3POU - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF E.COLI OMPF PORIN IN LIPIDIC CUBIC PHASE: SPACE GROUP H32, LARGE UNIT CELL

Authors :   R. G. Efremov, L. A. Sazanov

Date :   23 Nov 10 (Deposition) - 07 Mar 12 (Release) - 20 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Beta Barrel, Membrane Protein, Solute Transport, Pore (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. G. Efremov, L. A. Sazanov
Structure Of Escherichia Coli Ompf Porin From Lipidic Mesophase.
J. Struct. Biol. V. 178 311 2012
PubMed-ID: 22484237 | Reference-DOI: 10.1016/J.JSB.2012.03.005

Molecule 1 - OMPF PROTEIN
	Chains	:	A
	Fragment	:	UNP RESIDUES 23-362
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	511693
	Strain	:	BL21
	Synonym	:	OUTER MEMBRANE PROTEIN F

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	OLC	4	Ligand/Ion	(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	OLC	12	Ligand/Ion	(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:23 , TYR A:98 , TYR A:157 , GLY A:159 , ASP A:172 , VAL A:311 , VAL A:334 , HOH A:369	BINDING SITE FOR RESIDUE OLC A 341
2	AC2	SOFTWARE	TYR A:180	BINDING SITE FOR RESIDUE OLC A 342
3	AC3	SOFTWARE	SER A:177 , ILE A:178 , ALA A:190 , TRP A:214	BINDING SITE FOR RESIDUE OLC A 343
4	AC4	SOFTWARE	LEU A:218 , ILE A:273	BINDING SITE FOR RESIDUE OLC A 344

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

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GRAM_NEG_PORIN	PS00576	General diffusion Gram-negative porins signature.	OMPF_ECOLI	317-333	1	A:295-311

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GRAM_NEG_PORIN	PS00576	General diffusion Gram-negative porins signature.	OMPF_ECOLI	317-333	3	A:295-311

(no "Exon" information available for 3POU)

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:340
 aligned with OMPF_ECOLI | P02931 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:340
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
           OMPF_ECOLI    23 AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 362
               SCOP domains d3poua_ A: Porin                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeeeeeeeeeeeee............ee..eeeeeeeeeee....eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeee..hhhhhh.....................eeeeeeeeee.........eeeeeeee......hhhhh...eeeeeeeeee..eeeeeeeeeee.hhhhhh.......eeeeeeeeeeeee..eeeeeeeeeee...eee......eee..eeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee....eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GRAM_NEG_PORIN   ----------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pou A   1 AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 340
                                    10        20        30        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

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Membrane and cell surface proteins and peptides (2046)

Fold: Transmembrane beta-barrels (143)

Superfamily: Porins (99)

Family: Porin (49)

Protein domain: Porin (40)

Escherichia coli, different sequences [TaxId: 562] (27)

d3poua_

(no "CATH Domain" information available for 3POU)

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

Asymmetric Unit(hide GO term definitions)

Chain A (OMPF_ECOLI | P02931)

molecular function
	GO:0042912	colicin transmembrane transporter activity	Enables the transfer of a colicin from one side of a membrane to the other. Colicins are a group of antibiotics produced by E. coli and related species that are encoded by a group of naturally occurring plasmids, e.g. Col E1.
	GO:0015238	drug transmembrane transporter activity	Enables the directed movement of a drug from one side of a membrane to the other. A drug is any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	GO:0015075	ion transmembrane transporter activity	Enables the transfer of an ion from one side of a membrane to the other.
	GO:0015288	porin activity	Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
biological process
	GO:0043213	bacteriocin transport	The directed movement of a bacteriocin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Bacteriocins are a group of antibiotics produced by bacteria and are encoded by a group of naturally occurring plasmids, e.g. Col E1. Bacteriocins are toxic to bacteria closely related to the bacteriocin producing strain.
	GO:0006855	drug transmembrane transport	The process in which a drug is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0034220	ion transmembrane transport	A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	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: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:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	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.
	GO:0046930	pore complex	Any small opening in a membrane that allows the passage of gases and/or liquids.

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
		OLC	[ 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 3pou)

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
	3pou
		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
	OMPF_ECOLI \| P02931
		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

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
	OMPF_ECOLI \| P02931
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

2pox
3poq	THE SAME PROTEIN AND SPACEGROUP BUT DIFFERENT UNIT CELL AND PACKING

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

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