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(-) Description

Title :  BETA PIX-SH3 COMPLEXED WITH A CBL-B PEPTIDE
 
Authors :  D. Jozic, N. Cardenes, Y. L. Deribe, G. Moncalian, D. Hoeller, Y. Groemping, I. Dikic, K. Rittinger, J. Bravo
Date :  03 Aug 05  (Deposition) - 11 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,D
Biol. Unit 1:  A,B,D  (2x)
Keywords :  Adaptor Proteins, Cin85, Pix/Cool, Cbl, Protein-Protein Interaction, X-Ray, Endocytosis, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Jozic, N. Cardenes, Y. L. Deribe, G. Moncalian, D. Hoeller, Y. Groemping, I. Dikic, K. Rittinger, J. Bravo
Cbl Promotes Clustering Of Endocytic Adaptor Proteins.
Nat. Struct. Mol. Biol. V. 12 972 2005
PubMed-ID: 16228008  |  Reference-DOI: 10.1038/NSMB1000
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePGEX
    FragmentBETA-PIX SH3A
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymPAK-INTERACTING EXCHANGE FACTOR BETA, BETA-PIX
 
Molecule 2 - 8-RESIDUE PEPTIDE FROM A SIGNAL TRANSDUCTION PROTEIN CBL-B
    ChainsD
    EngineeredYES
    FragmentRESIDUES 904-911
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE CAN BE NATURALLY FOUND IN HOMO SAPIENS (HUMAN)CBL-B
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABD
Biological Unit 1 (2x)ABD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2AK5)

(-) Sites  (0, 0)

(no "Site" information available for 2AK5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AK5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro B:65 -Ser B:66

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AK5)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.ARHG7_RAT6-65
 
  2A:6-65
B:6-65
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.ARHG7_RAT6-65
 
  4A:6-65
B:6-65

(-) Exons   (3, 5)

Asymmetric Unit (3, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000179471ENSRNOE00000277809chr16:82635476-82635312165ARHG7_RAT1-55552A:6-55
B:3-55
50
53
1.2bENSRNOT000000179472bENSRNOE00000350383chr16:82603278-8260319287ARHG7_RAT56-84292A:56-65
B:56-66
10
11
1.3ENSRNOT000000179473ENSRNOE00000342668chr16:82581873-8258178985ARHG7_RAT85-113290--
1.4ENSRNOT000000179474ENSRNOE00000338153chr16:82580441-82580311131ARHG7_RAT113-156440--
1.5ENSRNOT000000179475ENSRNOE00000299788chr16:82577209-82577008202ARHG7_RAT157-224680--
1.6ENSRNOT000000179476ENSRNOE00000123133chr16:82567614-8256752689ARHG7_RAT224-253300--
1.7ENSRNOT000000179477ENSRNOE00000128814chr16:82560132-8256003895ARHG7_RAT254-285320--
1.8ENSRNOT000000179478ENSRNOE00000123260chr16:82559813-8255971896ARHG7_RAT285-317330--
1.9ENSRNOT000000179479ENSRNOE00000123318chr16:82554748-82554626123ARHG7_RAT317-358420--
1.10ENSRNOT0000001794710ENSRNOE00000123372chr16:82550615-82550477139ARHG7_RAT358-404470--
1.11ENSRNOT0000001794711ENSRNOE00000123438chr16:82549894-8254983560ARHG7_RAT405-424200--
1.12ENSRNOT0000001794712ENSRNOE00000129046chr16:82549272-82549126147ARHG7_RAT425-473490--
1.13ENSRNOT0000001794713ENSRNOE00000123551chr16:82546857-8254677187ARHG7_RAT474-502290--
1.14ENSRNOT0000001794714ENSRNOE00000123615chr16:82541663-8254158579ARHG7_RAT503-529270--
1.15ENSRNOT0000001794715ENSRNOE00000123672chr16:82541425-82541286140ARHG7_RAT529-575470--
1.16ENSRNOT0000001794716ENSRNOE00000127997chr16:82538706-82538482225ARHG7_RAT576-650750--
1.17ENSRNOT0000001794717ENSRNOE00000123730chr16:82536831-8253673894ARHG7_RAT651-682320--
1.18aENSRNOT0000001794718aENSRNOE00000123790chr16:82534037-8253394890ARHG7_RAT682-712310--
1.21ENSRNOT0000001794721ENSRNOE00000123923chr16:82524702-82524603100ARHG7_RAT712-745340--
1.22ENSRNOT0000001794722ENSRNOE00000124026chr16:82524361-8252430755ARHG7_RAT745-763190--
1.23ENSRNOT0000001794723ENSRNOE00000389941chr16:82523402-825212262177ARHG7_RAT764-803400--

