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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   STRUCTURE OF C12-LF11 BOUND TO THE DPC MICELLES

Authors :   B. Japelj

Date :   06 Apr 06 (Deposition) - 13 Feb 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

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

Reference :   B. Japelj, M. Zorko, A. Majerle, P. Pristovsek, S. Sanchez-Gomez, G. M. Tejada, I. Moriyon, S. E. Blondelle, K. Brandenburg, J. Andra, K. Lohner, R. Jerala
The Acyl Group As The Central Element Of The Structural Organization Of Antimicrobial Lipopeptide.
J. Am. Chem. Soc. V. 129 1022 2007
PubMed-ID: 17263370 | Reference-DOI: 10.1021/JA067419V
(for further references see the PDB file header)

Molecule 1 - LACTOFERRIN-BASED SYNTHETIC PEPTIDE C12-LF11
	Chains	:	A
	Engineered	:	YES
	Synthetic	:	YES


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (2, 2)

No.	Name	Count	Type	Full Name
1	DAO	1	Ligand/Ion	LAURIC ACID
2	NH2	1	Mod. Amino Acid	AMINO GROUP

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:1 , GLN A:2 , TRP A:3 , GLN A:4	BINDING SITE FOR RESIDUE DAO A 13

(no "SS Bond" information available for 2GMC)

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

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_013505	K	47	R	TRFL_HUMAN	Polymorphism	1126478	A	K	9	R

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

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

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.5a	ENST00000231751	5a	ENSE00001814982	chr3:46506653-46506315	339	TRFL_HUMAN	1-15	15	0	-	-
1.8b	ENST00000231751	8b	ENSE00001591766	chr3:46501309-46501146	164	TRFL_HUMAN	15-69	55	1	A:1-12	12
1.9	ENST00000231751	9	ENSE00001078630	chr3:46497888-46497780	109	TRFL_HUMAN	70-106	37	0	-	-
1.10a	ENST00000231751	10a	ENSE00002201536	chr3:46497468-46497286	183	TRFL_HUMAN	106-167	62	0	-	-
1.12b	ENST00000231751	12b	ENSE00001078629	chr3:46496932-46496785	148	TRFL_HUMAN	167-216	50	0	-	-
1.13a	ENST00000231751	13a	ENSE00000825947	chr3:46495850-46495795	56	TRFL_HUMAN	216-235	20	0	-	-
1.14	ENST00000231751	14	ENSE00000825946	chr3:46492163-46491985	179	TRFL_HUMAN	235-294	60	0	-	-
1.15	ENST00000231751	15	ENSE00000767141	chr3:46491518-46491344	175	TRFL_HUMAN	295-353	59	0	-	-
1.16b	ENST00000231751	16b	ENSE00000767140	chr3:46490508-46490354	155	TRFL_HUMAN	353-404	52	0	-	-
1.17	ENST00000231751	17	ENSE00000492524	chr3:46488889-46488799	91	TRFL_HUMAN	405-435	31	0	-	-
1.18	ENST00000231751	18	ENSE00000767138	chr3:46487984-46487931	54	TRFL_HUMAN	435-453	19	0	-	-
1.19	ENST00000231751	19	ENSE00000492526	chr3:46486927-46486772	156	TRFL_HUMAN	453-505	53	0	-	-
1.20	ENST00000231751	20	ENSE00000492527	chr3:46485073-46484932	142	TRFL_HUMAN	505-552	48	0	-	-
1.22a	ENST00000231751	22a	ENSE00000767135	chr3:46482974-46482907	68	TRFL_HUMAN	552-575	24	0	-	-
1.23a	ENST00000231751	23a	ENSE00001292001	chr3:46480971-46480787	185	TRFL_HUMAN	575-636	62	0	-	-
1.24c	ENST00000231751	24c	ENSE00000825945	chr3:46479620-46479431	190	TRFL_HUMAN	637-700	64	0	-	-
1.25c	ENST00000231751	25c	ENSE00001289842	chr3:46477720-46477136	585	TRFL_HUMAN	700-710	11	0	-	-

NMR Structure

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:12
 aligned with TRFL_HUMAN | P02788 from UniProtKB/Swiss-Prot  Length:710

