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 LGG-1 COMPLEXED WITH A UNC-51 PEPTIDE
 
Authors :  Y. Watanabe, Y. Fujioka, N. N. Noda
Date :  05 Oct 15  (Deposition) - 30 Dec 15  (Release) - 30 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Autophagy, Ubiquitin-Like, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Wu, Y. Watanabe, X. Y. Guo, X. Qi, P. Wang, H. Y. Zhao, Z. Wang, Y. Fujioka, H. Zhang, J. Q. Ren, T. C. Fang, Y. X. Shen, W. Feng, J. J. Hu, N. N. Noda, H. Zhang
Structural Basis Of The Differential Function Of The Two C. Elegans Atg8 Homologs, Lgg-1 And Lgg-2, In Autophagy
Mol. Cell V. 60 914 2015
PubMed: search  |  Reference-DOI: 10.1016/J.MOLCEL.2015.11.019

(-) Compounds

Molecule 1 - PROTEIN LGG-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEX-6P
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-116
    Gene: LGG-1, C32D5.9
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
 
Molecule 2 - SERINE/THREONINE-PROTEIN KINASE UNC-51
    Chains: C, D
    Engineered: YES
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Synonym: UNC-51 AIM
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1CD14Ligand/IonCADMIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:0 , GLY A:116 , GLY B:-2 , HOH B:313binding site for residue CD A 201
02AC2SOFTWAREGLU A:17binding site for residue CD A 202
03AC3SOFTWAREASP A:45 , HOH A:301 , HIS B:42 , HOH B:320 , HOH B:351binding site for residue CD A 203
04AC4SOFTWAREASP A:97 , HOH A:328 , ASP B:19 , HOH B:333 , HOH B:345binding site for residue CD A 204
05AC5SOFTWAREHIS A:98 , HOH A:310 , HOH A:336 , HOH A:338 , HOH A:339 , HOH A:341binding site for residue CD A 205
06AC6SOFTWAREASP A:27 , ASP B:54 , HOH B:327 , HOH B:335 , HOH B:344binding site for residue CD A 206
07AC7SOFTWAREHOH A:303 , HOH B:324 , HOH B:337 , HOH B:346binding site for residue CD A 207
08AC8SOFTWAREASP A:54 , ASP B:27 , HOH B:331 , HOH B:343binding site for residue CD A 208
09AC9SOFTWAREGLY A:-2 , HIS B:0 , GLY B:116 , HOH B:313binding site for residue CD B 201
10AD1SOFTWAREHIS A:99 , HOH A:311 , HOH A:335 , HIS B:99 , HOH B:340 , HOH B:347binding site for residue CD B 202
11AD2SOFTWAREGLU B:17 , HOH D:406binding site for residue CD B 203
12AD3SOFTWAREASP B:111binding site for residue CD B 204
13AD4SOFTWAREHIS B:98 , HOH B:302 , HOH B:311 , HOH B:338 , HOH B:349 , HOH B:354binding site for residue CD B 205
14AD5SOFTWAREHIS A:42 , GLN A:69 , HOH A:302 , HOH A:340 , ASP B:45 , HOH B:321binding site for residue CD B 206

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5AZG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AZG)

(-) 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:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee............eeeee...hhhhhhhhhhhhh........eee..........hhhhhhhhhh.....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5azg A  -2 GPHMKWAYKEENNFEKRRAEGDKIRRKYPDRIPVIVEKAPKSKLHDLDKKKYLVPSDLTVGQFYFLIRKRIQLRPEDALFFFVNNVIPQTMTTMGQLYQDHHEEDLFLYIAYSDESVYG 116
                                     7        17        27        37        47        57        67        77        87        97       107         


Chain B from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee............eeeee...hhhhhhhhhhhhh........eeee.........hhhhhhhhhh.....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5azg B  -2 GPHMKWAYKEENNFEKRRAEGDKIRRKYPDRIPVIVEKAPKSKLHDLDKKKYLVPSDLTVGQFYFLIRKRIQLRPEDALFFFVNNVIPQTMTTMGQLYQDHHEEDLFLYIAYSDESVYG 116
                                     7        17        27        37        47        57        67        77        87        97       107         


Chain C from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5azg C 357 DFTFL 361


Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...ee. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5azg D 356 TDFTFL 361
   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 5AZG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (44, 49)

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
    CD  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5azg)
 
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
  5azg
    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
  LGG1_CAEEL | Q09490
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  UNC51_CAEEL | Q23023
    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
  LGG1_CAEEL | Q09490
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  UNC51_CAEEL | Q23023
    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
        LGG1_CAEEL | Q09490: 5azf

(-) Related Entries Specified in the PDB File

5azf 5AZF CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT PEPTIDE.
5azh