Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  ION SELECTIVITY OF OMPF PORIN SOAKED IN 0.2M KBR
 
Authors :  D. Balasundaresan, L. Blachowicz, B. Roux
Date :  22 Jul 13  (Deposition) - 23 Oct 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Porin, Outer Membrane Protein, Beta-Barrel, Ion Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Dhakshnamoorthy, B. K. Ziervogel, L. Blachowicz, B. Roux
A Structural Study Of Ion Permeation In Ompf Porin From Anomalous X-Ray Diffraction And Molecular Dynamics Simulations.
J. Am. Chem. Soc. V. 135 16561 2013
PubMed-ID: 24106986  |  Reference-DOI: 10.1021/JA407783A

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN F
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPR272
    Expression System Strain: K12
    Expression System Taxid: 83333
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 23-362
    Gene: B0929, CMLB, COA, CRY, JW0912, OMPF, TOLF
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: OUTER MEMBRANE PROTEIN 1A, OUTER MEMBRANE PROTEIN B, OUTER MEMBRANE PROTEIN IA, PORIN OMPF

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A 
Biological Unit 2 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1BR12Ligand/IonBROMIDE ION
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:123 , HOH A:659BINDING SITE FOR RESIDUE BR A 401
02AC2SOFTWAREASN A:69 , ARG A:100 , ASP A:126 , GLY A:134 , ARG A:163 , HOH A:572BINDING SITE FOR RESIDUE BR A 402
03AC3SOFTWAREALA A:261 , ILE A:273BINDING SITE FOR RESIDUE BR A 403
04AC4SOFTWAREARG A:167 , HOH A:553BINDING SITE FOR RESIDUE BR A 404
05AC5SOFTWAREASN A:69 , SER A:70 , ALA A:75BINDING SITE FOR RESIDUE BR A 405
06AC6SOFTWARELYS A:89 , ARG A:140 , ASN A:141 , SER A:142 , HOH A:607 , HOH A:610BINDING SITE FOR RESIDUE BR A 406
07AC7SOFTWARETYR A:63 , GLN A:76 , HOH A:543BINDING SITE FOR RESIDUE MG A 407
08AC8SOFTWAREGLN B:262 , ARG B:270BINDING SITE FOR RESIDUE BR B 401
09AC9SOFTWARESER B:125 , BR B:404BINDING SITE FOR RESIDUE BR B 402
10BC1SOFTWAREASN B:69 , GLU B:71 , THR B:81 , BR B:405 , HOH B:638BINDING SITE FOR RESIDUE BR B 403
11BC2SOFTWARESER B:125 , ARG B:167 , ARG B:168 , BR B:402 , HOH B:610BINDING SITE FOR RESIDUE BR B 404
12BC3SOFTWAREGLN B:66 , GLY B:67 , ASN B:68 , ASN B:69 , BR B:403BINDING SITE FOR RESIDUE BR B 405
13BC4SOFTWAREASP B:113 , HOH B:566BINDING SITE FOR RESIDUE BR B 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LSH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LSH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LSH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LSH)

(-) Exons   (0, 0)

(no "Exon" information available for 4LSH)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4lsha_ A: Porin                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeeee...........ee..eeeeeeeeeeeee..eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeee..hhhhhh.....................eeeeeeeeeehhhhhh...eeeeeeee..............eeeeeeeeee..eeeeeeeeeee.hhhhhh.......eeeeeeeeeeeee..eeeeeeeeeee...eeee....eeee..eeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee....eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lsh A   1 AEIGNKVDLYGKAVGLHYFSKGGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 340
                              ||    14        24 ||     35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335     
                              3|                26|                                                                                                                                                                                                                                                                                                                        
                               8                 28                                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4lshb_ B: Porin                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeee...........ee..eeeeeeeeeeeee..eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeee..hhhhhh.....................eeeeeeeeeehhhhhh...eeeeeeee..............eeeeeeeeee..eeeeeeeeeee.hhhhhh.......eeeeeeeeeeeee..eeeeeeeeeee...eeee....eeee..eeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee....eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lsh B   1 AEGNKVDLYGKAVGLHYFSKGGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 340
                             ||     15        25||      36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    
                             2|                26|                                                                                                                                                                                                                                                                                                                        
                              8                 28
   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, 2)

Asymmetric Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LSH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LSH)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

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
    BR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4lsh)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

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 | Biol. Unit 2 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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4lsh
    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

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

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        OMPF_ECOLI | P02931: 1bt9 1gfm 1gfn 1gfo 1gfp 1gfq 1hxt 1hxu 1hxx 1mpf 1opf 2omf 2zfg 2zld 3fyx 3hw9 3hwb 3k19 3k1b 3o0e 3poq 3pou 3pox 4d5u 4gcp 4gcq 4gcs 4jfb 4lse 4lsf 4lsi

(-) Related Entries Specified in the PDB File

4lse 4lsf 4lsi