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 THE UNLIGANDED FORM OF HCN2 CNBD
 
Authors :  V. A. Klenchin, B. Chanda
Date :  02 May 16  (Deposition) - 30 Nov 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hcn Channels, Cyclic Nucleotide Regulated Channels, Cyclic Nucleotide Binding Domain, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. P. Goldschen-Ohm, V. A. Klenchin, D. S. White, J. B. Cowgill, Q. Cui, R. H. Goldsmith, B. Chanda
Structure And Dynamics Underlying Elementary Ligand Binding Events In Human Pacemaking Channels.
Elife V. 5 2016
PubMed-ID: 27858593  |  Reference-DOI: 10.7554/ELIFE.20797

(-) Compounds

Molecule 1 - MALTOSE-BINDING PERIPLASMIC PROTEIN,POTASSIUM/SODIUM HYPERPOLARIZATION-ACTIVATED CYCLIC NUCLEOTIDE-GATED CHANNEL 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: MALE, Z5632, ECS5017, HCN2, BCNG2, HAC1
    Organism Common: MOUSE
    Organism Taxid: 83334, 10090
    Synonym: MBP,MMBP,MALTODEXTRIN-BINDING PROTEIN,BRAIN CYCLIC NUCLEOTIDE-GATED CHANNEL 2,BCNG-2,HYPERPOLARIZATION-ACTIVATED CATION CHANNEL 1,HAC-1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1MAL2Ligand/IonMALTOSE
2NO33Ligand/IonNITRATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MAL1Ligand/IonMALTOSE
2NO31Ligand/IonNITRATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1MAL1Ligand/IonMALTOSE
2NO32Ligand/IonNITRATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:-214 , ASP A:-304 , TRP A:-307 , TRP A:-29 , GLU A:-216 , ALA A:-306 , ARG A:-303 , ASN A:-357 , PRO A:-215 , ASP A:-355 , GLU A:-258 , LYS A:-354 , HOH A:809 , HOH A:810 , HOH A:815 , HOH A:827 , HOH A:882binding site for residue MAL A 701
2AC2SOFTWAREGLY A:581 , ARG A:591 , THR A:592binding site for residue NO3 A 702
3AC3SOFTWARETYR B:-214 , ASP B:-304 , TRP B:-307 , TRP B:-29 , GLU B:-216 , ALA B:-306 , ARG B:-303 , PRO B:-215 , ASP B:-355 , LYS B:-354 , GLU B:-258 , ASN B:-357 , HOH B:810 , HOH B:856 , HOH B:875binding site for residue MAL B 701
4AC4SOFTWAREGLY B:581 , ARG B:591 , THR B:592 , NO3 B:703binding site for residue NO3 B 702
5AC5SOFTWAREVAL B:564 , GLY B:581 , GLU B:582 , NO3 B:702binding site for residue NO3 B 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JON)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys B:567 -Gly B:568

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JON)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JON)

(-) Exons   (0, 0)

(no "Exon" information available for 5JON)

(-) 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:509
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....hhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhh.......eeeee..hhhhhhhh........hhhhhh..hhhhhhhhee..ee..eeeeee..eeeee.........hhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh..eeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeehhhhhhhhhhhh..eeee............eeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..eeeee....eee.......eeeeeee..eeee.....eeee....eehhhhhh.......eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jon A -367 IEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNAAELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLD  634
                                  -358      -348      -338      -328      -318      -308      -298      -288      -278      -268      -258      -248      -238      -228      -218      -208      -198      -188      -178      -168      -158      -148      -138      -128      -118      -108       -98       -88       -78       -68       -58       -48       -38       -28       -18        -8       495       505       515       525       535       545       555       565       575       585       595       605       615       625         
                                                                                                                                                                                                                                                                                                                                                                                                           0|                                                                                                                                            
                                                                                                                                                                                                                                                                                                                                                                                                          494                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:506
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....hhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh......eeeee..hhhhhhhh........hhhhhh..hhhhhhh.ee..ee..eeeeee..eeeee.........hhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh..eeeee....eeeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeehhhhhhhhhhhh..eeee............eeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhh.....ee.hhhhhhhhh.hhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.eeeee....eee.......eeeeeee..eeee.....eeee....eehhhhhhh......eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jon B -368 KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNAAELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAI  630
                                  -359      -349      -339      -329      -319      -309      -299      -289      -279      -269      -259      -249      -239      -229      -219      -209      -199      -189      -179      -169      -159      -149      -139      -129      -119      -109       -99       -89       -79       -69       -59       -49       -39       -29       -19        -9       494       504       514       524       534       544       554       564       574       584       594       604       614       624      
                                                                                                                                                                                                                                                                                                                                                                                                            0|                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                                           494
   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 5JON)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JON)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JON)

(-) Gene Ontology  (32, 33)

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
    MAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NO3  [ 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 ]
 
  Cis Peptide Bonds
    Lys B:567 - Gly B:568   [ RasMol ]  
 
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
  5jon
    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
  HCN2_MOUSE | O88703
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  MALE_ECO57 | P0AEY0
    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
  HCN2_MOUSE | O88703
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MALE_ECO57 | P0AEY0
    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
        HCN2_MOUSE | O88703: 1q3e 1q43 1q5o 2q0a 3bpz 3etq 3ffq 4eqf 5khg 5khh 5khi 5khj 5khk
        MALE_ECO57 | P0AEY0: 1a7l 1anf 1dmb 1ez9 1ezo 1ezp 1fqa 1fqb 1fqc 1fqd 1hsj 1iud 1jvx 1jvy 1jw4 1jw5 1lax 1lls 1mdp 1mdq 1mg1 1mh3 1mh4 1mpb 1mpc 1mpd 1n3w 1n3x 1nl5 1nmu 1omp 1peb 1r6z 1svx 1t0k 1y4c 1ytv 1ziu 1zjl 1zkb 1zmg 2v93 3io4 3io6 3mbp 3osq 3osr 3vd8 4feb 4mbp 4my2 4wgi 4wrn 4wth 4wvg 4wvh 4wvi 4wvj 4xa2 4xai 4xaj 4xhs 4ys9 5bmy 5c7r 5cl1 5dfm 5e24 5e7u 5edu 5fio 5ii4 5jj4 5jtq 5jtr 5k94 5ldf 5lof 5t03 5t05 5t0a 5ttd

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5JON)