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

(-) Description

Title :  COHESIN SUBUNIT PDS5 IN COMPLEX WITH SCC1
 
Authors :  B. -G. Lee, M. Jansma, K. Nasmyth, J. Lowe
Date :  27 Nov 15  (Deposition) - 13 Apr 16  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A,E
Keywords :  Heat Repeat Cohesin Subunit, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. G. Lee, M. B. Roig, M. Jansma, N. Petela, J. Metson, K. Nasmyth, J. Low
Crystal Structure Of The Cohesin Gatekeeper Pds5 And In Complex With Kleisin Scc1.
Cell Rep V. 14 2108 2016
PubMed-ID: 26923598  |  Reference-DOI: 10.1016/J.CELREP.2016.02.020

(-) Compounds

Molecule 1 - COHESIN SUBUNIT PDS5, KLTH0D07062P,KLTH0D07062P, KLTH0D07062P,COHESIN SUBUNIT PDS5, KLTH0D07062P,KLTH0D07062P, KLTH0D07062P,COHESIN SUBUNIT PDS5, KLTH0D07062P,KLTH0D07062P, KLTH0D07062P,COHESIN SUBUNIT PDS5, KLTH0D07062P,KLTH0D07062P
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PHIS17
    Expression System Taxid: 469008
    Expression System Variant: C41
    Expression System Vector Type: PLASMID
    Gene: KLTH0D07062G,PDS5, KLTH0D07062G
    Organism Common: YEAST
    Organism Scientific: LACHANCEA THERMOTOLERANS
    Organism Taxid: 381046, 559295
    Other Details: THE UNK RESIDUES ARE PART OF CHAIN A, BUT WE COULD NOT CORRECT THE EXACT RESIDUES DUE TO LOW RESOLUTION MAP
    Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284
 
Molecule 2 - KLTH0G16610P
    Chains: E
    Engineered: YES
    Organism Common: YEAST
    Organism Scientific: LACHANCEA THERMOTOLERANS (STRAIN ATCC 56472 / CBS 6340 / NRRL Y-8284)
    Organism Taxid: 559295
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 40)

Asymmetric/Biological Unit (1, 40)
No.NameCountTypeFull Name
1UNK40Mod. Amino Acid

(-) Sites  (0, 0)

(no "Site" information available for 5F0O)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F0O)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:806 -Pro A:807
2Tyr A:935 -Pro A:936
3Phe A:965 -Ile A:966

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F0O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F0O)

(-) Exons   (0, 0)

(no "Exon" information available for 5F0O)

(-) Sequences/Alignments

Asymmetric/Biological 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:1018
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhh.hhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhh...hhhhhhh............hhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhh.hhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhh........hhhhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..................hhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.............hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5f0o A    1 xxxxxxxxxxxxxxxxxLERYRADLIDRKILRNKDHGVRAFAACCLSDILRLYAPDAPYTDKELTEIFRLFLAQLKLLQEPENGYLTQQTYLINNLLEYRSIVILTDLPSSSQLVEELFNIFYSPTNSTIQGNMFTAIGGILGEVISECDSLPMSALKMVFNKFLSHKRAESLDGIPGFEISLIICQTYSNRLGRHFIKFYSEIMYEVLGEASSAYKTLVKIGNLTSELWKYAPELVGSVTGLLYQLLCSDNELFRESATKCVSKMLGTHSLINFAVAHSDTYKIWLSKMADISPHVRQAWVSEIPSILMSRSDLSDDISKGLAKALIDSDHTVRLSAIQTFHEVPVKRLWECLPNAAVFAGLVHLTRETRRDLRDECIDAVARIYTESIESIPKTNENKEIWGVVETIPSACFNLYYINDLEINMKVDLLTFEKFLPLGLSNEEFVQRLLTLLQGFNEKAFSSFYAFNRRQDQMSTVLWKFIEFCEETNSQSPAASLSDTKLIKTVEWISSGFPSHLNVEQILLAFRELNDRRLYRLIKVAVAETSKHLTVRNAVSELFKRLEEPELFRKKNIKIESRFTRDNFSTVFRVLIYRAAPIIFNISNLPSFLNTSNEDEKALKRQLIDNISIIKPGIFKDQVKNLVTIITTLSLAEAMRTVYKISKTFFFQKLEDYAKEGNPLEAKYAIKLLGLAPNAAEYLSEVATAILPLDLKSKHFASNVLVLAEITKMQPQLLEKDSTEIVGLLIKDVLLSNDVVGDEDDQQAWFSDEDIYTGKADALSAKVFSLKLFANKIKVMAMTHAFTERTLKLFFYLVASGGELVSESNTDNYPTPANYQNKLRCCAGLHILKITKIAFIKPQDISKLMNLVEDESLEVRSSFIGRLKDFLGDGSISIKFLPLVFFTAYEPDQALRTSTKMWINYTLSKENFRKGTFFERALPRLIHFIAHHPDVAEGLRLLTGLTTAIDYLVFYADSVLKASNLALLYYLAGRVRQYxxxxxxxxxxxxxxxxxxxxxxx 2022
                            ||||||||10||||||||82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     ||247       257       267       277||     295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685  ||   698       708       718       737       747   ||  768       778       788       798       808       818       828       838       848       858       868       878       888       905       915       925       935       945       955    || 969       979       989       999      1009      1019      1029      1039      1049      1059      1074      1084      1094      1104    ||2004||||||2014||||||||
                            ||||||||9-UNK|||80                                                                                                                                                           238|                               278|                                                                                                                                                                                                                                                                                                                                                                                                              688|                               726|            751|                                                                                                                                  896|                                                     960|                                                                                                  1067|                                1109|||||2008-UNK|2017-UNK|
                            1-UNK|||10-UNK|||                                                                                                                                                             244                                287                                                                                                                                                                                                                                                                                                                                                                                                               692                                736             763                                                                                                                                   904                                                      965                                                                                                   1073                                 2000-UNK|2009-UNK|2018-UNK
                             2-UNK|| 11-UNK||                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                2001-UNK|2010-UNK|2019-UNK
                              3-UNK|  12-UNK|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 2002-UNK|2011-UNK|2020-UNK
                               4-UNK   13-UNK                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  2003-UNK 2012-UNK 2021-UNK
                                5-UNK   14-UNK                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  2004-UNK 2013-UNK 2022-UNK
                                 6-UNK   15-UNK                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  2005-UNK 2014-UNK    
                                  7-UNK   16-UNK                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  2006-UNK 2015-UNK   
                                   8-UNK   17-UNK                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  2007-UNK 2016-UNK  


Chain E from PDB  Type:PROTEIN  Length:17
                                                  
               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 ----------------- Transcript
                5f0o E  125 SQYLLQDAVTEREVLLV  141
                                   134
   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 5F0O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F0O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F0O)

(-) Gene Ontology  (28, 34)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    UNK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 5f0o)
 
  Cis Peptide Bonds
    Leu A:806 - Pro A:807   [ RasMol ]  
    Phe A:965 - Ile A:966   [ RasMol ]  
    Tyr A:935 - Pro A:936   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  5f0o
    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
  C5DGP8_LACTC | C5DGP8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  C5DNF8_LACTC | C5DNF8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  C5DGP8_LACTC | C5DGP8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  C5DNF8_LACTC | C5DNF8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        C5DGP8_LACTC | C5DGP8: 5f0n

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5F0O)