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
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)

(-) Description

Title :  NEAR-ATOMIC RESOLUTION CRYO-EM RECONSTRUCTION OF PELORUSIDE-STABILIZED MICROTUBULE
 
Authors :  E. H. Kellogg, E. Nogales
Date :  10 Aug 16  (Deposition) - 01 Feb 17  (Release) - 08 Mar 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (26x)
Keywords :  Peloruside, Microtubule, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. H. Kellogg, N. M. Hejab, S. Howes, P. Northcote, J. H. Miller, J. F. Diaz, K. H. Downing, E. Nogales
Insights Into The Distinct Mechanisms Of Action Of Taxane And Non-Taxane Microtubule Stabilizers From Cryo-Em Structures.
J. Mol. Biol. V. 429 633 2017
PubMed-ID: 28104363  |  Reference-DOI: 10.1016/J.JMB.2017.01.001

(-) Compounds

Molecule 1 - TUBULIN ALPHA CHAIN
    Chains: A
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
 
Molecule 2 - TUBULIN BETA CHAIN
    Chains: B
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: BETA-TUBULIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (26x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4POU1Ligand/IonPELORUSIDE A
Biological Unit 1 (3, 78)
No.NameCountTypeFull Name
1GDP26Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GTP26Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4POU26Ligand/IonPELORUSIDE A

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , GLN A:11 , ALA A:12 , GLN A:15 , GLU A:71 , ASP A:98 , ALA A:99 , ALA A:100 , ASN A:101 , SER A:140 , GLY A:143 , GLY A:144 , THR A:145 , GLY A:146 , ILE A:171 , THR A:179 , GLU A:183 , ASN A:206 , TYR A:224 , ASN A:228 , MG A:502 , LYS B:254binding site for residue GTP A 501
2AC2SOFTWAREGLU A:71 , GTP A:501binding site for residue MG A 502
3AC3SOFTWAREGLN B:11 , CYS B:12 , GLN B:15 , SER B:140 , GLY B:144 , THR B:145 , GLY B:146 , ASP B:179 , GLU B:183 , ASN B:206 , TYR B:224 , ASN B:228binding site for residue GDP B 501
4AC4SOFTWAREPHE B:296 , ASP B:297 , ALA B:298 , LYS B:299 , ARG B:308 , TYR B:312binding site for residue POU B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5SYC)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:273 -Pro A:274
2Ala B:273 -Pro B:274

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5SYC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5SYC)

(-) Exons   (0, 0)

(no "Exon" information available for 5SYC)

(-) 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:424
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhhhhhhhhhhhhhhhhh..........eee.....eee.eeeee...hhhhhhhhh..........eee.......hhhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh.....eeeeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh........eeeee....hhhhhhh..hhhhhhhhhh...............eeeeeeeeee..hhhhhhhhhhhhhhh............eeeeee................eeeeeeeee.hhhhhhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5syc A   1 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGV 437
                                    10        20        30    ||  53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433    
                                                             35|                                                                                                                                                                                                                                                                                                                                                                                                    
                                                              49                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:426
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhhhhh...........hhhhhhhhh.eeee...eeee.eeeee..hhhhhhhhhh.hhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.eee..hhhhhhhhhh......eeeeeee.............hhhhhhhhhhhhhhh....hhhhh.eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeee........eeeeeeeee..hhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5syc B   1 MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQ 436
                                    10        20        30        40   ||   52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       370       380       390       400       410       420       430      
                                                                      44|                                                                                                                                                                                                                                                                                                                      360|                                                                   
                                                                       47                                                                                                                                                                                                                                                                                                                       369
   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  (0, 0)

(no "SCOP Domain" information available for 5SYC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5SYC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5SYC)

(-) Gene Ontology  (16, 32)

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
    GDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    POU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:273 - Pro A:274   [ RasMol ]  
    Ala B:273 - Pro B:274   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5syc
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  B6A7R0_PIG | B6A7R0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TBA1B_PIG | Q2XVP4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TBB_PIG | P02554
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  B6A7R0_PIG | B6A7R0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TBA1B_PIG | Q2XVP4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TBB_PIG | P02554
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        B6A7R0_PIG | B6A7R0: 5sye 5syf 5syg
        TBA1B_PIG | Q2XVP4: 3j8x 3j8y 3jak 3jal 3jar 3jas 3jat 3jaw 4zhq 4zi7 4zol 5ca0 5ezy 5fnv 5jqg 5kmg 5sye 5syf 5syg
        TBB_PIG | P02554: 1ffx 1ia0 1jff 1sa0 1sa1 1tub 1tvk 2hxf 2hxh 2wbe 3j6e 3j6f 3j6g 3j6h 3j6p 3j7i 3jak 3jal 3jar 3jas 3jat 3jaw 4abo 4zhq 4zi7 4zol 5bmv 5fnv 5jqg 5kmg 5sye 5syf 5syg

(-) Related Entries Specified in the PDB File

5sye 5syf 5syg