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 :  CRYSTAL STRUCTURE OF HUMAN GLTP BOUND WITH 12:0 MONOSULFATIDE
 
Authors :  V. R. Samygina, B. Ochoa-Lizarralde, L. Malinina
Date :  13 Sep 12  (Deposition) - 10 Apr 13  (Release) - 10 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Gltp-Fold, Lipid Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. R. Samygina, B. Ochoa-Lizarralde, A. N. Popov, A. Cabo-Bilbao, F. Goni-De-Cerio, J. G. Molotkovsky, D. J. Patel, R. E. Brown, L. Malinina
Structural Insights Into Lipid-Dependent Reversible Dimerization Of Human Gltp.
Acta Crystallogr. , Sect. D V. 69 603 2013
PubMed-ID: 23519669  |  Reference-DOI: 10.1107/S0907444913000024

(-) Compounds

Molecule 1 - GLYCOLIPID TRANSFER PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GLTP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GLTP

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1EIS1Ligand/IonN-{(2S,3R,4E)-3-HYDROXY-1-[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]OCTADEC-4-EN-2-YL}DODECANAMIDE
2MYS2Ligand/IonPENTADECANE
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1EIS2Ligand/IonN-{(2S,3R,4E)-3-HYDROXY-1-[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]OCTADEC-4-EN-2-YL}DODECANAMIDE
2MYS4Ligand/IonPENTADECANE
3NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:41 , PHE A:42 , ILE A:45 , ASP A:48 , ASN A:52 , LEU A:92 , ALA A:93 , TRP A:96 , PHE A:103 , LEU A:136 , HIS A:140 , PHE A:148 , TYR A:207 , MYS A:302 , HOH A:418 , HOH A:514 , HOH A:536 , HOH A:568 , HOH A:602BINDING SITE FOR RESIDUE EIS A 301
2AC2SOFTWAREPHE A:33 , LEU A:37 , PHE A:103 , PHE A:107 , LEU A:152 , PHE A:183 , EIS A:301 , HOH A:615BINDING SITE FOR RESIDUE MYS A 302
3AC3SOFTWARELYS A:87 , LEU A:205 , ASN A:206 , TYR A:207 , HOH A:622BINDING SITE FOR RESIDUE MYS A 303
4AC4SOFTWAREHOH A:431 , HOH A:511 , HOH A:544 , HOH A:606 , HOH A:627 , HOH A:650BINDING SITE FOR RESIDUE NA A 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H2Z)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:85 -Pro A:86

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H2Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H2Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4H2Z)

(-) 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:203
                                                                                                                                                                                                                                           
               SCOP domains d4h2za_ A: Glycolipid transfer protein, GLTP                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2z A   7 HLLKPLPADKQIETGPFLEAVSHLPPFFDCLGSPVFTPIKADISGNITKIKAVYDTNPAKFRTLQNILEVEKEMYGAEWPKVGATLALMWLKRGLRFIQVFLQSICDGERDENHPNLIRVNATKAYEMALKKYHGWIVQKIFQAALYAAPYKSDFLKALSKGQNVTEEECLEKIRLFLVNYTATIDVIYEMYTQMNAELNYKV 209
                                    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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H2Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H2Z)

(-) Gene Ontology  (12, 12)

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
    EIS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MYS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:85 - Pro A:86   [ 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
  4h2z
    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
  GLTP_HUMAN | Q9NZD2
    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
  GLTP_HUMAN | Q9NZD2
    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
        GLTP_HUMAN | Q9NZD2: 1swx 1sx6 2euk 2eum 2evd 2evl 2evs 2evt 3ric 3rwv 3rzn 3s0i 3s0k 4gh0 4ghp 4ghs 4gix 4gjq 4gvt 4gxd 4gxg

(-) Related Entries Specified in the PDB File

4gh0 4gxd