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 :  Y78 ESTER MUTANT OF KCSA IN HIGH K+
 
Authors :  K. Matulef, F. I. Valiyaveetil
Date :  18 Sep 13  (Deposition) - 30 Oct 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (4x)
Keywords :  Membrane Protein, Channel, Ester, Unnatural Amino Acid, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Matulef, A. G. Komarov, C. A. Costantino, F. I. Valiyaveetil
Using Protein Backbone Mutagenesis To Dissect The Link Between Ion Occupancy And C-Type Inactivation In K+ Channels.
Proc. Natl. Acad. Sci. Usa V. 110 17886 2013
PubMed-ID: 24128761  |  Reference-DOI: 10.1073/PNAS.1314356110

(-) Compounds

Molecule 1 - ANTIBODY FAB FRAGMENT HEAVY CHAIN
    Cell: HYBRIDOMA
    Chains: A
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Common: PICHIA PASTORIS
    Expression System Taxid: 4922
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - ANTIBODY FAB FRAGMENT LIGHT CHAIN
    Cell: HYBRIDOMA
    Chains: B
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Common: PICHIA PASTORIS
    Expression System Taxid: 4922
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - PH-GATED POTASSIUM CHANNEL KCSA
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 22-124
    Gene: KCSA, SKC1
    Organism Scientific: STREPTOMYCES LIVIDANS
    Organism Taxid: 1916
    Synonym: STREPTOMYCES LIVIDANS K+ CHANNEL, SKC1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (4x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1DGA1Ligand/IonDIACYL GLYCEROL
2K6Ligand/IonPOTASSIUM ION
3TYF1Mod. Amino Acid(2S)-2-HYDROXY-3-(4-HYDROXYPHENYL)PROPANOIC ACID
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1DGA-1Ligand/IonDIACYL GLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3TYF-1Mod. Amino Acid(2S)-2-HYDROXY-3-(4-HYDROXYPHENYL)PROPANOIC ACID
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1DGA4Ligand/IonDIACYL GLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3TYF4Mod. Amino Acid(2S)-2-HYDROXY-3-(4-HYDROXYPHENYL)PROPANOIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:30 , GLU B:53 , PRO C:63 , LEU C:86 , HOH C:1113BINDING SITE FOR RESIDUE DGA C 1001
2AC2SOFTWAREGLY C:77 , TYF C:78BINDING SITE FOR RESIDUE K C 1002
3AC3SOFTWARETHR C:75 , VAL C:76 , K C:1004BINDING SITE FOR RESIDUE K C 1003
4AC4SOFTWARETHR C:75 , K C:1003BINDING SITE FOR RESIDUE K C 1004
5AC5SOFTWAREK C:1007BINDING SITE FOR RESIDUE K C 1006
6AC6SOFTWAREK C:1006BINDING SITE FOR RESIDUE K C 1007

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:145 -A:200
3B:23 -B:88
4B:134 -B:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:151 -Pro A:152
2Glu A:153 -Pro A:154
3Trp A:193 -Pro A:194
4Ser B:7 -Pro B:8
5Trp B:94 -Pro B:95
6Tyr B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MSW)

(-) 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:219
                                                                                                                                                                                                                                                           
               SCOP domains d4mswa1 A:1-118 Immunoglobulin heavy chain variable domain, VH                                                        d4mswa2 A:119-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeee.....eeeeeee........eeeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.......ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4msw A   1 QVQLQQPGAELVKPGASVKLSCKASGYTFTSDWIHWVKQRPGHGLEWIGEIIPSYGRANYNEKIQKKATLTADKSSSTAFMQLSSLTSEDSAVYYCARERGDGYFAVWGAGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSSWPSETVTCNVAHPASSTKVDKKIVPRD 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d4mswb1 B:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d4mswb2 B:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4msw B   1 DILLTQSPAILSVSPGERVSFSCRASQSIGTDIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIANYYCQQSNRWPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain C from PDB  Type:PROTEIN  Length:103
                                                                                                                                       
               SCOP domains d4mswc_ C: Potassium channel protein                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 4msw C  22 SALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGxGDLYPVTLWGRLVAVVVMVAGITSFGLVTAALATWFVGREQERRGH 124
                                    31        41        51        61        71      | 81        91       101       111       121   
                                                                                   78-TYF
   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  (5, 5)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

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
    DGA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TYF  [ 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 ]
 
  Cis Peptide Bonds
    Glu A:153 - Pro A:154   [ RasMol ]  
    Phe A:151 - Pro A:152   [ RasMol ]  
    Ser B:7 - Pro B:8   [ RasMol ]  
    Trp A:193 - Pro A:194   [ RasMol ]  
    Trp B:94 - Pro B:95   [ RasMol ]  
    Tyr B:140 - Pro B:141   [ 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
  4msw
    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
  KCSA_STRLI | P0A334
    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
  KCSA_STRLI | P0A334
    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
        KCSA_STRLI | P0A334: 1bl8 1f6g 1j95 1jq1 1jq2 1jvm 1k4c 1k4d 1r3i 1r3j 1r3k 1r3l 1s33 1s5h 1zwi 2a9h 2atk 2bob 2boc 2dwd 2dwe 2h8p 2hg5 2hjf 2hvj 2hvk 2ih1 2ih3 2itc 2itd 2jk5 2nlj 2p7t 2qto 2w0f 3eff 3f5w 3f7v 3f7y 3fb5 3fb6 3fb7 3fb8 3gb7 3hpl 3ifx 3iga 3ogc 3or6 3or7 3pjs 3stl 3stz 4lbe 4lcu 4uuj 5e1a 5ebl 5ebm 5ebw 5ec1 5ec2 5j9p

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4MSW)