Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MYO5B GLOBULAR TAIL DOMAIN IN COMPLEX WITH ACTIVE RAB11A
 
Authors :  O. Pylypenko, W. Attanda, C. Gauquelin, A. Houdusse
Date :  29 Jul 13  (Deposition) - 20 Nov 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dil, Protein Transport-Contractile Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Pylypenko, W. Attanda, C. Gauquelin, M. Lahmani, D. Coulibaly, B. Baron, S. Hoos, M. A. Titus, P. England, A. M. Houdusse
Structural Basis Of Myosin V Rab Gtpase-Dependent Cargo Recognition.
Proc. Natl. Acad. Sci. Usa V. 110 20443 2013
PubMed-ID: 24248336  |  Reference-DOI: 10.1073/PNAS.1314329110

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-11A
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentDILUTE DOMAIN RESIDUES 1456-1848
    GeneRAB11A, RAB11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRAB-11, YL8
 
Molecule 2 - UNCONVENTIONAL MYOSIN-VB
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 1-177
    GeneMYO5B, KIAA1119
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1BEF2Ligand/IonBERYLLIUM TRIFLUORIDE ION
2GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3GOL1Ligand/IonGLYCEROL
4MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1BEF1Ligand/IonBERYLLIUM TRIFLUORIDE ION
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3GOL1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BEF1Ligand/IonBERYLLIUM TRIFLUORIDE ION
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3GOL-1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:25 , THR A:43 , BEF A:202 , GDP A:203 , HOH A:303 , HOH A:311BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWARESER A:20 , LYS A:24 , THR A:43 , GLY A:69 , MG A:201 , GDP A:203 , HOH A:303 , HOH A:311 , HOH A:320 , HOH A:433BINDING SITE FOR RESIDUE BEF A 202
3AC3SOFTWAREGLY A:21 , VAL A:22 , GLY A:23 , LYS A:24 , SER A:25 , ASN A:26 , PHE A:36 , ASN A:37 , LEU A:38 , SER A:40 , ASN A:124 , LYS A:125 , ASP A:127 , SER A:154 , ALA A:155 , LEU A:156 , MG A:201 , BEF A:202 , HOH A:303 , HOH A:311 , HOH A:361 , HOH A:386BINDING SITE FOR RESIDUE GDP A 203
4AC4SOFTWAREARG A:74 , TRP A:105 , GLU A:108 , HOH A:441BINDING SITE FOR RESIDUE GOL A 204
5AC5SOFTWARESER C:25 , THR C:43 , BEF C:202 , GDP C:203 , HOH C:336 , HOH C:339BINDING SITE FOR RESIDUE MG C 201
6AC6SOFTWARESER C:20 , LYS C:24 , SER C:42 , THR C:43 , GLY C:69 , MG C:201 , GDP C:203 , HOH C:305 , HOH C:336BINDING SITE FOR RESIDUE BEF C 202
7AC7SOFTWAREGLY C:21 , VAL C:22 , GLY C:23 , LYS C:24 , SER C:25 , ASN C:26 , PHE C:36 , ASN C:37 , LEU C:38 , SER C:40 , ASN C:124 , LYS C:125 , ASP C:127 , LEU C:128 , SER C:154 , ALA C:155 , LEU C:156 , MG C:201 , BEF C:202 , HOH C:307 , HOH C:320 , HOH C:336 , HOH C:339BINDING SITE FOR RESIDUE GDP C 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LX0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LX0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LX0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LX0)

(-) Exons   (0, 0)

(no "Exon" information available for 4LX0)

(-) 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:171
                                                                                                                                                                                                            
               SCOP domains d4lx0a_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhh..hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lx0 A    7 EYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVS  177
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176 

