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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Biological Unit 7 (Jmol Viewer)

Description

Title :   HUMAN BETA-DEFENSIN-1 (MUTANT SER8ALA)

Authors :   J. Lubkowski, M. Pazgier

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

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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),C (1x)
Biol. Unit 7: B (1x),D (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

Molecule 1 - BETA-DEFENSIN 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAED4
	Expression System Strain	:	BL21(DE3)PLYSE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	HUMAN BETA-DEFENSIN 1, RESIDUES 33-68
	Gene	:	DEFB1, BD1, HBD1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BD-1, DEFENSIN, BETA 1, HBD-1

Structural Features

Chains, Units

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)
Biological Unit 6 (1x)	:	A (1x)		C (1x)
Biological Unit 7 (1x)	:		B (1x)		D (1x)

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 7)

Asymmetric Unit (2, 7)

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

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 2)

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

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 5 (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 6 (2, 2)

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

Biological Unit 7 (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	SO4	2	Ligand/Ion	SULFATE ION

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:3 , HOH A:126 , ASP C:1 , HIS C:2 , CYS C:27 , TYR C:28 , ARG C:29 , HOH C:101 , HOH C:107 , HOH C:274	BINDING SITE FOR RESIDUE SO4 C 401
2	AC2	SOFTWARE	ASP A:1 , HIS A:2 , CYS A:27 , TYR A:28 , ARG A:29 , HOH A:117 , HOH A:126 , HOH A:317 , TYR C:3 , HOH C:101	BINDING SITE FOR RESIDUE SO4 A 402
3	AC3	SOFTWARE	ASP A:1 , GLY A:25 , THR A:26 , HOH A:219 , ARG B:29 , ASN D:4 , HOH D:306	BINDING SITE FOR RESIDUE SO4 D 403
4	AC4	SOFTWARE	TYR B:3 , HOH B:160 , ASP D:1 , HIS D:2 , CYS D:27 , TYR D:28 , ARG D:29 , HOH D:102 , HOH D:171 , HOH D:245 , HOH D:314	BINDING SITE FOR RESIDUE SO4 D 404
5	AC5	SOFTWARE	ASP B:1 , HIS B:2 , CYS B:27 , TYR B:28 , ARG B:29 , HOH B:141 , HOH B:160 , HOH B:196 , TYR D:3 , HOH D:102	BINDING SITE FOR RESIDUE SO4 B 405
6	AC6	SOFTWARE	ASP B:1 , GLY B:25 , THR B:26 , HOH B:110 , HOH B:128 , HOH B:201 , ARG C:29 , HOH C:248	BINDING SITE FOR RESIDUE SO4 B 406
7	AC7	SOFTWARE	ASP C:1 , GLY C:25 , THR C:26 , HOH C:238 , HOH C:304	BINDING SITE FOR RESIDUE ACT C 410

SS Bonds (12, 12)

Asymmetric Unit

No.	Residues
1	A:5	-	A:34
2	A:12	-	A:27
3	A:17	-	A:35
4	B:5	-	B:34
5	B:12	-	B:27
6	B:17	-	B:35
7	C:5	-	C:34
8	C:12	-	C:27
9	C:17	-	C:35
10	D:5	-	D:34
11	D:12	-	D:27
12	D:17	-	D:35

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2NLC)

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/C	V	6	I
2	UniProt	VAR_014925	A	48	V	DEFB1_HUMAN	Polymorphism	1800967	A/C	A	16	V
3	UniProt	VAR_014926	C	67	S	DEFB1_HUMAN	Polymorphism	1800968	A/C	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	B/D	V	6	I
2	UniProt	VAR_014925	A	48	V	DEFB1_HUMAN	Polymorphism	1800967	B/D	A	16	V
3	UniProt	VAR_014926	C	67	S	DEFB1_HUMAN	Polymorphism	1800968	B/D	C	35	S

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

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 2NLC)

Exons (1, 4)

Asymmetric Unit (1, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000297439	1	ENSE00001087806	chr8:6735544-6735319	226	DEFB1_HUMAN	1-21	21	0	-	-
1.2	ENST00000297439	2	ENSE00001087807	chr8:6728348-6728097	252	DEFB1_HUMAN	21-68	48	4	A:1-36 B:1-36 C:1-36 D:1-36	36 36 36 36

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 d2nlca_ 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
                  2nlc A  1 DHYNCVSAGGQCLYSACPIFTKIQGTCYRGKAKCCK 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 d2nlcb_ 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
                  2nlc B  1 DHYNCVSAGGQCLYSACPIFTKIQGTCYRGKAKCCK 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 d2nlcc_ 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
                  2nlc C  1 DHYNCVSAGGQCLYSACPIFTKIQGTCYRGKAKCCK 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 d2nlcd_ D: automated matches         SCOP domains
               CATH domains ------------------------------------ CATH domains
           Pfam domains (1) Defensin_beta-2nlcD01 D:1-36         Pfam domains (1)
           Pfam domains (2) Defensin_beta-2nlcD02 D:1-36         Pfam domains (2)
           Pfam domains (3) Defensin_beta-2nlcD03 D:1-36         Pfam domains (3)
           Pfam domains (4) Defensin_beta-2nlcD04 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
                  2nlc D  1 DHYNCVSAGGQCLYSACPIFTKIQGTCYRGKAKCCK 36
                                    10        20        30

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		→ 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

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Defensin-like (59)

Superfamily: Defensin-like (59)

Family: Defensin (50)

Protein domain: automated matches (20)

Human (Homo sapiens) [TaxId: 9606] (17)

1a	d2nlca_	A:
1b	d2nlcb_	B:
1c	d2nlcc_	C:
1d	d2nlcd_	D:

CATH Domains (0, 0)

(no "CATH Domain" information available for 2NLC)

Pfam Domains (1, 4)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Defensin (30)

Family: Defensin_beta (14)

Homo sapiens (Human) (13)

1a	Defensin_beta-2nlcD01	D:1-36
1b	Defensin_beta-2nlcD02	D:1-36
1c	Defensin_beta-2nlcD03	D:1-36
1d	Defensin_beta-2nlcD04	D:1-36

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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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	DEFB1_HUMAN \| P60022	:	1e4s 1iju 1ijv 1kj5 2nlb 2nld 2nle 2nlf 2nlg 2nlh 2nlp 2nlq 2nls 2plz

Related Entries Specified in the PDB File

1ijv	HUMAN BETA-DEFENSIN-1
2nlb	HUMAN BETA-DEFENSIN-1 (MUTANT ASN4ALA)
2nld	HUMAN BETA-DEFENSIN-1 (MUTANT GLN11ALA)
2nle	HUMAN BETA-DEFENSIN-1 (MUTANT GLN11ALA)
2nlf	HUMAN BETA-DEFENSIN-1 (MUTANT LEU13GLU)
2nlg	HUMAN BETA-DEFENSIN-1 (MUTANT LYS22GLU)
2nlh	HUMAN BETA-DEFENSIN-1 (MUTANT GLN24ALA)
2nlp
2nlq
2nls