    Alignment length:12
                                    48  
            TRFL_HUMAN   39 FQWQRNMRKVRG 50
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) --------R--- SAPs(SNPs)
                    PROSITE ------------ PROSITE
               Transcript 1 Exon 1.8b    Transcript 1
                  2gmc A  1 FQWQRNIRKVRx 12
                                    10 |
                                      12-NH2

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 '\|'

(no "SCOP Domain" information available for 2GMC)

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

(no "Pfam Domain" information available for 2GMC)

NMR Structure(hide GO term definitions)

Chain A (TRFL_HUMAN | P02788)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	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).
	GO:0043539	protein serine/threonine kinase activator activity	Binds to and increases the activity of a protein serine/threonine kinase.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
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:0019732	antifungal humoral response	An immune response against a fungus mediated through a body fluid. An example of this process is the antifungal humoral response in Drosophila melanogaster.
	GO:0060349	bone morphogenesis	The process in which bones are generated and organized.
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	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:0006959	humoral immune response	An immune response mediated through a body fluid.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0002227	innate immune response in mucosa	Any process of the innate immune response that takes place in the mucosal tissues.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0033214	iron assimilation by chelation and transport	A process in which iron (Fe3+) is solubilized by ferric iron-specific chelators, known as siderophores, excreted by a cell; the iron-siderophore complex is then transported into the cell by specific cell surface receptors.
	GO:0055072	iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
	GO:0044793	negative regulation by host of viral process	A process in which a host organism stops, prevents or reduces the frequency, rate or extent of a process being mediated by a virus with which it is infected.
	GO:0032780	negative regulation of ATPase activity	Any process that stops or reduces the rate of ATP hydrolysis by an ATPase.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0031665	negative regulation of lipopolysaccharide-mediated signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of signaling in response to detection of lipopolysaccharide.
	GO:2001205	negative regulation of osteoclast development	Any process that stops, prevents or reduces the frequency, rate or extent of osteoclast development.
	GO:1900229	negative regulation of single-species biofilm formation in or on host organism	Any process that stops, prevents or reduces the frequency, rate or extent of single-species biofilm formation in or on host organism.
	GO:2000308	negative regulation of tumor necrosis factor (ligand) superfamily member 11 production	Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor (ligand) superfamily member 11 production.
	GO:0045071	negative regulation of viral genome replication	Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
	GO:0048525	negative regulation of viral process	Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process in which a virus is a participant.
	GO:0001503	ossification	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:1900159	positive regulation of bone mineralization involved in bone maturation	Any process that activates or increases the frequency, rate or extent of bone mineralization involved in bone maturation.
	GO:1902732	positive regulation of chondrocyte proliferation	Any process that increases the frequency, rate or extent of the multiplication or reproduction of chondrocytes by cell division, resulting in the expansion of their population. A chondrocyte is a polymorphic cell that forms cartilage.
	GO:0045669	positive regulation of osteoblast differentiation	Any process that activates or increases the frequency, rate or extent of osteoblast differentiation.
	GO:0033690	positive regulation of osteoblast proliferation	Any process that activates or increases the rate or extent of osteoblast proliferation.
	GO:0071902	positive regulation of protein serine/threonine kinase activity	Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity.
	GO:0034145	positive regulation of toll-like receptor 4 signaling pathway	Any process that activates or increases the frequency, rate, or extent of toll-like receptor 4 signaling pathway.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0001817	regulation of cytokine production	Any process that modulates the frequency, rate, or extent of production of a cytokine.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0032680	regulation of tumor necrosis factor production	Any process that modulates the frequency, rate, or extent of tumor necrosis factor production.
	GO:0001895	retina homeostasis	A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0097013	phagocytic vesicle lumen	The volume enclosed by the membrane of a phagocytic vesicle.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0030141	secretory granule	A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
	GO:0042581	specific granule	Granule with a membranous, tubular internal structure, found primarily in mature neutrophil cells. Most are released into the extracellular fluid. Specific granules contain lactoferrin, lysozyme, vitamin B12 binding protein and elastase.

NMR Structure
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Description

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Ligands, Modified Residues, Ions (2, 2)

Sites (1, 1)

SS Bonds (0, 0)

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