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(-) Description

Title :  HUMAN NEURONAL RAB6B IN THREE INTERMEDIATE FORMS
 
Authors :  F. M. Vellieux, S. Tcherniuk, I. Garcia-Saez, F. Kozielski
Date :  26 Jan 07  (Deposition) - 29 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Human Neuron, Rab6B, Gdp Mg No3 Complex, Gdp Mg Complex, Gdp Complex, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. M. Vellieux, S. Tcherniuk, I. Garcia-Saez, F. Kozielski
3D Structure Of Human Neuronal Rab6B In Three Intermediate Forms
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-6B
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES IN DATABASE 13-174
    GeneRAB6B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRAB6B

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1GDP3Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3NO31Ligand/IonNITRATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3NO31Ligand/IonNITRATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3NO3-1Ligand/IonNITRATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3NO3-1Ligand/IonNITRATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:22 , SER A:23 , LYS A:26 , TYR A:42 , THR A:45 , ALA A:70 , GLY A:71 , GDP A:602 , MG A:603 , HOH A:736BINDING SITE FOR RESIDUE NO3 A 601
2AC2SOFTWARETHR A:27 , THR A:45 , NO3 A:601 , GDP A:602 , HOH A:608 , HOH A:609BINDING SITE FOR RESIDUE MG A 603
3AC3SOFTWARETHR B:27 , GDP B:702 , HOH B:710 , HOH B:711 , HOH B:767 , HOH B:768BINDING SITE FOR RESIDUE MG B 703
4AC4SOFTWARESER A:23 , VAL A:24 , GLY A:25 , LYS A:26 , THR A:27 , SER A:28 , PHE A:38 , ASP A:39 , ASN A:40 , TYR A:42 , ASN A:126 , LYS A:127 , ASP A:129 , LEU A:130 , SER A:156 , ALA A:157 , LYS A:158 , NO3 A:601 , MG A:603 , HOH A:608 , HOH A:609 , HOH A:612 , HOH A:719 , THR B:113BINDING SITE FOR RESIDUE GDP A 602
5AC5SOFTWARESER B:23 , VAL B:24 , GLY B:25 , LYS B:26 , THR B:27 , SER B:28 , PHE B:38 , ASP B:39 , ASN B:126 , LYS B:127 , ASP B:129 , LEU B:130 , SER B:156 , ALA B:157 , LYS B:158 , MG B:703 , HOH B:709 , HOH B:711 , HOH B:731 , HOH B:767BINDING SITE FOR RESIDUE GDP B 702
6AC6SOFTWARESER C:23 , VAL C:24 , GLY C:25 , LYS C:26 , THR C:27 , SER C:28 , PHE C:38 , ALA C:70 , ARG C:112 , THR C:113 , GLU C:114 , ARG C:115 , GLY C:116 , ASN C:126 , LYS C:127 , ASP C:129 , LEU C:130 , SER C:156 , ALA C:157 , LYS C:158 , HOH C:862 , HOH C:869 , HOH C:882 , HOH C:902BINDING SITE FOR RESIDUE GDP C 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E9S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2E9S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E9S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E9S)

(-) Exons   (7, 21)

Asymmetric Unit (7, 21)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002852081bENSE00001829040chr3:133614660-133614241420RAB6B_HUMAN1-24243A:13-24
B:13-24
C:14-24
12
12
11
1.4bENST000002852084bENSE00001078189chr3:133583486-13358342859RAB6B_HUMAN24-43203A:24-43
B:24-40
C:24-41
20
17
18
1.5ENST000002852085ENSE00001018393chr3:133560507-13356045454RAB6B_HUMAN44-61183A:44-61
B:49-61
C:50-61
18
13
12
1.6bENST000002852086bENSE00001696426chr3:133560234-133560129106RAB6B_HUMAN62-97363A:62-97
B:62-97 (gaps)
C:62-97 (gaps)
36
36
36
1.7ENST000002852087ENSE00002178939chr3:133558461-133558350112RAB6B_HUMAN97-134383A:97-134
B:97-134
C:97-134
38
38
38
1.8bENST000002852088bENSE00001078188chr3:133557103-13355701094RAB6B_HUMAN134-165323A:134-165
B:134-165
C:134-165
32
32
32
1.9ENST000002852089ENSE00001078185chr3:133553485-13355341967RAB6B_HUMAN166-188233A:166-176 (gaps)
B:166-176 (gaps)
C:166-176 (gaps)
13
13
13
1.10bENST0000028520810bENSE00001409669chr3:133547696-1335430834614RAB6B_HUMAN188-208210--

