2NLP - JenaLib

Title :   HUMAN BETA-DEFENSIN-1 (MUTANT GLN24GLU)

Authors :   J. Lubkowski, M. Pazgier

Date :   20 Oct 06 (Deposition) - 31 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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 (1x),B (1x),C (1x),D (1x)
Biol. Unit 6: A (1x),B (1x)
Biol. Unit 7: C,D  (1x)
Biol. Unit 8: B (1x),C (1x),D (1x)
Biol. Unit 9: A (1x),B (1x),C (1x)

Keywords :   Antimicrobial, Chemotactic, Defensin, Mutant, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Pazgier, A. Prahl, D. M. Hoover, J. Lubkowski
Studies Of The Biological Properties Of Human Beta-Defensin 1.
J. Biol. Chem. V. 282 1819 2007
PubMed-ID: 17071614 | Reference-DOI: 10.1074/JBC.M607210200
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 5 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 6 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 7 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 8 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 9 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:3 , HOH A:108 , HOH A:129 , HOH A:215 , ASP B:1 , HIS B:2 , CYS B:27 , TYR B:28 , ARG B:29 , HOH D:137	BINDING SITE FOR RESIDUE SO4 A 37
2	AC2	SOFTWARE	ASP A:1 , HIS A:2 , CYS A:27 , TYR A:28 , ARG A:29 , HOH A:108 , TYR B:3 , HOH D:127 , HOH D:137	BINDING SITE FOR RESIDUE SO4 D 37
3	AC3	SOFTWARE	HOH A:102 , HOH A:111 , HOH A:115 , HOH A:300 , TYR C:3 , ASP D:1 , HIS D:2 , CYS D:27 , TYR D:28 , ARG D:29	BINDING SITE FOR RESIDUE SO4 A 38
4	AC4	SOFTWARE	HOH A:105 , HOH A:111 , HOH A:115 , HOH A:121 , HOH A:148 , ASP C:1 , HIS C:2 , CYS C:27 , TYR C:28 , ARG C:29 , TYR D:3	BINDING SITE FOR RESIDUE SO4 A 39
5	AC5	SOFTWARE	ASP B:1 , GLY B:25 , THR B:26 , HOH B:260 , HOH B:310 , HOH B:314 , HOH B:347 , ASP C:1 , ASN C:4	BINDING SITE FOR RESIDUE SO4 B 37
6	AC6	SOFTWARE	ASP A:1 , GLY A:25 , THR A:26 , HOH A:221 , HOH A:358	BINDING SITE FOR RESIDUE SO4 A 40

SS Bonds (12, 12)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 12)

Asymmetric Unit (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_018405	V	38	I	DEFB1_HUMAN	Polymorphism	2738047	A/B/C/D	V	6	I
2	UniProt	VAR_014925	A	48	V	DEFB1_HUMAN	Polymorphism	1800967	A/B/C/D	A	16	V
3	UniProt	VAR_014926	C	67	S	DEFB1_HUMAN	Polymorphism	1800968	A/B/C/D	C	35	S

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

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_018405	V	38	I	DEFB1_HUMAN	Polymorphism	2738047	A	V	6	I
2	UniProt	VAR_014925	A	48	V	DEFB1_HUMAN	Polymorphism	1800967	A	A	16	V
3	UniProt	VAR_014926	C	67	S	DEFB1_HUMAN	Polymorphism	1800968	A	C	35	S

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

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_018405	V	38	I	DEFB1_HUMAN	Polymorphism	2738047	B	V	6	I
2	UniProt	VAR_014925	A	48	V	DEFB1_HUMAN	Polymorphism	1800967	B	A	16	V
3	UniProt	VAR_014926	C	67	S	DEFB1_HUMAN	Polymorphism	1800968	B	C	35	S

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

Biological Unit 3 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_018405	V	38	I	DEFB1_HUMAN	Polymorphism	2738047	C	V	6	I
2	UniProt	VAR_014925	A	48	V	DEFB1_HUMAN	Polymorphism	1800967	C	A	16	V
3	UniProt	VAR_014926	C	67	S	DEFB1_HUMAN	Polymorphism	1800968	C	C	35	S

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

Biological Unit 4 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_018405	V	38	I	DEFB1_HUMAN	Polymorphism	2738047	D	V	6	I
2	UniProt	VAR_014925	A	48	V	DEFB1_HUMAN	Polymorphism	1800967	D	A	16	V
3	UniProt	VAR_014926	C	67	S	DEFB1_HUMAN	Polymorphism	1800968	D	C	35	S

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

Biological Unit 5 (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_018405	V	38	I	DEFB1_HUMAN	Polymorphism	2738047	A/B/C/D	V	6	I
2	UniProt	VAR_014925	A	48	V	DEFB1_HUMAN	Polymorphism	1800967	A/B/C/D	A	16	V
3	UniProt	VAR_014926	C	67	S	DEFB1_HUMAN	Polymorphism	1800968	A/B/C/D	C	35	S