2.2dENST000002641222dENSE00001340691chr3:105587887-105587580308CBLB_HUMAN-00--
2.3ENST000002641223ENSE00002109512chr3:105586435-105586254182CBLB_HUMAN1-56560--
2.4ENST000002641224ENSE00002192869chr3:105572508-105572258251CBLB_HUMAN57-140840--
2.5ENST000002641225ENSE00001686511chr3:105495386-105495240147CBLB_HUMAN140-189500--
2.6ENST000002641226ENSE00001628201chr3:105470462-105470306157CBLB_HUMAN189-241530--
2.7ENST000002641227ENSE00001692048chr3:105464882-105464761122CBLB_HUMAN242-282410--
2.8ENST000002641228ENSE00001696958chr3:105459475-105459338138CBLB_HUMAN282-328470--
2.9ENST000002641229ENSE00001616258chr3:105456102-10545601588CBLB_HUMAN328-357300--
2.10ENST0000026412210ENSE00001694160chr3:105452984-105452853132CBLB_HUMAN358-401440--
2.11ENST0000026412211ENSE00001654827chr3:105439094-105438891204CBLB_HUMAN402-469680--
2.12ENST0000026412212ENSE00001767402chr3:105423017-105422832186CBLB_HUMAN470-531620--
2.13aENST0000026412213aENSE00001607504chr3:105421303-105420938366CBLB_HUMAN532-6531220--
2.14ENST0000026412214ENSE00000774846chr3:105412432-10541233895CBLB_HUMAN654-685320--
2.15ENST0000026412215ENSE00000774845chr3:105404310-105404164147CBLB_HUMAN685-734500--
2.16bENST0000026412216bENSE00000774844chr3:105400662-10540056895CBLB_HUMAN734-766330--
2.16dENST0000026412216dENSE00000774843chr3:105400454-105400323132CBLB_HUMAN766-810450--
2.17ENST0000026412217ENSE00000774842chr3:105397415-105397275141CBLB_HUMAN810-857480--
2.18bENST0000026412218bENSE00000774841chr3:105389196-105389077120CBLB_HUMAN857-897410--
2.19dENST0000026412219dENSE00001755904chr3:105378073-1053743053769CBLB_HUMAN897-982861D:904-9118

(-) 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:60
 aligned with ARHG7_RAT | O55043 from UniProtKB/Swiss-Prot  Length:646

    Alignment length:60
                                    15        25        35        45        55        65
            ARHG7_RAT     6 NSQLVVRAKFNFQQTNEDELSFSKGDVIHVTRVEEGGWWEGTHNGRTGWFPSNYVREIKP  65
               SCOP domains d2ak5a_ A: automated matches                                 SCOP domains
               CATH domains 2ak5A00 A:6-65 SH3 Domains                                   CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..................eeeeee.....eeeeee..eeeeee...eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE SH3  PDB: A:6-65 UniProt: 6-65                               PROSITE
               Transcript 1 Exon 1.1  PDB: A:6-55 UniProt: 1-55 [INCOMPLETE]  Exon 1.2b  Transcript 1
                 2ak5 A   6 NSQLVVRAKFNFQQTNEDELSFSKGDVIHVTRVEEGGWWEGTHNGRTGWFPSNYVREIKP  65
                                    15        25        35        45        55        65

Chain B from PDB  Type:PROTEIN  Length:64
 aligned with ARHG7_RAT | O55043 from UniProtKB/Swiss-Prot  Length:646

    Alignment length:64
                                    12        22        32        42        52        62    
            ARHG7_RAT     3 DNANSQLVVRAKFNFQQTNEDELSFSKGDVIHVTRVEEGGWWEGTHNGRTGWFPSNYVREIKPS  66
               SCOP domains d2ak5b_ B: automated matches                                     SCOP domains
               CATH domains 2ak5B00 B:3-66 SH3 Domains                                       CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee..................eeeeee.....eeeeee..eeeeee...eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SH3  PDB: B:6-65 UniProt: 6-65                              - PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-55 UniProt: 1-55 [INCOMPLETE]     Exon 1.2b   Transcript 1
                 2ak5 B   3 GSANSQLVVRAKFNFQQTNEDELSFSKGDVIHVTRVEEGGWWEGTHNGRTGWFPSNYVREIKPS  66
                                    12        22        32        42        52        62    

Chain D from PDB  Type:PROTEIN  Length:8
 aligned with CBLB_HUMAN | Q13191 from UniProtKB/Swiss-Prot  Length:982

    Alignment length:8
           CBLB_HUMAN   904 RPPKPRPR 911
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
               Transcript 2 2.19d    Transcript 2
                 2ak5 D 904 RPPKPRPR 911

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AK5)

(-) Gene Ontology  (40, 43)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ARHG7_RAT | O55043)
molecular function
    GO:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0043615    astrocyte cell migration    The orderly movement of an astrocyte, a class of large neuroglial (macroglial) cells in the central nervous system, the largest and most numerous neuroglial cells in the brain and spinal cord.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0030032    lamellipodium assembly    Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    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:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

Chain D   (CBLB_HUMAN | Q13191)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0001784    phosphotyrosine residue binding    Interacting selectively and non-covalently with a phosphorylated tyrosine residue within a protein.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006607    NLS-bearing protein import into nucleus    The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0023051    regulation of signaling    Any process that modulates the frequency, rate or extent of a signaling process.
    GO:0009629    response to gravity    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gravitational stimulus.
    GO:0009725    response to hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
    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.
cellular component
    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:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARHG7_RAT | O550432df6 2g6f 2p4r 2w6b 3l4f 3qjn
        CBLB_HUMAN | Q131912bz8 2do6 2j6f 2jnh 2ldr 2ooa 2oob 3pfv 3vgo 3zni

(-) Related Entries Specified in the PDB File

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