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(-) Description

Title :  CATALYTIC DOMAIN OF SST2 F403W MUTANT BOUND TO UBIQUITIN
 
Authors :  A. N. Bueno
Date :  21 Apr 15  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Helix-Beta-Helix Sandwich, Ubiquitin, Zinc Metalloprotease, Endosome, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. N. Bueno
Structure Of The Catalytic Domain Of Sst2 Mutant F403W Boun To Ubiquitin At 2. 3 Angstroms
To Be Published
PubMed: search

(-) 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-6P-1
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 245-435
    Gene: SST2, SPAC19B12.10
    Mutation: YES
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843
    Synonym: SUPPRESSOR OF STE12 DELETION PROTEIN 2
 
Molecule 2 - POLYUBIQUITIN-B
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Taxid: 562
    Expression System Vector Type: ROSETTA
    Fragment: UNP RESIDUES 77-152
    Gene: UBB
    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  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:341 , HIS A:343 , ASP A:354 , GLY B:76binding site for residue ZN A 501
2AC2SOFTWAREHIS A:356 , CYS A:397 , HIS A:404 , HIS A:406binding site for residue ZN A 502
3AC3SOFTWAREALA A:252 , TYR A:253 , LEU A:260 , ARG A:384 , VAL A:414 , ALA A:415 , HIS A:419 , LYS A:426binding site for residue EDO A 503
4AC4SOFTWAREHOH A:614 , THR B:7 , LEU B:8 , LEU B:69 , VAL B:70 , LEU B:71binding site for residue EDO B 101
5AC5SOFTWARELEU A:334 , THR B:7 , LEU B:8 , THR B:9 , GLY B:10binding site for residue EDO B 102
6AC6SOFTWAREHIS C:341 , HIS C:343 , ASP C:354 , GLY D:76binding site for residue ZN C 501
7AC7SOFTWAREHIS C:356 , CYS C:397 , HIS C:404 , HIS C:406binding site for residue ZN C 502
8AC8SOFTWARETYR C:264binding site for residue EDO C 503
9AC9SOFTWARETHR D:7 , LEU D:8 , LEU D:69 , VAL D:70 , LEU D:71binding site for residue EDO D 101

(-) SS Bonds  (0, 0)

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

(-) 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 4ZFT)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZFT)

(-) 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.eeeeehhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee..eee....eee.hhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh...eeeeeehhhheeeeeee..hhhhhhhhhh.............eee......eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zft A 249 KIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLWHPHEGKVYTMVAQPGHVREINSKLQVVDLR 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:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 4zft B  -1 GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                     8        18        28        38        48        58        68        


Chain C from PDB  Type:PROTEIN  Length:183
                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeehhhhhhhhhhhhhhhhh....eeeeeeee...eeeeeeeee..eee....eee.hhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh...eeeeeehhhheeeeeee..hhhhhhhhhh.............eee......eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zft C 251 HAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLWHPHEGKVYTMVAQPGHVREINSKLQVVDLR 433
                                   260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430   


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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (102, 103)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SST2_SCHPO | Q9P371: 4jxe 4k1r 4ms7 4msd 4msj 4msm 4msq 4nql 4pqt 4zd4 4zd5 4zfr
        UBB_HUMAN | P0CG47: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1yx5 1yx6 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2hth 2ibi 2j7q 2jf5 2jzz 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2l0f 2l0t 2mbb 2mro 2msg 2n13 2nr2 2o6v 2ojr 2pe9 2pea 2w9n 2wdt 2xew 2xk5 2y5b 2zcb 3a33 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3oj3 3oj4 3ons 3phd 3ptf 3zlz 3znh 4uel 4uf6 4whv 4wlr 4wur 4wzp 4xof 4zfr 4zpz 4zux 5bnb 5caw 5cra 5cvm 5cvn 5cvo 5d0k 5d0m 5dfl 5dk8 5e6j 5edv 5emz 5eya 5gjq 5go7 5go8 5gob 5goc 5god 5gog 5goh 5goi 5goj 5gok 5ibk 5ifr 5j8p 5jbv 5jby 5jg6 5jp3 5jtj 5jtv 5k9p 5kgf 5khy 5l8h 5l8w 5l9t 5ln1 5lrv 5lrw 5lrx 5m93 5mnj 5n2w 5n38 5nl5 5nlj 5nvg 5tof 5tog 5ulf 5ulh 5ulk 5v1y 5v1z 5vey 5vf0 5w46 5x3m 5x3n 5x3o 5xbo 5xdp 5xk4 5xk5

(-) Related Entries Specified in the PDB File

2znv AMSH-LP E292A BOUND TO LYS63-LINKED UBIQUITIN DIMER
4k1r CATALYTIC DOMAIN OF SST2 BOUND TO UBIQUITIN
4msm CATALYTIC MUTANT OF SST2 E286A BOUND TO UBIQUITIN
4msq CATALYTIC DOMAIN OF SST2 BOUND TO UBIQUITIN
4zfr