Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR, ALPHA-ISOFORM
 
Authors :  L. Peng, K. Zeng, A. Heine, B. Moyer, S. E. Greasley, P. Kuhn, W. E. Balch, I. A. Wilson
Date :  11 Oct 99  (Deposition) - 25 Oct 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.04
Chains :  Asym./Biol. Unit :  A
Keywords :  Ultra-High Resolution, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Luan, A. Heine, K. Zeng, B. Moyer, S. E. Greasely, P. Kuhn, W. E. Balch, I. A. Wilson
A New Functional Domain Of Guanine Nucleotide Dissociation Inhibitor (Alpha-Gdi) Involved In Rab Recycling.
Traffic V. 1 270 2000
PubMed-ID: 11208110  |  Reference-DOI: 10.1034/J.1600-0854.2000.010309.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:117 , LYS A:118 , ASN A:130 , HOH A:1032 , HOH A:1169 , HOH A:1324BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWARETYR A:192 , ARG A:193 , THR A:194 , HOH A:1064 , HOH A:1066 , HOH A:1316BINDING SITE FOR RESIDUE SO4 A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D5T)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:47 -Pro A:48
2Glu A:374 -Pro A:375

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D5T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1D5T)

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000160931ENSBTAE00000395537X:23762869-2376291951GDIA_BOVIN1-17171A:1-1717
1.2ENSBTAT000000160932ENSBTAE00000244799X:23763999-23764106108GDIA_BOVIN18-53361A:18-5336
1.3ENSBTAT000000160933ENSBTAE00000130996X:23764264-23764363100GDIA_BOVIN54-87341A:54-8734
1.4ENSBTAT000000160934ENSBTAE00000131001X:23764512-23764646135GDIA_BOVIN87-132461A:87-13246
1.5ENSBTAT000000160935ENSBTAE00000131002X:23765114-23765312199GDIA_BOVIN132-198671A:132-19867
1.6ENSBTAT000000160936ENSBTAE00000131007X:23765579-23765710132GDIA_BOVIN198-242451A:198-24245
1.7ENSBTAT000000160937ENSBTAE00000131011X:23766257-23766356100GDIA_BOVIN242-275341A:242-27534
1.8ENSBTAT000000160938ENSBTAE00000131012X:23766709-23766880172GDIA_BOVIN276-333581A:276-33358
1.9ENSBTAT000000160939ENSBTAE00000131015X:23767184-23767328145GDIA_BOVIN333-381491A:333-38149
1.10ENSBTAT0000001609310ENSBTAE00000131017X:23767454-2376750855GDIA_BOVIN381-399191A:381-39919
1.11ENSBTAT0000001609311ENSBTAE00000131035X:23767599-237686311033GDIA_BOVIN400-449501A:400-43132

