3B9Z - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE NITROSOMONAS EUROPAEA RH PROTEIN COMPLEXED WITH CARBON DIOXIDE

Authors :   X. Li, S. Jayachandran, H-H. T. Nguyen, M. K. Chan

Date :   07 Nov 07 (Deposition) - 18 Dec 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Carbon Dioxide, Channel, Rh Protein, Co2, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Li, S. Jayachandran, H. H. Nguyen, M. K. Chan
Structure Of The Nitrosomonas Europaea Rh Protein.
Proc. Natl. Acad. Sci. Usa V. 104 19279 2007
PubMed-ID: 18040042 | Reference-DOI: 10.1073/PNAS.0709710104
(for further references see the PDB file header)

Molecule 1 - AMMONIUM TRANSPORTER FAMILY RH-LIKE PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	METHYLOCOCCUS CAPSULATUS
	Expression System Taxid	:	414
	Fragment	:	RESIDUES 31-418
	Gene	:	RH50, NE0448
	Organism Scientific	:	NITROSOMONAS EUROPAEA ATCC 19718
	Organism Taxid	:	228410
	Strain	:	IFO 14298

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	BOG	2	Ligand/Ion	B-OCTYLGLUCOSIDE
2	CO2	1	Ligand/Ion	CARBON DIOXIDE
3	UNL	1	Ligand/Ion	UNKNOWN LIGAND

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	BOG	6	Ligand/Ion	B-OCTYLGLUCOSIDE
2	CO2	3	Ligand/Ion	CARBON DIOXIDE
3	UNL	3	Ligand/Ion	UNKNOWN LIGAND

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:90 , PRO A:99 , HOH A:678	BINDING SITE FOR RESIDUE BOG A 1
2	AC2	SOFTWARE	PHE A:129 , PHE A:248 , HOH A:632 , HOH A:712 , HOH A:719 , HOH A:728	BINDING SITE FOR RESIDUE BOG A 419
3	AC3	SOFTWARE	PHE A:61 , ASP A:201 , SER A:204 , VAL A:261 , ASN A:265	BINDING SITE FOR RESIDUE CO2 A 420
4	AC4	SOFTWARE	PHE A:110 , SER A:163 , ALA A:164 , PHE A:218 , ALA A:219 , ILE A:222 , HOH A:545	BINDING SITE FOR RESIDUE UNL A 421

(no "SS Bond" information available for 3B9Z)

(no "Cis Peptide Bond" information available for 3B9Z)

(no "SAP(SNP)/Variant" information available for 3B9Z)

(no "PROSITE Motif" information available for 3B9Z)

(no "Exon" information available for 3B9Z)

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:388
 aligned with Q82X47_NITEU | Q82X47 from UniProtKB/TrEMBL  Length:425

    Alignment length:388
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410        
         Q82X47_NITEU    31 EINEARLVAQYNYSINILAMLLVGFGFLMVFVRRYGFSATTGTYLVVATGLPLYILLRANGIFGHALTPHSVDAVIYAEFAVATGLIAMGAVLGRLRVFQYALLALFIVPVYLLNEWLVLDNASGLTEGFQDSAGSIAIHAFGAYFGLGVSIALTTAAQRAQPIESDATSDRFSMLGSMVLWLFWPSFATAIVPFEQMPQTIVNTLLALCGATLATYFLSALFHKGKASIVDMANAALAGGVAIGSVCNIVGPVGAFVIGLLGGAISVVGFVFIQPMLESKAKTIDTCGVHNLHGLPGLLGGFSAILIVPGIAVAQLTGIGITLALALIGGVIAGALIKLTGTTKQAYEDSHEFIHLAGPEDEHKAERLVLEAKTEIQGLKNRIDAAV 418
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b9zA00 A:31-418 Ammonium transporter AmtB like domains                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b9z A  31 EINEARLVAQYNYSINILAMLLVGFGFLMVFVRRYGFSATTGTYLVVATGLPLYILLRANGIFGHALTPHSVDAVIYAEFAVATGLIAMGAVLGRLRVFQYALLALFIVPVYLLNEWLVLDNASGLTEGFQDSAGSIAIHAFGAYFGLGVSIALTTAAQRAQPIESDATSDRFSMLGSMVLWLFWPSFATAIVPFEQMPQTIVNTLLALCGATLATYFLSALFHKGKASIVDMANAALAGGVAIGSVCNIVGPVGAFVIGLLGGAISVVGFVFIQPMLESKAKTIDTCGVHNLHGLPGLLGGFSAILIVPGIAVAQLTGIGITLALALIGGVIAGALIKLTGTTKQAYEDSHEFIHLAGPEDEHKAERLVLEAKTEIQGLKNRIDAAV 418
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410

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 3B9Z)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Ammonium transporter fold (31)

Homologous Superfamily: Ammonium transporter AmtB like domains (31)

Nitrosomonas europaea atcc 19718. Organism_taxid: 228410. Strain: ifo14298. (3)

3b9zA00

A:31-418

(no "Pfam Domain" information available for 3B9Z)

Asymmetric Unit(hide GO term definitions)

Chain A (Q82X47_NITEU | Q82X47)

molecular function
	GO:0008519	ammonium transmembrane transporter activity	Enables the transfer of ammonium from one side of a membrane to the other. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals.
biological process
	GO:0072488	ammonium transmembrane transport	The directed movement of ammonium across a membrane by means of some agent such as a transporter or pore. Ammonium is the cation NH4+.
	GO:0015696	ammonium transport	The directed movement of ammonium into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric 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
		BOG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CO2	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		UNL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3b9z)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3b9z
		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
	Q82X47_NITEU \| Q82X47
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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

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
	Q82X47_NITEU \| Q82X47
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q82X47_NITEU \| Q82X47	:	3b9w 3b9y 3bhs

3b9y	CRYSTAL STRUCTURE OF THE NITROSOMONAS EUROPAEA RH PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File