2AT5 - JenaLib

Title :   1.22 A CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS CONTAINING FE(III) DEUTEROPORPHYRIN IX COMPLEXED WITH NITRIC OXIDE AT PH 5.6

Authors :   A. M. Amoia, W. R. Montfort

Date :   24 Aug 05 (Deposition) - 22 Aug 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.22

Chains :   Asym./Biol. Unit : X

Keywords :   Lipocalin, Beta Barrel, Ferrous, Heme Analog, Fe(Iii) Deuteroporphyrin Ix, Nitric Oxide, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Amoia, W. R. Montfort
Heme Distortion In Nitrophorin 4: High Resolution Structures Of Mutated Positions L123V And L133V And Heme Altered Proteins
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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 X from PDB  Type:PROTEIN  Length:184
 aligned with NP4_RHOPR | Q94734 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:184
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    
            NP4_RHOPR    22 ACTKNAIAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYHYDPKTQDTFYDVSELQVESLGKYTANFKKVDKNGNVKVAVTAGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDAAAGDKVKSAVSAATLEFSKFISTKENNCAYDNDSLKSLLTK 205
               SCOP domains d2at5x_ X: Nitrophorin 4                                                                                                                                                                 SCOP domains
               CATH domains 2at5X00 X:1-184  [code=2.40.128.20, no name defined]                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhheeeeeeeeeeee.hhhhh....eeeeeeeee..eeeeeeeee......eeeeeeeeeeee..eeeee.eee.....eee.....eeeeeeeeee...eeeeeeeeee..eeeeeeeeeee.......hhhhhhhhhhh..hhhhhee........hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2at5 X   1 ACTKNAIAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYHYDPKTQDTFYDVSELQVESLGKYTANFKKVDKNGNVKVAVTAGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDAAAGDKVKSAVSAATLEFSKFISTKENNCAYDNDSLKSLLTK 184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain X (NP4_RHOPR | Q94734)

molecular function
	GO:0051381	histamine binding	Interacting selectively and non-covalently with histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0070026	nitric oxide binding	Interacting selectively and non-covalently with nitric oxide (NO).
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0050880	regulation of blood vessel size	Any process that modulates the size of blood vessels.
	GO:0042311	vasodilation	An increase in the internal diameter of blood vessels, especially arterioles or capillaries, due to relaxation of smooth muscle cells that line the vessels, and usually resulting in a decrease in blood pressure.
cellular component
	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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		FDE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2at5)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2at5
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	NP4_RHOPR \| Q94734
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	NP4_RHOPR \| Q94734
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description