -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF5_HUMAN	65-93	1	- - - D:3-31

Biological Unit 5 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF5_HUMAN	65-93	8	A:3-31 B:3-31 C:3-31 D:3-31

Biological Unit 6 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF5_HUMAN	65-93	8	A:3-31 B:3-31 C:3-31 D:3-31

Biological Unit 7 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEFENSIN	PS00269	Mammalian defensins signature.	DEF5_HUMAN	65-93	8	A:3-31 B:3-31 C:3-31 D:3-31

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 DEF5_HUMAN | Q01523 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:32
                                    72        82        92  
            DEF5_HUMAN   63 ATCYCRTGRCATRESLSGVCEISGRLYRLCCR 94
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------H----------------------- SAPs(SNPs)
                    PROSITE --DEFENSIN  PDB: A:3-31        - PROSITE
               Transcript 1 Exon 1.2  PDB: A:1-32            Transcript 1
                  1zmp A  1 ATCYCRTGRCATRESLSGVCEISGRLYRLCCR 32
                                    10        20        30

Chain B from PDB  Type:PROTEIN  Length:32
 aligned with DEF5_HUMAN | Q01523 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:32
                                    72        82        92  
            DEF5_HUMAN   63 ATCYCRTGRCATRESLSGVCEISGRLYRLCCR 94
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------H----------------------- SAPs(SNPs)
                    PROSITE --DEFENSIN  PDB: B:3-31        - PROSITE
               Transcript 1 Exon 1.2  PDB: B:1-32            Transcript 1
                  1zmp B  1 ATCYCRTGRCATRESLSGVCEISGRLYRLCCR 32
                                    10        20        30

Chain C from PDB  Type:PROTEIN  Length:32
 aligned with DEF5_HUMAN | Q01523 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:32
                                    72        82        92  
            DEF5_HUMAN   63 ATCYCRTGRCATRESLSGVCEISGRLYRLCCR 94
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------H----------------------- SAPs(SNPs)
                    PROSITE --DEFENSIN  PDB: C:3-31        - PROSITE
               Transcript 1 Exon 1.2  PDB: C:1-32            Transcript 1
                  1zmp C  1 ATCYCRTGRCATRESLSGVCEISGRLYRLCCR 32
                                    10        20        30

Chain D from PDB  Type:PROTEIN  Length:25
 aligned with DEF5_HUMAN | Q01523 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:31
                                    72        82        92 
            DEF5_HUMAN   63 ATCYCRTGRCATRESLSGVCEISGRLYRLCC 93
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author ...eee...------..eeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) --------H---------------------- SAPs(SNPs)
                    PROSITE --DEFENSIN  PDB: D:3-31         PROSITE
               Transcript 1 Exon 1.2  PDB: D:1-31 (gaps)    Transcript 1
                  1zmp D  1 ATCYCRTGR------LSGVCEISGRLYRLCC 31
                                    |-     |  20        30 
                                    9     16

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DEF5_HUMAN | Q01523)

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:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	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.
	GO:0034774	secretory granule lumen	The volume enclosed by the membrane of a secretory granule.
	GO:0030133	transport vesicle	Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (11, 11)

SS Bonds (11, 11)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 4)

PROSITE Motifs (1, 4)

Exons (1, 4)

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