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

(-) Description

Title :  CRYO-EM STRUCTURE OF GLUTAMATE DEHYDROGENASE AT 1.8 A RESOLUTION
 
Authors :  A. Merk, A. Bartesaghi, S. Banerjee, V. Falconieri, P. Rao, L. Earl, J. M S. Subramaniam
Date :  17 May 16  (Deposition) - 08 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Glutamate Dehydrogenase, Small Metabolic Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Merk, A. Bartesaghi, S. Banerjee, V. Falconieri, P. Rao, M. I. Davis R. Pragani, M. B. Boxer, L. A. Earl, J. L. Milne, S. Subramaniam
Breaking Cryo-Em Resolution Barriers To Facilitate Drug Discovery.
Cell V. 165 1698 2016
PubMed-ID: 27238019  |  Reference-DOI: 10.1016/J.CELL.2016.05.040

(-) Compounds

Molecule 1 - GLUTAMATE DEHYDROGENASE 1, MITOCHONDRIAL
    Chains: A, B, C, D, E, F
    EC Number: 1.4.1.3
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: GDH 1

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5K12)

(-) Sites  (0, 0)

(no "Site" information available for 5K12)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K12)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr A:87 -Pro A:88
2Thr B:87 -Pro B:88
3Thr C:87 -Pro C:88
4Thr D:87 -Pro D:88
5Thr E:87 -Pro E:88
6Thr F:87 -Pro F:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K12)

(-) Exons   (0, 0)

(no "Exon" information available for 5K12)

(-) Sequences/Alignments

Asymmetric/Biological 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:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeee.....eeeeeeeeee.......eeeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh......hhhhh....hhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k12 A  53 KPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKV 489
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   ||  375       385       395       405       415       425       435       445       455       465       475       485    
                                                                                                                                                                                                       226|                                                                                                                       
                                                                                                                                                                                                        370                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeee.....eeeeeeeeee.......eeeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh......hhhhh....hhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k12 B  53 KPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKV 489
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   ||  375       385       395       405       415       425       435       445       455       465       475       485    
                                                                                                                                                                                                       226|                                                                                                                       
                                                                                                                                                                                                        370                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeee.....eeeeeeeeee.......eeeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh......hhhhh....hhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k12 C  53 KPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKV 489
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   ||  375       385       395       405       415       425       435       445       455       465       475       485    
                                                                                                                                                                                                       226|                                                                                                                       
                                                                                                                                                                                                        370                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeee.....eeeeeeeeee.......eeeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh......hhhhh....hhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k12 D  53 KPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKV 489
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   ||  375       385       395       405       415       425       435       445       455       465       475       485    
                                                                                                                                                                                                       226|                                                                                                                       
                                                                                                                                                                                                        370                                                                                                                       


Chain E from PDB  Type:PROTEIN  Length:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeee.....eeeeeeeeee.......eeeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh......hhhhh....hhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k12 E  53 KPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKV 489
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   ||  375       385       395       405       415       425       435       445       455       465       475       485    
                                                                                                                                                                                                       226|                                                                                                                       
                                                                                                                                                                                                        370                                                                                                                       


Chain F from PDB  Type:PROTEIN  Length:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeee.....eeeeeeeeee.......eeeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh......hhhhh....hhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k12 F  53 KPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKV 489
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   ||  375       385       395       405       415       425       435       445       455       465       475       485    
                                                                                                                                                                                                       226|                                                                                                                       
                                                                                                                                                                                                        370
   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 5K12)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K12)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K12)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 5k12)
 
  Sites
(no "Sites" information available for 5k12)
 
  Cis Peptide Bonds
    Thr A:87 - Pro A:88   [ RasMol ]  
    Thr B:87 - Pro B:88   [ RasMol ]  
    Thr C:87 - Pro C:88   [ RasMol ]  
    Thr D:87 - Pro D:88   [ RasMol ]  
    Thr E:87 - Pro E:88   [ RasMol ]  
    Thr F:87 - Pro F:88   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  5k12
    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
  DHE3_BOVIN | P00366
    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)
  1.4.1.3
    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
  DHE3_BOVIN | P00366
    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
        DHE3_BOVIN | P00366: 1hwy 1hwz 1nqt 1nr7 3etd 3ete 3etg 3jcz 3jd0 3jd1 3jd2 3jd3 3jd4 3mvo 3mvq 3mw9 3qmu

(-) Related Entries Specified in the PDB File

5k0z 5k10 5k11