(-) 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:164
 aligned with RAB6B_HUMAN | Q9NRW1 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:166
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172      
          RAB6B_HUMAN    13 KFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNLNSFQQTSKWIDDVRTERGSDVIIMLVGNKTDLADKRQITIEEGEQRAKELSVMFIETSAKTGYNVKQLFRRVASALPGME 178
               SCOP domains d2e9sa_ A: automated matches                                                                                                                                           SCOP domains
               CATH domains 2e9sA00 A:13-176 P-loop containing nucleotide triphosphate hydrolases                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh--hh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b   -------------------Exon 1.5          Exon 1.6b  PDB: A:62-97             ------------------------------------Exon 1.8b  PDB: A:134-165       Exon 1.9      Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.4b           -----------------------------------------------------Exon 1.7  PDB: A:97-134               -------------------------------------------- Transcript 1 (2)
                 2e9s A  13 KFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNLNSFQQTSKWIDDVRTERGSDVIIMLVGNKTDLADKRQITIEEGEQRAKELSVMFIETSAKTGYNVKQLFRRVASAL--LE 176
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 |  | 
                                                                                                                                                                                           174  | 
                                                                                                                                                                                              175 

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with RAB6B_HUMAN | Q9NRW1 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:166
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172      
          RAB6B_HUMAN    13 KFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNLNSFQQTSKWIDDVRTERGSDVIIMLVGNKTDLADKRQITIEEGEQRAKELSVMFIETSAKTGYNVKQLFRRVASALPGME 178
               SCOP domains d2e9sb_ B: automated matches                                                                                                                                           SCOP domains
               CATH domains 2e9sB00 B:13-176 P-loop cont        aining nucleotide trip      hosphate hydrolases                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh....--------...eeeeee..eeeeeeee...------.hhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhh--hh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b   -------------------Exon 1.5          Exon 1.6b  PDB: B:62-97 (gaps)      ------------------------------------Exon 1.8b  PDB: B:134-165       Exon 1.9      Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.4b           -----------------------------------------------------Exon 1.7  PDB: B:97-134               -------------------------------------------- Transcript 1 (2)
                 2e9s B  13 KFKLVFLGEQSVGKTSLITRFMYDSFDN--------DFLSKTMYLEDRTVRLQLWDTA------SLIPSYIRDSTVAVVVYDITNLNSFQQTSKWIDDVRTERGSDVIIMLVGNKTDLADKRQITIEEGEQRAKELSVMFIETSAKTGYNVKQLFRRVASAL--LE 176
                                    22        32       | -      | 52        62       | -    |   82        92       102       112       122       132       142       152       162       172 |  | 
                                                      40       49                   70     77                                                                                              174  | 
                                                                                                                                                                                              175 

Chain C from PDB  Type:PROTEIN  Length:154
 aligned with RAB6B_HUMAN | Q9NRW1 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:165
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173     
          RAB6B_HUMAN    14 FKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNLNSFQQTSKWIDDVRTERGSDVIIMLVGNKTDLADKRQITIEEGEQRAKELSVMFIETSAKTGYNVKQLFRRVASALPGME 178
               SCOP domains d2e9sc_ C: automated matches                                                                                                                                          SCOP domains
               CATH domains 2e9sC00 C:14-176 P-loop cont        aining nucleotide triphosp hate hydrolases                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhh.....--------.eeeeeee..eeeeeeeee.......-.hhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhh..hhhhhhhhhhhh..eeeee......hhhhhhhhhhhhh--hh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  -------------------Exon 1.5          Exon 1.6b  PDB: C:62-97 (gaps)      ------------------------------------Exon 1.8b  PDB: C:134-165       Exon 1.9      Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.4b           -----------------------------------------------------Exon 1.7  PDB: C:97-134               -------------------------------------------- Transcript 1 (2)
                 2e9s C  14 FKLVFLGEQSVGKTSLITRFMYDSFDNT--------FLSKTMYLEDRTVRLQLWDTAGQERF-SLIPSYIRDSTVAVVVYDITNLNSFQQTSKWIDDVRTERGSDVIIMLVGNKTDLADKRQITIEEGEQRAKELSVMFIETSAKTGYNVKQLFRRVASAL--LE 176
                                    23        33       | -      | 53        63        73 | |    83        93       103       113       123       133       143       153       163       173|  | 
                                                      41       50                       75 |                                                                                              174  | 
                                                                                          77                                                                                                 175 

   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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E9S)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (RAB6B_HUMAN | Q9NRW1)
molecular function
    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:0031489    myosin V binding    Interacting selectively and non-covalently with a class V myosin; myosin V is a dimeric molecule involved in intracellular transport.
    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).
biological process
    GO:0006891    intra-Golgi vesicle-mediated transport    The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).
    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:0042147    retrograde transport, endosome to Golgi    The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport.
    GO:0006890    retrograde vesicle-mediated transport, Golgi to ER    The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
    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: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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0005793    endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAB6B_HUMAN | Q9NRW12fe4 2ffq

(-) Related Entries Specified in the PDB File

2fe4 RAB6B-GDP
2ffq RAB6B-GTP GAMMA-S