Chain B from PDB  Type:PROTEIN  Length:382
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eee.hhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhh..........hhhhhhhhhhhh............................hhhhh..hhhhh....eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lx0 B 1447 LYFQGAMQVTVQRKEKDFQGMLEYHKEDEALLIRNLVTDLKPQMLSGTVPCLPAYILYMCIRHADYTNDDLKVHSLLTSTINGIKKVLKKHNDDFEMTSFWLSNTCRLLHCLKQYSGDEGFMTQNTAKQNEHCLKNFDLTEYRQVLSDLSIQIYQQLIKIAEGVLQPMIVSAMLENESIQGLSNSYCLEAIIRQMNAFHTVMCDQGLDPEIILQVFKQLFYMINAVTLNNLLLRKDVCSWSTGMQLRYNISQLEEWLRGRNLHQSGAVQTMEPLIQAAQLLQLKKKTQEDAEAICSLCTSLSTQQIVKILNLYTPLNEFEERVTVAFIRTIQAQLQERNDPQQLLLDAKHMFPVLFPFNPSSLTMDSIHIPACLNLEFLNEV 1848
                                 |1458      1468      1478      1488      1498      1508      1518      1528      1538      1548      1558      1568      1578      1588      1598      1608      1618      1628  ||  1656      1666      1676      1686      1696      1706      1716      1726      1736      1746      1756      1766      1776      1786      1796      1806      1816      1826      1836      1846  
                              1452|                                                                                                                                                                            1631|                                                                                                                                                                                                      
                               1455                                                                                                                                                                             1650                                                                                                                                                                                                      

Chain C from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                            
               SCOP domains d4lx0c_ C: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhh..hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lx0 C    7 EYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVS  177
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176 

Chain D from PDB  Type:PROTEIN  Length:380
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.............ee.hhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhh..........hhhhhhhhhhhh..........................hhhhh..hhhhh....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lx0 D 1443 NLYFQGSMQVTVQRKEKDFQGMLEYHKEDEALLIRNLVTDLKPQMLSGTVPCLPAYILYMCIRHADYTNDDLKVHSLLTSTINGIKKVLKKHNDDFEMTSFWLSNTCRLLHCLKQYSGDEGFMTQNTAKQNEHCLKNFDLTEYRQVLSDLSIQIYQQLIKIAEGVLQPMIVSAMLENESIQGLNSYCLEAIIRQMNAFHTVMCDQGLDPEIILQVFKQLFYMINAVTLNNLLLRKDVCSWSTGMQLRYNISQLEEWLRGRNLHQSGAVQTMEPLIQAAQLLQLKKKTQEDAEAICSLCTSLSTQQIVKILNLYTPLNEFEERVTVAFIRTIQAQLQERNDQLLLDAKHMFPVLFPFNPSSLTMDSIHIPACLNLEFLNEV 1848
                                 |1457      1467      1477      1487      1497      1507      1517      1527      1537      1547      1557      1567      1577      1587      1597      1607      1617      1627  ||  1656      1666      1676      1686      1696      1706      1716      1726      1736      1746      1756      1766      1776      1786      1796      1806|     1818      1828      1838      1848
                              1448|                                                                                                                                                                            1630|                                                                                                                                                        1806|                                       
                               1454                                                                                                                                                                             1650                                                                                                                                                         1809                                       

   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  (0, 0)

(no "CATH Domain" information available for 4LX0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LX0)

(-) Gene Ontology  (66, 77)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    BEF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4lx0)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) 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
  4lx0
    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
  MYO5B_HUMAN | Q9ULV0
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  RB11A_HUMAN | P62491
    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
  MYO5B_HUMAN | Q9ULV0
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RB11A_HUMAN | P62491
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MYO5B_HUMAN | Q9ULV04j5m 4lnz 4lwz
        RB11A_HUMAN | P624911oiv 1oiw 1oix 1yzk 2d7c 2gzd 2gzh 2hv8 4c4p 4d0l 4d0m 4lwz 4uj3 4uj4 4uj5 5c46 5c4g 5euq 5ez5 5fbl 5fbq 5fbr 5fbv 5fbw 5jcz

(-) Related Entries Specified in the PDB File

4lwz 4lx1 4lx2