Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SPATIAL STRUCTURE OF THE LENTIL LIPID TRANSFER PROTEIN IN COMPLEX WITH ANIONIC LYSOLIPID LPPG
 
Authors :  K. S. Mineev, Z. O. Shenkarev, A. S. Arseniev, D. N. Melnikova, E. I. Fink T. V. Ovchinnikova
Date :  17 Aug 16  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Plant Defense Peptide Lipid Transfer Protein Lens Culinaris Complex With Lipid, Structure From Cyana 3. 0, Lipid Transfer, Lipid Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. O. Shenkarev, D. N. Melnikova, E. I. Finkina, S. V. Sukhanov, I. A. Boldyrev, A. K. Gizatullina, K. S. Mineev, A. S. Arseniev, T. V. Ovchinnikova
Ligand Binding Properties Of The Lentil Lipid Transfer Protein: Molecular Insight Into The Possible Mechanism Of Lipid Uptake.
Biochemistry V. 56 1785 2017
PubMed-ID: 28266846  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B01079

(-) Compounds

Molecule 1 - NON-SPECIFIC LIPID-TRANSFER PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: LENTIL
    Organism Scientific: LENS CULINARIS
    Organism Taxid: 3864
    Synonym: LTP2

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1PGM1Ligand/Ion1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)]
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1PGM1Ligand/Ion1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)]

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:8 , LEU A:15 , LEU A:35 , LEU A:36 , LEU A:52 , LYS A:53 , ALA A:55 , ALA A:56 , ALA A:67 , ILE A:82binding site for residue PGM A 101

(-) SS Bonds  (4, 4)

NMR Structure
No.Residues
1A:4 -A:51
2A:14 -A:28
3A:29 -A:74
4A:49 -A:88

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Gly A:23 -Pro A:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LQV)

(-) Sequences/Alignments

NMR Structure
   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:93
                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..hhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh............hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  5lqv A  1 AISCGAVTSDLSPCLTYLTGGPGPSPQCCGGVKKLLAAANTTPDRQAACNCLKSAAGSITKLNTNNAAALPGKCGVNIPYKISTTTNCNTVKF 93
                                    10        20        30        40        50        60        70        80        90
   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 5LQV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)

 Visualization

(-) Interactive Views

NMR Structure
  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
    PGM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:23 - Pro A:24   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models 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
  5lqv
    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
  NLTP2_LENCU | A0AT29
    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
  NLTP2_LENCU | A0AT29
    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
        NLTP2_LENCU | A0AT29: 2mal

(-) Related Entries Specified in the PDB File

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