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 :  CRYSTAL STRUCTURE OF CNG MIMICKING NAK-ETPP MUTANT IN COMPLEX WITH RB+
 
Authors :  M. De March, L. M. R. Napolitano, S. Onesti
Date :  01 Sep 14  (Deposition) - 01 Jul 15  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (4x)
Keywords :  Alpha Helical Membrane Protein, Chimera Channel, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Napolitano, I. Bisha, M. De March, A. Marchesi, M. Arcangeletti N. Demitri, M. Mazzolini, A. Rodriguez, A. Magistrato, S. Onesti, A. Laio, V. Torre
A Structural, Functional, And Computational Analysis Suggests Pore Flexibility As The Base For The Poor Selectivity Of Cng Channels.
Proc. Natl. Acad. Sci. Usa V. 112 E3619 2015
PubMed-ID: 26100907  |  Reference-DOI: 10.1073/PNAS.1503334112

(-) Compounds

Molecule 1 - POTASSIUM CHANNEL PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector: PQE60
    Fragment: RESIDUES 20-110
    Gene: BC_0669
    Mutation: YES
    Organism Scientific: BACILLUS CEREUS ATCC 14579
    Organism Taxid: 226900
    Strain: ATCC 14579 / DSM 31

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): A 
Biological Unit 2 (4x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1GLY10Mod. Amino AcidGLYCINE
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3RB6Ligand/IonRUBIDIUM ION
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1GLY20Mod. Amino AcidGLYCINE
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3RB-1Ligand/IonRUBIDIUM ION
Biological Unit 2 (2, 24)
No.NameCountTypeFull Name
1GLY20Mod. Amino AcidGLYCINE
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3RB-1Ligand/IonRUBIDIUM ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:63 , VAL A:64 , RB A:202 , RB A:203BINDING SITE FOR RESIDUE RB A 201
02AC2SOFTWARETHR A:63 , RB A:201BINDING SITE FOR RESIDUE RB A 202
03AC3SOFTWAREVAL A:64 , GLY A:65 , RB A:201BINDING SITE FOR RESIDUE RB A 203
04AC4SOFTWAREGLU A:46 , GLY A:47 , GLN B:71 , GLY B:209BINDING SITE FOR RESIDUE MPD A 204
05AC5SOFTWARELEU A:81 , PHE A:93BINDING SITE FOR RESIDUE GLY A 205
06AC6SOFTWARETHR A:34BINDING SITE FOR RESIDUE GLY A 206
07AC7SOFTWAREHOH A:310BINDING SITE FOR RESIDUE GLY A 207
08AC8SOFTWARESER A:43 , GLY A:47 , LEU A:48 , HOH A:302BINDING SITE FOR RESIDUE GLY A 208
09AC9SOFTWAREARG A:49 , PRO A:50 , ILE A:51BINDING SITE FOR RESIDUE GLY A 209
10BC1SOFTWAREVAL B:64 , GLY B:65 , RB B:203BINDING SITE FOR RESIDUE RB B 201
11BC2SOFTWARETHR B:63 , RB B:203BINDING SITE FOR RESIDUE RB B 202
12BC3SOFTWARETHR B:63 , VAL B:64 , RB B:201 , RB B:202BINDING SITE FOR RESIDUE RB B 203
13BC4SOFTWAREARG B:49 , GLY B:208 , HOH B:312BINDING SITE FOR RESIDUE MPD B 204
14BC5SOFTWAREASN B:100BINDING SITE FOR RESIDUE GLY B 205
15BC6SOFTWARESER B:37BINDING SITE FOR RESIDUE GLY B 206
16BC7SOFTWAREHOH B:302BINDING SITE FOR RESIDUE GLY B 207
17BC8SOFTWAREMPD B:204 , GLY B:209 , HOH B:312BINDING SITE FOR RESIDUE GLY B 208
18BC9SOFTWAREMPD A:204 , ARG B:49 , GLN B:71 , GLY B:208BINDING SITE FOR RESIDUE GLY B 209

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R8C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4R8C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R8C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R8C)

(-) Exons   (0, 0)

(no "Exon" information available for 4R8C)

(-) 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:84
                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 4r8c A  25 QVLFVLTILTLISGTIFYSTVEGLRPIDALYFSVVTLTTVGETPPPQTDFGKIFTILYIFIGIGLVFGFIHKLAVNVQLPSILS 108
                                    34        44        54        64        74        84        94       104    


Chain B from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4r8c B  21 DKEFQVLFVLTILTLISGTIFYSTVEGLRPIDALYFSVVTLTTVGETPPPQTDFGKIFTILYIFIGIGLVFGFIHKLAVNVQLPSILSNLVP 112
                                    30        40        50        60        70        80        90       100       110
   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  (0, 0)

(no "SCOP Domain" information available for 4R8C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R8C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R8C)

(-) Gene Ontology  (2, 2)

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
    GLY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    RB  [ 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 ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4r8c)
 
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
  4r8c
    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
  Q81HW2_BACCR | Q81HW2
    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

(-) 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
  Q81HW2_BACCR | Q81HW2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q81HW2_BACCR | Q81HW2: 2ahy 2ahz 2q67 2q68 2q69 2q6a 3e83 3e86 3e89 3e8b 3e8f 3e8g 3e8h 3k03 3k04 3k06 3k08 3k0d 3k0g 3t1c 3t2m 3t4d 3t4z 3tcu 3tet 4pdl 4pdm 4pdr 4pdv 4r50 4r6z 4r7c 4rai 4ro2 4zbm

(-) Related Entries Specified in the PDB File

3k0d CRYSTAL STRUCTURE OF CNG MIMICKING NAK MUTANT, NAK-ETPP, K+ COMPLEX
3k0g CRYSTAL STRUCTURE OF CNG MIMICKING NAK MUTANT, NAK-ETPP, NA+ COMPLEX
4r50
4r6z
4r7c
4r8b
4rai
4rar