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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF GGA1-GAE
 
Authors :  M. Inoue, T. Shiba, Y. Yamada, K. Ihara, M. Kawasaki, R. Kato, K. Nakayam S. Wakatsuki
Date :  21 Aug 06  (Deposition) - 17 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  C,D  (1x)
Biol. Unit 6:  A,B  (1x)
Keywords :  Ig Fold, Adaptin, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Inoue, T. Shiba, K. Ihara, Y. Yamada, S. Hirano, H. Kamikubo, M. Kataoka, M. Kawasaki, R. Kato, K. Nakayama, S. Wakatsuki
Molecular Basis For Autoregulatory Interaction Between Gae Domain And Hinge Region Of Gga1
Traffic V. 8 904 2007
PubMed-ID: 17506864  |  Reference-DOI: 10.1111/J.1600-0854.2007.00577.X

(-) Compounds

Molecule 1 - ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX4T-2
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentGAE DOMAIN, RESIDUES 507-639
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGOLGI-LOCALIZED, GAMMA EAR-CONTAINING, ARF-BINDING PROTEIN 1, GAMMA-ADAPTIN RELATED PROTEIN 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D
Biological Unit 5 (1x)  CD
Biological Unit 6 (1x)AB  

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2DWY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DWY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAEPS50180 Gamma-adaptin ear (GAE) domain profile.GGA1_HUMAN510-631  1C:510-631
Biological Unit 1 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAEPS50180 Gamma-adaptin ear (GAE) domain profile.GGA1_HUMAN510-631  0-
Biological Unit 2 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAEPS50180 Gamma-adaptin ear (GAE) domain profile.GGA1_HUMAN510-631  0-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAEPS50180 Gamma-adaptin ear (GAE) domain profile.GGA1_HUMAN510-631  1C:510-631
Biological Unit 4 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAEPS50180 Gamma-adaptin ear (GAE) domain profile.GGA1_HUMAN510-631  0-
Biological Unit 5 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAEPS50180 Gamma-adaptin ear (GAE) domain profile.GGA1_HUMAN510-631  1C:510-631
Biological Unit 6 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAEPS50180 Gamma-adaptin ear (GAE) domain profile.GGA1_HUMAN510-631  0-

(-) Exons   (4, 13)

Asymmetric Unit (4, 13)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003436321aENSE00001813421chr22:38004482-38004910429GGA1_HUMAN1-15150--
1.7cENST000003436327cENSE00002140158chr22:38010197-3801028185GGA1_HUMAN15-43290--
1.8aENST000003436328aENSE00001612880chr22:38012929-3801300476GGA1_HUMAN43-68260--
1.9cENST000003436329cENSE00001683976chr22:38014455-3801455399GGA1_HUMAN69-101330--
1.10fENST0000034363210fENSE00000880168chr22:38016245-38016368124GGA1_HUMAN102-143420--
1.11bENST0000034363211bENSE00000880169chr22:38016820-38016920101GGA1_HUMAN143-176340--
1.12cENST0000034363212cENSE00000653934chr22:38017623-3801770381GGA1_HUMAN177-203270--
1.13ENST0000034363213ENSE00000880172chr22:38019334-38019474141GGA1_HUMAN204-250470--
1.14bENST0000034363214bENSE00000880174chr22:38019559-3801964082GGA1_HUMAN251-278280--
1.14eENST0000034363214eENSE00001286815chr22:38020976-38021083108GGA1_HUMAN278-314370--
1.15aENST0000034363215aENSE00000653938chr22:38021804-38021956153GGA1_HUMAN314-365520--
1.16ENST0000034363216ENSE00000653944chr22:38025469-3802553365GGA1_HUMAN365-386220--
1.17aENST0000034363217aENSE00000653945chr22:38026005-38026177173GGA1_HUMAN387-444580--
1.18bENST0000034363218bENSE00000653946chr22:38026910-38027106197GGA1_HUMAN444-510671-
-
C:507-510
-
-
-
4
-
1.19ENST0000034363219ENSE00000653947chr22:38028003-38028172170GGA1_HUMAN510-566574A:511-566
B:511-566
C:510-566 (gaps)
D:511-566
56
56
57
56
1.20ENST0000034363220ENSE00000653948chr22:38028412-38028522111GGA1_HUMAN567-603374A:567-603
B:567-603
C:567-603
D:567-603
37
37
37
37
1.21dENST0000034363221dENSE00001823052chr22:38028608-38029571964GGA1_HUMAN604-639364A:604-639
B:604-636
C:604-639
D:604-639
36
33
36
36

(-) 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:129
 aligned with GGA1_HUMAN | Q9UJY5 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:129
                                   520       530       540       550       560       570       580       590       600       610       620       630         
           GGA1_HUMAN   511 NILPVTVYDQHGFRILFHFARDPLPGRSDVLVVVVSMLSTAPQPIRNIVFQSAVPKVMKVKLQPPSGTELPAFNPIVHPSAITQVLLLANPQKEKVRLRYKLTFTMGDQTYNEMGDVDQFPPPETWGSL 639
               SCOP domains d2dwya_ A: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeee.........eeeeeeeeee......eeeeeeee...........................eeeeeeeee........eeeeeeeee..eeeeeeeee....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GAE  PDB: - UniProt: 510-631                                                                                             -------- PROSITE
           Transcript 1 (1) --------------------------------------------------------Exon 1.20  PDB: A:567-603            Exon 1.21d  PDB: A:604-639           Transcript 1 (1)
           Transcript 1 (2) Exon 1.19  PDB: A:511-566 UniProt: 510-566 [INCOMPLETE] ------------------------------------------------------------------------- Transcript 1 (2)
                 2dwy A 511 NILPVTVYDQHGFRILFHFARDPLPGRSDVLVVVVSMLSTAPQPIRNIVFQSAVPKVMKVKLQPPSGTELPAFNPIVHPSAITQVLLLANPQKEKVRLRYKLTFTMGDQTYNEMGDVDQFPPPETWGSL 639
                                   520       530       540       550       560       570       580       590       600       610       620       630         

