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
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)

(-) Description

Title :  RICE NONSPECIFIC LIPID TRANSFER PROTEIN
 
Authors :  J. Y. Lee, K. S. Min, H. Cha, D. H. Shin, K. Y. Hwang, S. W. Suh
Date :  09 Oct 97  (Deposition) - 16 Dec 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Lipid Transport, Alpha-Helical Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Y. Lee, K. Min, H. Cha, D. H. Shin, K. Y. Hwang, S. W. Suh
Rice Non-Specific Lipid Transfer Protein: The 1. 6 A Crystal Structure In The Unliganded State Reveals A Small Hydrophobic Cavity.
J. Mol. Biol. V. 276 437 1998
PubMed-ID: 9512714  |  Reference-DOI: 10.1006/JMBI.1997.1550
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NONSPECIFIC LIPID TRANSFER PROTEIN
    Chains: A
    Fragment: FOUR-HELIX BUNDLE
    Organ: SEED
    Organism Common: RICE
    Organism Scientific: ORYZA SATIVA
    Organism Taxid: 4530

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CXS2Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CXS4Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:2 , GLY A:4 , SER A:24 , ALA A:26 , SER A:71 , HOH A:101 , HOH A:104 , HOH A:154BINDING SITE FOR RESIDUE SO4 A 216
2AC2SOFTWAREPRO A:23 , LYS A:72 , SER A:84 , ILE A:85 , ASP A:86 , ARG A:89 , HOH A:111 , HOH A:152 , CXS A:211BINDING SITE FOR RESIDUE CXS A 201
3AC3SOFTWAREALA A:21 , GLY A:22 , PRO A:23 , PRO A:78 , ARG A:89 , HOH A:102 , HOH A:105 , CXS A:201BINDING SITE FOR RESIDUE CXS A 211

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:3 -A:50
2A:13 -A:27
3A:28 -A:73
4A:48 -A:87

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:22 -Pro A:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RZL)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PLANT_LTPPS00597 Plant lipid transfer proteins signature.NLTP1_ORYSI94-115  1A:69-90
NLTP1_ORYSJ94-115  1A:69-90
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PLANT_LTPPS00597 Plant lipid transfer proteins signature.NLTP1_ORYSI94-115  2A:69-90
NLTP1_ORYSJ94-115  2A:69-90

(-) Exons   (0, 0)

(no "Exon" information available for 1RZL)

(-) 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:91
 aligned with NLTP1_ORYSI | A2ZHF1 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:91
                                    35        45        55        65        75        85        95       105       115 
          NLTP1_ORYSI    26 ITCGQVNSAVGPCLTYARGGAGPSAACCSGVRSLKAAASTTADRRTACNCLKNAARGIKGLNAGNAASIPSKCGVSVPYTISASIDCSRVS 116
               SCOP domains d1rzla_ A: Plant non-specific lipid-transfer protein (ns-LTP, ns-LTP1)                      SCOP domains
               CATH domains 1rzlA00 A:1-91 Plant lipid-transfer and hydrophobic proteins                                CATH domains
               Pfam domains Tryp_alpha_amyl-1rzlA01 A:1-87                                                         ---- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------PLANT_LTP  PDB: A:69-9- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 1rzl A   1 ITCGQVNSAVGPCLTYARGGAGPSAACCSGVRSLKAAASTTADRRTACNCLKNAARGIKGLNAGNAASIPSKCGVSVPYTISASIDCSRVS  91
                                    10        20        30        40        50        60        70        80        90 


Chain A from PDB  Type:PROTEIN  Length:91
 aligned with NLTP1_ORYSJ | Q0IQK9 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:91
                                    35        45        55        65        75        85        95       105       115 
          NLTP1_ORYSJ    26 ITCGQVNSAVGPCLTYARGGAGPSAACCSGVRSLKAAASTTADRRTACNCLKNAARGIKGLNAGNAASIPSKCGVSVPYTISASIDCSRVS 116
               SCOP domains d1rzla_ A: Plant non-specific lipid-transfer protein (ns-LTP, ns-LTP1)                      SCOP domains
               CATH domains 1rzlA00 A:1-91 Plant lipid-transfer and hydrophobic proteins                                CATH domains
               Pfam domains Tryp_alpha_amyl-1rzlA01 A:1-87                                                         ---- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------PLANT_LTP  PDB: A:69-9- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 1rzl A   1 ITCGQVNSAVGPCLTYARGGAGPSAACCSGVRSLKAAASTTADRRTACNCLKNAARGIKGLNAGNAASIPSKCGVSVPYTISASIDCSRVS  91
                                    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  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Prolamin (17)

(-) Gene Ontology  (3, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (NLTP1_ORYSI | A2ZHF1)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
biological process
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

Chain A   (NLTP1_ORYSJ | Q0IQK9)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
biological process
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

 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
    CXS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:22 - Pro A:23   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  1rzl
    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
  NLTP1_ORYSI | A2ZHF1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  NLTP1_ORYSJ | Q0IQK9
    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
  NLTP1_ORYSI | A2ZHF1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  NLTP1_ORYSJ | Q0IQK9
    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
        NLTP1_ORYSI | A2ZHF1: 1bv2 1uva 1uvb 1uvc
        NLTP1_ORYSJ | Q0IQK9: 1bv2 1uva 1uvb 1uvc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RZL)