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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C3BOT-NAD-RALA COMPLEX REVEALS A NOVEL TYPE OF ACTION OF A BACTERIAL EXOENZYME
 
Authors :  A. Pautsch, M. Vogelsgesang, J. Trankle, C. Herrmann, K. Aktories
Date :  12 Jul 05  (Deposition) - 11 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Exoenzyme C3, Bacterial Adp-Ribosyltransferase, Ral, Rho, Gdp- Binding, Protein Binding-Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Pautsch, M. Vogelsgesang, J. Trankle, C. Herrmann, K. Aktories
Crystal Structure Of The C3Bot-Rala Complex Reveals A Novel Type Of Action Of A Bacterial Exoenzyme.
Embo J. V. 24 3670 2005
PubMed-ID: 16177825  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600813
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAL-A
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-2T
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneRALA, RAL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - MONO-ADP-RIBOSYLTRANSFERASE C3
    ChainsB
    EC Number2.4.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-2T
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneC3
    Organism ScientificCLOSTRIDIUM BOTULINUM D PHAGE
    Organism Taxid29342
    SynonymEXOENZYME C3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:28 , GDP A:500 , HOH A:508 , HOH A:519 , HOH A:526 , HOH A:593BINDING SITE FOR RESIDUE MG A 300
2AC2SOFTWAREGLY A:24 , VAL A:25 , GLY A:26 , LYS A:27 , SER A:28 , ALA A:29 , GLU A:41 , ASP A:42 , ASN A:127 , LYS A:128 , ASP A:130 , LEU A:131 , SER A:157 , ALA A:158 , LYS A:159 , MG A:300 , HOH A:504 , HOH A:507 , HOH A:508 , HOH A:519 , HOH A:523 , HOH A:526 , HOH A:579BINDING SITE FOR RESIDUE GDP A 500
3AC3SOFTWARETHR B:80 , ALA B:83 , SER B:84 , ASN B:87 , ARG B:91 , ARG B:128 , GLY B:129 , ASP B:130 , ASP B:131 , ALA B:133 , TYR B:134 , ARG B:167 , GLU B:169 , SER B:174 , THR B:175 , PHE B:183 , ARG B:186 , GLN B:212 , GLU B:214 , HOH B:414 , HOH B:424 , HOH B:461 , HOH B:498 , HOH B:499 , HOH B:500BINDING SITE FOR RESIDUE NAD B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A9K)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:181 -Asp A:182

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A9K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A9K)

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000000052571aENSE00001829077chr7:39663082-39663424343RALA_HUMAN-00--
1.3aENST000000052573aENSE00000832451chr7:39726230-39726380151RALA_HUMAN1-38381A:13-3826
1.4bENST000000052574bENSE00000679279chr7:39729981-39730189209RALA_HUMAN39-108701A:39-10870
1.5ENST000000052575ENSE00000679282chr7:39736284-39736458175RALA_HUMAN108-166591A:108-16659
1.8dENST000000052578dENSE00001270055chr7:39745722-397477232002RALA_HUMAN167-206401A:167-18216

(-) 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:170
 aligned with RALA_HUMAN | P11233 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:170
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182
           RALA_HUMAN    13 ALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTAGQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRAEQWNVNYVETSAKTRANVDKVFFDLMREIRARKMED 182
               SCOP domains d2a9ka_ A: Ras-related protein RalA                                                                                                                                        SCOP domains
               CATH domains 2a9kA00 A:13-182 P-loop containing nucleotide triphosphate hydrolases                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee......hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeehhhhhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:13-38   Exon 1.4b  PDB: A:39-108 UniProt: 39-108                              ----------------------------------------------------------Exon 1.8d        Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------Exon 1.5  PDB: A:108-166 UniProt: 108-166                  ---------------- Transcript 1 (2)
                 2a9k A  13 ALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTAGQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRAEQWNVNYVETSAKTRANVDKVFFDLMREIRARKMED 182
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain B from PDB  Type:PROTEIN  Length:207
 aligned with ARC3_CBDP | P15879 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:207
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       
            ARC3_CBDP    45 TYQEFTNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGVINGFPSNLIKQVELLDKSFNKMKTPENIMLFRGDDPAYLGTEFQNTLLNSNGTINKTAFEKAKAKFLNKDRLEYGYISTSLMNVSQFAGRPIITKFKVAKGSKAGYIDPISAFAGQLEMLLPRHSTYHIDDMRLSSDGKQIIITATMMGTAINPK 251
               SCOP domains d2a9kb_ B: Exoenzyme c3                                                                                                                                                                                         SCOP domains
               CATH domains 2a9kB00 B:45-251 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhh..........hhhhhhhhhhhhh..eeee...eeee....hhhhhh.eeeeeee......ee.hhhh......eeee...eeeeeeeeee......eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a9k B  45 TYQEFTNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGVINGFPSNLIKQVELLDKSFNKMKTPENIMLFRGDDPAYLGTEFQNTLLNSNGTINKTAFEKAKAKFLNKDRLEYGYISTSLMNVSQFAGRPIITKFKVAKGSKAGYIDPISAFAGQLEMLLPRHSTYHIDDMRLSSDGKQIIITATMMGTAINPK 251
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       

   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  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A9K)

(-) Gene Ontology  (40, 41)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RALA_HUMAN | P11233)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0031755    Edg-2 lysophosphatidic acid receptor binding    Interacting selectively and non-covalently with an Edg-2 lysophosphatidic acid receptor.
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0017022    myosin binding    Interacting selectively and non-covalently with any part of a myosin complex; myosins are any of a superfamily of molecular motor proteins that bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    GO:0031532    actin cytoskeleton reorganization    A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0000910    cytokinesis    The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:0061024    membrane organization    A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
    GO:0051665    membrane raft localization    Any process in which membrane rafts are transported to, or maintained in, a specific location. Membrane rafts are small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes.
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0051491    positive regulation of filopodium assembly    Any process that activates or increases the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
    GO:0017157    regulation of exocytosis    Any process that modulates the frequency, rate or extent of exocytosis.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0032154    cleavage furrow    The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    GO:0030139    endocytic vesicle    A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B   (ARC3_CBDP | P15879)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016763    transferase activity, transferring pentosyl groups    Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006471    protein ADP-ribosylation    The transfer, from NAD, of ADP-ribose to protein amino acids.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARC3_CBDP | P158791g24 1gze 1gzf 1uzi 2a78 2bov 2c89 2c8a 2c8b 2c8c 2c8d 2c8e 2c8f 2c8g 2c8h
        RALA_HUMAN | P112331uad 1zc3 1zc4 2a78 2bov

(-) Related Entries Specified in the PDB File

1g24 EXOENZYME C3, CLOSTRIDIUM BOTULINUM
1u8z RALA-GDP
1u90 RALA-GTP
1uad RALA-GPPNHP-SEC5
2a78 RALA-GDP-C3BOT COMPLEX
2bov RALA-GDP-C3BOT COMPLEX