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(-) Description

Title :  LIPID BINDING IN RICE NONSPECIFIC LIPID TRANSFER PROTEIN-1 COMPLEXES FROM ORYZA SATIVA
 
Authors :  H. -C. Cheng, P. -T. Cheng, P. Peng, P. -C. Lyu, Y. -J. Sun
Date :  19 Jan 04  (Deposition) - 19 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Lipid Transport, Ltp 1, Pap 1, Rice, Fatty Acid Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. -C. Cheng, P. -T. Cheng, P. Peng, P. -C. Lyu, Y. -J. Sun
Lipid Binding In Rice Nonspecific Lipid Transfer Protein-1 Complexes From Oryza Sativa
Protein Sci. V. 13 2304 2004
PubMed-ID: 15295114  |  Reference-DOI: 10.1110/PS.04799704

(-) Compounds

Molecule 1 - NONSPECIFIC LIPID TRANSFER PROTEIN
    Chains: A
    Organism Common: RICE
    Organism Scientific: ORYZA SATIVA
    Organism Taxid: 4530
    Other Details: COMPLEXED WITH PALMITIC ACID
    Synonym: LTP 1, PAP 1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PAM2Ligand/IonPALMITOLEIC ACID
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1PAM4Ligand/IonPALMITOLEIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:10 , ALA A:17 , SER A:24 , LEU A:34 , LYS A:35 , ALA A:38 , ARG A:44 , ILE A:69 , PRO A:78 , ILE A:81 , PAM A:1093BINDING SITE FOR RESIDUE PAM A1092
2AC2SOFTWARELEU A:51 , ALA A:63 , ILE A:81 , SER A:82 , ALA A:83 , SER A:84 , ILE A:85 , PAM A:1092BINDING SITE FOR RESIDUE PAM A1093

(-) 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  (0, 0)

(no "Cis Peptide Bond" information available for 1UVB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1UVB)

(-) 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 d1uvba_ A: Plant non-specific lipid-transfer protein (ns-LTP, ns-LTP1)                      SCOP domains
               CATH domains 1uvbA00 A:1-91 Plant lipid-transfer and hydrophobic proteins                                CATH domains
               Pfam domains Tryp_alpha_amyl-1uvbA01 A:1-87                                                         ---- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhh............hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------PLANT_LTP  PDB: A:69-9- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 1uvb 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 d1uvba_ A: Plant non-specific lipid-transfer protein (ns-LTP, ns-LTP1)                      SCOP domains
               CATH domains 1uvbA00 A:1-91 Plant lipid-transfer and hydrophobic proteins                                CATH domains
               Pfam domains Tryp_alpha_amyl-1uvbA01 A:1-87                                                         ---- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhh............hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------PLANT_LTP  PDB: A:69-9- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 1uvb 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)
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  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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NLTP1_ORYSI | A2ZHF1: 1bv2 1rzl 1uva 1uvc
        NLTP1_ORYSJ | Q0IQK9: 1bv2 1rzl 1uva 1uvc

(-) Related Entries Specified in the PDB File

1bv2 LIPID TRANSFER PROTEIN FROM RICE SEEDS, NMR , 14 STRUCTURES
1mzm RICE NONSPECIFIC LIPID TRANSFER PROTEIN
1rzl RICE NONSPECIFIC LIPID TRANSFER PROTEIN
1uva RICE NONSPECIFIC LIPID TRANSFER PROTEIN
1uvc RICE NONSPECIFIC LIPID TRANSFER PROTEIN