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 SCHIZOSACCHAROMYCES POMBE AMSH-LIKE PROTEASE SST2 CATALYTIC DOMAIN BOUND TO UBIQUITIN
 
Authors :  R. K. Shrestha, J. A. Ronau, C. Das
Date :  18 Sep 13  (Deposition) - 18 Jun 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ubiquitin, Deubiquitination, Helix-Beta-Helix Sandwich, Zinc Metalloprotease, Lysine 63-Linked Polyubiquitin, Cytosol, Endosome, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Shrestha, J. A. Ronau, C. W. Davies, R. G. Guenette, E. R. Strieter L. N. Paul, C. Das
Insights Into The Mechanism Of Deubiquitination By Jamm Deubiquitinases From Cocrystal Structures Of The Enzyme Wit The Substrate And Product.
Biochemistry V. 53 3199 2014
PubMed-ID: 24787148  |  Reference-DOI: 10.1021/BI5003162

(-) Compounds

Molecule 1 - AMSH-LIKE PROTEASE SST2
    Chains: A, C
    EC Number: 3.4.19.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6-P1
    Expression System Strain: ROSETTA
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 245-435
    Gene: SST2, SPAC19B12.10
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 284812
    Strain: 972/ATCC 24843
    Synonym: SUPPRESSOR OF STE12 DELETION PROTEIN 2
 
Molecule 2 - UBIQUITIN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6-P1
    Expression System Strain: ROSETTA
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 77-152
    Gene: UBC, UBIQUITIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1EDO13Ligand/Ion1,2-ETHANEDIOL
2PO41Ligand/IonPHOSPHATE ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2PO4-1Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2PO41Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:356 , CYS A:397 , HIS A:404 , HIS A:406BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREHIS A:341 , HIS A:343 , ASP A:354 , GLY B:76BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWAREASP A:315 , GLN A:346 , PHE A:349 , HOH A:684 , GLY B:76BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWAREILE A:290 , LEU A:325 , GLN A:329 , THR A:336 , TYR A:361 , LEU B:8 , LEU B:71 , EDO B:101BINDING SITE FOR RESIDUE EDO A 504
05AC5SOFTWARETHR A:281 , LYS A:282 , HOH A:617BINDING SITE FOR RESIDUE EDO A 505
06AC6SOFTWARELYS A:258 , GLN A:362 , PRO A:366 , ASP A:387 , HOH A:693BINDING SITE FOR RESIDUE EDO A 506
07AC7SOFTWAREPRO A:388 , GLN A:392BINDING SITE FOR RESIDUE EDO A 507
08AC8SOFTWAREEDO A:504 , THR B:7 , LEU B:8 , LEU B:69 , VAL B:70 , LEU B:71BINDING SITE FOR RESIDUE EDO B 101
09AC9SOFTWAREILE B:44 , ALA B:46 , GLY B:47 , HIS B:68BINDING SITE FOR RESIDUE EDO B 102
10BC1SOFTWAREHIS C:356 , CYS C:397 , HIS C:404 , HIS C:406BINDING SITE FOR RESIDUE ZN C 501
11BC2SOFTWAREHIS C:341 , HIS C:343 , ASP C:354 , GLY D:76BINDING SITE FOR RESIDUE ZN C 502
12BC3SOFTWARELYS C:409 , THR C:412 , MET C:413BINDING SITE FOR RESIDUE PO4 C 503
13BC4SOFTWAREILE C:382 , GLN C:416 , GLU C:422 , HOH C:635BINDING SITE FOR RESIDUE EDO C 504
14BC5SOFTWARETHR A:313 , ASP A:315 , GLU C:311 , THR C:316 , CYS C:317 , GLY C:318 , HOH C:642 , ARG D:74 , HOH D:203BINDING SITE FOR RESIDUE EDO C 505
15BC6SOFTWARELEU C:325 , GLN C:329 , THR C:336 , TYR C:361 , LEU D:8 , LEU D:71 , EDO D:101BINDING SITE FOR RESIDUE EDO C 506
16BC7SOFTWAREASP C:315 , GLN C:346 , PHE C:349 , GLY D:76BINDING SITE FOR RESIDUE EDO C 507
17BC8SOFTWAREEDO C:506 , THR D:7 , LEU D:8 , LEU D:69 , VAL D:70 , LEU D:71BINDING SITE FOR RESIDUE EDO D 101
18BC9SOFTWAREPHE C:326 , ASP C:330 , LYS D:6 , THR D:7 , LEU D:8 , HIS D:68BINDING SITE FOR RESIDUE EDO D 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:387 -Pro A:388
2Gln A:416 -Pro A:417
3Asp C:387 -Pro C:388
4Gln C:416 -Pro C:417