(-) Sequences/Alignments

Asymmetric/Biological 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:433
 aligned with GDIA_BOVIN | P21856 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:433
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428   
           GDIA_BOVIN     - --MDEEYDVIVLGTGLTECILSGIMSVNGKKVLHMDRNPYYGGESSSITPLEELYKRFQLLEGPPETMGRGRDWNVDLIPKFLMANGQLVKMLLYTEVTRYLDFKVVEGSFVYKGGKIYKVPSTETEALASNLMGMFEKRRFRKFLVFVANFDENDPKTFEGVDPQNTSMRDVYRKFDLGQDVIDFTGHALALYRTDDYLDQPCLETINRIKLYSESLARYGKSPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPVDDIIMENGKVVGVKSEGEVARCKQLICDPSYVPDRVRKAGQVIRIICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISYAHNVAAQGKYIAIASTTVETTDPEKEVEPALELLEPIDQKFVAISDLYEPIDDGSESQVFCSCSYDATTHFETTCNDIKDIYKRMAGSAFDF 431
               SCOP domains d1d5ta1 A:-2-291,A:389-431 Guanine nucleotide dissociation inhibitor, GDI                                                                                                                                                                                                                            d1d5ta2 A:292-388 Guanine nucleotide dissociation inhibitor, GDI                                 d1d5ta1 A:-2-291,A:389-431                  SCOP domains
               CATH domains 1d5tA01 A:-2-57,A:224-294,A:387-431                        1d5tA02 A:58-118,A:295-386                                   1d5tA03 A:119-223 Guanine Nucleotide Dissociation Inhibitor, domain 1                                    1d5tA01 A:-2-57,A:224-294,A:387-431  [code=3.50.50.60, no name defined]1d5tA02 A:58-118,A:295-386 Guanine Nucleotide Dissociation Inhibitor, domain 2              1d5tA01 A:-2-57,A:224-294,A:387-431           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..hhhhhhhhhhhhhh...eeee...........ee.hhhhhhhhh......hhhhhhhhhh.ee.....ee..hhhhhhhhhhhhhhhh.eee..eeeeee..eeee...hhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhh.......hhhhhhhhh..hhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhhh..........eeeee..eeeeeee..eeee..eeee.hhhhhh.eeeeeeeeeeeeee............eeeeehhhhh.....eeeeeee.hhh......eeeeeeee....hhhhhhhhhhh......eeeeeeeeeeee........eee.........hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --Exon 1.1         Exon 1.2  PDB: A:18-53              Exon 1.3  PDB: A:54-87            --------------------------------------------Exon 1.5  PDB: A:132-198 UniProt: 132-198                          -------------------------------------------Exon 1.7  PDB: A:242-275          Exon 1.8  PDB: A:276-333 UniProt: 276-333                 -----------------------------------------------Exon 1.10          Exon 1.11  PDB: A:400-431        Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.4  PDB: A:87-132 UniProt: 87-132       -----------------------------------------------------------------Exon 1.6  PDB: A:198-242 UniProt: 198-242    ------------------------------------------------------------------------------------------Exon 1.9  PDB: A:333-381 UniProt: 333-381        -------------------------------------------------- Transcript 1 (2)
                 1d5t A  -2 HHMDEEYDVIVLGTGLTECILSGIMSVNGKKVLHMDRNPYYGGESSSITPLEELYKRFQLLEGPPETMGRGRDWNVDLIPKFLMANGQLVKMLLYTEVTRYLDFKVVEGSFVYKGGKIYKVPSTETEALASNLMGMFEKRRFRKFLVFVANFDENDPKTFEGVDPQNTSMRDVYRKFDLGQDVIDFTGHALALYRTDDYLDQPCLETINRIKLYSESLARYGKSPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPVDDIIMENGKVVGVKSEGEVARCKQLICDPSYVPDRVRKAGQVIRIICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISYAHNVAAQGKYIAIASTTVETTDPEKEVEPALGLLEPIDQKFVAISDLYEPIDDGSESQVFCSCSYDATTHFETTCNDIKDIYKRMAGSAFDF 431
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428   
                             ||                                                                                                                                                                                                                                                                                                                                                                                                                                              
                            -1|                                                                                                                                                                                                                                                                                                                                                                                                                                              
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                              

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D5T)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GDIA_BOVIN | P21856)
molecular function
    GO:0005092    GDP-dissociation inhibitor activity    Prevents the dissociation of GDP from a GTPase, thereby preventing GTP from binding.
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0005093    Rab GDP-dissociation inhibitor activity    Prevents the dissociation of GDP from the small GTPase Rab, thereby preventing GTP from binding.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0032482    Rab protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Rab family of proteins switching to a GTP-bound active state.
    GO:0050771    negative regulation of axonogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of axonogenesis.
    GO:0090315    negative regulation of protein targeting to membrane    Any process that decreases the frequency, rate or extent of the process of directing proteins towards a membrane, usually using signals contained within the protein.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:374 - Pro A:375   [ RasMol ]  
    Thr A:47 - Pro A:48   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1d5t
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GDIA_BOVIN | P21856
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  GDIA_BOVIN | P21856
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GDIA_BOVIN | P218561gnd 1lv0

(-) Related Entries Specified in the PDB File

1gnd GDI AT 1.81 ANGSTROM RESOLUTION