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with GGA1_HUMAN | Q9UJY5 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:126
                                   520       530       540       550       560       570       580       590       600       610       620       630      
           GGA1_HUMAN   511 NILPVTVYDQHGFRILFHFARDPLPGRSDVLVVVVSMLSTAPQPIRNIVFQSAVPKVMKVKLQPPSGTELPAFNPIVHPSAITQVLLLANPQKEKVRLRYKLTFTMGDQTYNEMGDVDQFPPPETW 636
               SCOP domains d2dwyb_ B: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..eeeeeee..........eeeeeeeeee.....eeeeeeeee.....eeee...................eeeeeeee........eeeeeeeee..eeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE GAE  PDB: - UniProt: 510-631                                                                                             ----- PROSITE
           Transcript 1 (1) --------------------------------------------------------Exon 1.20  PDB: B:567-603            Exon 1.21d  PDB: B:604-636        Transcript 1 (1)
           Transcript 1 (2) Exon 1.19  PDB: B:511-566 UniProt: 510-566 [INCOMPLETE] ---------------------------------------------------------------------- Transcript 1 (2)
                 2dwy B 511 NILPVTVYDQHGFRILFHFARDPLPGRSDVLVVVVSMLSTAPQPIRNIVFQSAVPKVMKVKLQPPSGTELPAFNPIVHPSAITQVLLLANPQKEKVRLRYKLTFTMGDQTYNEMGDVDQFPPPETW 636
                                   520       530       540       550       560       570       580       590       600       610       620       630      

Chain C from PDB  Type:PROTEIN  Length:132
 aligned with GGA1_HUMAN | Q9UJY5 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:133
                                   516       526       536       546       556       566       576       586       596       606       616       626       636   
           GGA1_HUMAN   507 IKPSNILPVTVYDQHGFRILFHFARDPLPGRSDVLVVVVSMLSTAPQPIRNIVFQSAVPKVMKVKLQPPSGTELPAFNPIVHPSAITQVLLLANPQKEKVRLRYKLTFTMGDQTYNEMGDVDQFPPPETWGSL 639
               SCOP domains d2dw yc_ C: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....-...eeeeee..eeeeeeee.........eeeeeeeeee.....eeeeeeeee.....eeee...................eeeeeeee........eeeeeeeee..eeeeeeeee....hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---GAE  PDB: C:510-631 UniProt: 510-631                                                                                      -------- PROSITE
           Transcript 1 (1) 1.18--------------------------------------------------------Exon 1.20  PDB: C:567-603            Exon 1.21d  PDB: C:604-639           Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.19  PDB: C:510-566 (gaps) UniProt: 510-566        ------------------------------------------------------------------------- Transcript 1 (2)
                 2dwy C 507 IKPS-ILPVTVYDQHGFRILFHFARDPLPGRSDVLVVVVSMLSTAPQPIRNIVFQSAVPKVMKVKLQPPSGTELPAFNPIVHPSAITQVLLLANPQKEKVRLRYKLTFTMGDQTYNEMGDVDQFPPPETWGSL 639
                               | | 516       526       536       546       556       566       576       586       596       606       616       626       636   
                             510 |                                                                                                                               
                               512                                                                                                                               

Chain D from PDB  Type:PROTEIN  Length:129
 aligned with GGA1_HUMAN | Q9UJY5 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:129
                                   520       530       540       550       560       570       580       590       600       610       620       630         
           GGA1_HUMAN   511 NILPVTVYDQHGFRILFHFARDPLPGRSDVLVVVVSMLSTAPQPIRNIVFQSAVPKVMKVKLQPPSGTELPAFNPIVHPSAITQVLLLANPQKEKVRLRYKLTFTMGDQTYNEMGDVDQFPPPETWGSL 639
               SCOP domains d2dwyd_ D: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeee.........eeeeeeeeee.....eeeeeeeeeee...eeee..................eeeeeeeee........eeeeeeeee..eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GAE  PDB: - UniProt: 510-631                                                                                             -------- PROSITE
           Transcript 1 (1) --------------------------------------------------------Exon 1.20  PDB: D:567-603            Exon 1.21d  PDB: D:604-639           Transcript 1 (1)
           Transcript 1 (2) Exon 1.19  PDB: D:511-566 UniProt: 510-566 [INCOMPLETE] ------------------------------------------------------------------------- Transcript 1 (2)
                 2dwy D 511 NILPVTVYDQHGFRILFHFARDPLPGRSDVLVVVVSMLSTAPQPIRNIVFQSAVPKVMKVKLQPPSGTELPAFNPIVHPSAITQVLLLANPQKEKVRLRYKLTFTMGDQTYNEMGDVDQFPPPETWGSL 639
                                   520       530       540       550       560       570       580       590       600       610       620       630         

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DWY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (GGA1_HUMAN | Q9UJY5)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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).
biological process
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    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:1901998    toxin transport    The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
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:0030131    clathrin adaptor complex    A membrane coat adaptor complex that links clathrin to a membrane.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GGA1_HUMAN | Q9UJY51j2j 1jwf 1jwg 1na8 1naf 1nwm 1o3x 1om9 1oxz 1py1 1ujj 1ujk 1x79 2dwx 3g2s 3g2t 3g2u 3g2v 3g2w

(-) Related Entries Specified in the PDB File

2dwx