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MSQ)

(-) 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:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....ee..eeee.hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee..eee....eee.hhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh...eeeeee....eeeeeee..hhhhhhhhhh.............eee......eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4msq A 249 KIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPGHVREINSKLQVVDLR 433
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428     


Chain B from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4msq B   0 SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                     9        19        29        39        49        59        69       


Chain C from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee.....ee..eeee.hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee..eee....eee.hhhhhhhhhhhhh.eeeeeeee........hhhhhhhhhhhhhhh...eeeeee....eeeeeee..hhhhhhhhhh.............eee......eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4msq C 248 FKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPGHVREINSKLQVVDLR 433
                                   257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427      


Chain D from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....eeee......hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee..ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4msq D   2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    11        21        31        41        51        61        71
   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 4MSQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (94, 95)

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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:387 - Pro A:388   [ RasMol ]  
    Asp C:387 - Pro C:388   [ RasMol ]  
    Gln A:416 - Pro A:417   [ RasMol ]  
    Gln C:416 - Pro C:417   [ RasMol ]  
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4msq
    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
  SST2_SCHPO | Q9P371
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  UBC_HUMAN | P0CG48
    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)
  3.4.19.-
    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
  SST2_SCHPO | Q9P371
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  UBC_HUMAN | P0CG48
    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
        SST2_SCHPO | Q9P371: 4jxe 4k1r 4ms7 4msd 4msj 4msm 4nql 4pqt 4zd4 4zd5 4zfr 4zft
        UBC_HUMAN | P0CG48: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1ogw 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1xqq 1yx5 1yx6 1zgu 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2gmi 2hth 2ibi 2j7q 2jf5 2jri 2jy6 2jzz 2k25 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2kx0 2l0f 2l0t 2l3z 2ld9 2lvo 2lvp 2lvq 2lz6 2mbo 2mbq 2mcn 2mi8 2mj5 2mor 2mre 2mws 2n2k 2nr2 2o6v 2ojr 2pe9 2pea 2rr9 2rsu 2ru6 2w9n 2wdt 2xew 2xk5 2y5b 2z59 2zcb 2zvn 2zvo 3a33 3alb 3aul 3b08 3b0a 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9o 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3ofi 3oj3 3oj4 3ons 3phd 3prm 3pt2 3ptf 3q3f 3rul 3tmp 3u30 3ugb 3v6c 3v6e 3vfk 3vuw 3vux 3vuy 3wxe 3wxf 3zlz 3znh 3zni 3znz 4ap4 4auq 4bos 4boz 4bvu 4ddg 4ddi 4dhj 4dhz 4fjv 4hk2 4hxd 4i6l 4i6n 4ig7 4ium 4jqw 4k1r 4k7s 4k7u 4k7w 4ksk 4ksl 4lcd 4ldt 4mdk 4mm3 4msm 4nqk 4un2 4v3k 4v3l 4wzp 4xok 4xol 4zqs 5a5b 5af4 5af5 5af6 5ait 5aiu 5b83 5c7j 5c7m 5e6j 5h07 5nl4 5nlf 5nli 5nmc

(-) Related Entries Specified in the PDB File

3rzu STRUCTURE OF CATALYTIC DOMAIN, HUMAN PROTEIN AMSH
4jxe STRUCTURE OF CATALYTIC DOMAIN, S.POMBE SSTE
4ms7 CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE SST2 CATALYTIC DOMAIN
4msd CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE AMSH-LIKE PROTEIN SST2 T319I MUTANT
4msj CRYSTAL STRUCTURE OF S. POMBE AMSH-LIKE PROTEASE SST2 CATALYTIC DOMAIN FROM P212121 SPACE GROUP
4msm CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE AMSH-LIKE PROTEASE SST2 E286A MUTANT BOUND TO UBIQUITIN