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

Biological Unit 6 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_018405	V	38	I	DEFB1_HUMAN	Polymorphism	2738047	A/B	V	6	I
2	UniProt	VAR_014925	A	48	V	DEFB1_HUMAN	Polymorphism	1800967	A/B	A	16	V
3	UniProt	VAR_014926	C	67	S	DEFB1_HUMAN	Polymorphism	1800968	A/B	C	35	S

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

Biological Unit 7 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_018405	V	38	I	DEFB1_HUMAN	Polymorphism	2738047	C/D	V	6	I
2	UniProt	VAR_014925	A	48	V	DEFB1_HUMAN	Polymorphism	1800967	C/D	A	16	V
3	UniProt	VAR_014926	C	67	S	DEFB1_HUMAN	Polymorphism	1800968	C/D	C	35	S

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

Biological Unit 8 (3, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_018405	V	38	I	DEFB1_HUMAN	Polymorphism	2738047	B/C/D	V	6	I
2	UniProt	VAR_014925	A	48	V	DEFB1_HUMAN	Polymorphism	1800967	B/C/D	A	16	V
3	UniProt	VAR_014926	C	67	S	DEFB1_HUMAN	Polymorphism	1800968	B/C/D	C	35	S

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

Biological Unit 9 (3, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_018405	V	38	I	DEFB1_HUMAN	Polymorphism	2738047	A/B/C	V	6	I
2	UniProt	VAR_014925	A	48	V	DEFB1_HUMAN	Polymorphism	1800967	A/B/C	A	16	V
3	UniProt	VAR_014926	C	67	S	DEFB1_HUMAN	Polymorphism	1800968	A/B/C	C	35	S

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

PROSITE Motifs (0, 0)

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:36
 aligned with DEFB1_HUMAN | P60022 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:36
                                    42        52        62      
           DEFB1_HUMAN   33 DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK 68
               SCOP domains d2nlpa_ A: automated matches         SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh..eee.........eeeee....eeee. Sec.struct. author
                 SAPs(SNPs) -----I---------V------------------S- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: A:1-36 UniProt: 21-68 Transcript 1
                  2nlp A  1 DHYNCVSSGGQCLYSACPIFTKIEGTCYRGKAKCCK 36
                                    10        20        30

Chain B from PDB  Type:PROTEIN  Length:36
 aligned with DEFB1_HUMAN | P60022 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:36
                                    42        52        62      
           DEFB1_HUMAN   33 DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK 68
               SCOP domains d2nlpb_ B: automated matches         SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh..eee.........eeeee....eeee. Sec.struct. author
                 SAPs(SNPs) -----I---------V------------------S- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: B:1-36 UniProt: 21-68 Transcript 1
                  2nlp B  1 DHYNCVSSGGQCLYSACPIFTKIEGTCYRGKAKCCK 36
                                    10        20        30

Chain C from PDB  Type:PROTEIN  Length:36
 aligned with DEFB1_HUMAN | P60022 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:36
                                    42        52        62      
           DEFB1_HUMAN   33 DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK 68
               SCOP domains d2nlpc_ C: automated matches         SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh..eee.........eeeee....eeee. Sec.struct. author
                 SAPs(SNPs) -----I---------V------------------S- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: C:1-36 UniProt: 21-68 Transcript 1
                  2nlp C  1 DHYNCVSSGGQCLYSACPIFTKIEGTCYRGKAKCCK 36
                                    10        20        30

Chain D from PDB  Type:PROTEIN  Length:36
 aligned with DEFB1_HUMAN | P60022 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:36
                                    42        52        62      
           DEFB1_HUMAN   33 DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK 68
               SCOP domains d2nlpd_ D: automated matches         SCOP domains
               CATH domains ------------------------------------ CATH domains
           Pfam domains (1) Defensin_beta-2nlpD01 D:1-36         Pfam domains (1)
           Pfam domains (2) Defensin_beta-2nlpD02 D:1-36         Pfam domains (2)
           Pfam domains (3) Defensin_beta-2nlpD03 D:1-36         Pfam domains (3)
           Pfam domains (4) Defensin_beta-2nlpD04 D:1-36         Pfam domains (4)
         Sec.struct. author hhhhhhhh..eee.........eeeee....eeee. Sec.struct. author
                 SAPs(SNPs) -----I---------V------------------S- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: D:1-36 UniProt: 21-68 Transcript 1
                  2nlp D  1 DHYNCVSSGGQCLYSACPIFTKIEGTCYRGKAKCCK 36
                                    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 (1, 4)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (16, 16)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DEFB1_HUMAN | P60022)

biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0002526	acute inflammatory response	Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
	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:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	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:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	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:0009617	response to bacterium	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
	GO:0033574	response to testosterone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.
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: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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