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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF D60A MUTANT OF ARABIDOPSIS ACD11 (ACCELERATED-CELL-DEATH 11) COMPLEXED WITH C2 CERAMIDE-1-PHOSPHATE (D18:1/2:0) AT 2.15 ANGSTROM RESOLUTION
 
Authors :  D. K. Simanshu, R. E. Brown, D. J. Patel
Date :  02 Dec 13  (Deposition) - 05 Feb 14  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Protein-Lipid Complexes, Pi-Bulge, Gltp-Fold, Lipid Transfer Protein, Cell Death, Ceramide-1-Phosphate, C1P, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. K. Simanshu, X. Zhai, D. Munch, D. Hofius, J. E. Markham, J. Bielawski, A. Bielawska, L. Malinina, J. G. Molotkovsky, J. W. Mundy, D. J. Patel, R. E. Brown
Arabidopsis Accelerated Cell Death 11, Acd11, Is A Ceramide-1-Phosphate Transfer Protein And Intermediary Regulator Of Phytoceramide Levels.
Cell Rep V. 6 388 2014
PubMed-ID: 24412362  |  Reference-DOI: 10.1016/J.CELREP.2013.12.023

(-) Compounds

Molecule 1 - ACCELERATED-CELL-DEATH 11
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ACD11, AT2G34690
    Mutation: YES
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: GLYCOLIPID TRANSFER PROTEIN, AT2G34690

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
11PW6Ligand/Ion(2S,3R,4E)-2-(ACETYLAMINO)-3-HYDROXYOCTADEC-4-EN-1-YLDIHYDROGEN PHOSPHATE
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
11PW2Ligand/Ion(2S,3R,4E)-2-(ACETYLAMINO)-3-HYDROXYOCTADEC-4-EN-1-YLDIHYDROGEN PHOSPHATE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
11PW2Ligand/Ion(2S,3R,4E)-2-(ACETYLAMINO)-3-HYDROXYOCTADEC-4-EN-1-YLDIHYDROGEN PHOSPHATE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
11PW2Ligand/Ion(2S,3R,4E)-2-(ACETYLAMINO)-3-HYDROXYOCTADEC-4-EN-1-YLDIHYDROGEN PHOSPHATE
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:59 , LYS A:64 , ARG A:99 , ARG A:103 , HIS A:143 , ILE A:147 , 1PW A:302 , HOH A:421 , HOH A:502 , LEU C:153 , TYR C:156BINDING SITE FOR RESIDUE 1PW A 301
2AC2SOFTWAREILE A:147 , 1PW A:301 , TRP C:145 , ARG C:148 , TYR C:156BINDING SITE FOR RESIDUE 1PW A 302
3AC3SOFTWAREPRO A:141 , 1PW C:301BINDING SITE FOR RESIDUE PEG A 303
4AC4SOFTWARELEU A:153 , TYR A:156 , GLY B:144 , TRP B:145 , ALA B:146 , ILE B:147 , ARG B:148 , 1PW B:302 , HOH B:490 , 1PW C:302BINDING SITE FOR RESIDUE 1PW B 301
5AC5SOFTWARETYR A:156 , MET B:59 , ALA B:60 , LYS B:64 , ARG B:99 , ARG B:103 , ILE B:147 , 1PW B:301BINDING SITE FOR RESIDUE 1PW B 302
6AC6SOFTWARESER B:152BINDING SITE FOR RESIDUE PEG B 303
7AC7SOFTWARETRP A:145 , ARG A:148 , PEG A:303 , HOH A:473 , TYR B:156 , HIS C:142 , HIS C:143 , GLY C:144 , ILE C:147 , ALA C:150 , HOH C:437 , HOH C:458BINDING SITE FOR RESIDUE 1PW C 301
8AC8SOFTWARETYR B:156 , 1PW B:301 , PHE C:56 , MET C:59 , ALA C:60 , LYS C:64 , ARG C:99 , ARG C:103 , ILE C:147 , HOH C:437 , HOH C:439BINDING SITE FOR RESIDUE 1PW C 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NTO)

(-) 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:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nto A   7 DKPLRKISAAFKKLAIIVNSPNPEVPVTQFSHACSLVSPLFGCLGIAFKFAEMAYVAKVDDLVRASSSISTLVVMMDKDIEADCVRKAGSHTRNLLRVKRGLDMVKVLFEQIIASEGDNSLKDPATKSYAQVFAPHHGWAIRKAVSLGMYALPTRAHLLNMLKEDEAAAKIHMQSYVNSSAPLITYLDNLFLSKQLGIDW 206
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206


Chain B from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nto B   6 ADKPLRKISAAFKKLAIIVNSPNPEVPVTQFSHACSLVSPLFGCLGIAFKFAEMAYVAKVDDLVRASSSISTLVVMMDKDIEADCVRKAGSHTRNLLRVKRGLDMVKVLFEQIIASEGDNSLKDPATKSYAQVFAPHHGWAIRKAVSLGMYALPTRAHLLNMLKEDEAAAKIHMQSYVNSSAPLITYLDNLFLSKQLGIDW 206
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205 


Chain C from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nto C   7 DKPLRKISAAFKKLAIIVNSPNPEVPVTQFSHACSLVSPLFGCLGIAFKFAEMAYVAKVDDLVRASSSISTLVVMMDKDIEADCVRKAGSHTRNLLRVKRGLDMVKVLFEQIIASEGDNSLKDPATKSYAQVFAPHHGWAIRKAVSLGMYALPTRAHLLNMLKEDEAAAKIHMQSYVNSSAPLITYLDNLFLSKQLGIDW 206
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206
   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 4NTO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

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
    1PW  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4nto)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  4nto
    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
  ACD11_ARATH | O64587
    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
  ACD11_ARATH | O64587
    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
        ACD11_ARATH | O64587: 4nt1 4nt2 4ntg 4nti

(-) Related Entries Specified in the PDB File

4nt1 4nt2 4ntg 4nti