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 :  AUTOMATED REFINEMENT OF DIFFRACTION DATA OBTAINED FROM AN ENDOTHIAPEPSIN CRYSTAL TREATED WITH FRAGMENT 132
 
Authors :  J. Schiebel, A. Heine, G. Klebe
Date :  28 Jun 16  (Deposition) - 03 Aug 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym./Biol. Unit :  A
Keywords :  Fragment Screening, Method Development, Aspartic Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Schiebel, S. G. Krimmer, K. Rower, A. Knorlein, X. Wang, A. Y. Park, M. Stieler, F. R. Ehrmann, K. Fu, N. Radeva, M. Krug, F. U. Huschmann, S. Glockner, M. S. Weiss, U. Mueller, G. Klebe, A. Heine
High-Throughput Crystallography: Reliable And Efficient Identification Of Fragment Hits.
Structure V. 24 1398 2016
PubMed-ID: 27452405  |  Reference-DOI: 10.1016/J.STR.2016.06.010

(-) Compounds

Molecule 1 - ENDOTHIAPEPSIN
    Chains: A
    EC Number: 3.4.23.22
    Organism Scientific: CRYPHONECTRIA PARASITICA
    Organism Taxid: 5116

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5P2E)

(-) Sites  (0, 0)

(no "Site" information available for 5P2E)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:255 -A:290

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:25 -Pro A:26
2Ser A:137 -Pro A:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5P2E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5P2E)

(-) Exons   (0, 0)

(no "Exon" information available for 5P2E)

(-) 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:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.......eeeeeee....eeeeeeee.....eee.....hhhhh......hhhhh...eeeeeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeeeeeehhhhhhh....eeee..hhhhh........hhhhhhhhhh...eeeee......eeeee............eeee........eeeeeeeee.....eeeeeeeee......eeehhhhhhhhhh.....eee....eeeee.......eeeee..eeeeehhhh.eeee......eeee.eee......eeehhhhhh..eeeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5p2e A   1 STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASEVDGQTIYTPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLTVTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKASLDSPVFTADLGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTSTGYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVSGAKSSSSVGGYVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGIGINIFGDVALKAAFVVFNGATTPTLGFASK 330
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
   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 5P2E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5P2E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5P2E)

(-) Gene Ontology  (4, 4)

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
(no "Ligands, Modified Residues, Ions" information available for 5p2e)
 
  Sites
(no "Sites" information available for 5p2e)
 
  Cis Peptide Bonds
    Ser A:137 - Pro A:138   [ RasMol ]  
    Thr A:25 - Pro A:26   [ 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
  5p2e
    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
  CARP_CRYPA | P11838
    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)
  3.4.23.22
    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
  CARP_CRYPA | P11838
    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
        CARP_CRYPA | P11838: 1e5o 1e80 1e81 1e82 1eed 1ent 1epl 1epm 1epn 1epo 1epp 1epq 1epr 1er8 1gkt 1gvt 1gvu 1gvv 1gvw 1gvx 1od1 1oew 1oex 2er0 2er6 2er7 2er9 2jji 2jjj 2v00 2vs2 3er3 3er5 3lzy 3pb5 3pbd 3pbz 3pcw 3pcz 3pgi 3pi0 3pld 3pll 3pm4 3pmu 3pmy 3prs 3psy 3pww 3q6y 3t6i 3t7p 3t7q 3t7x 3uri 3urj 3url 3wz6 3wz7 3wz8 4ape 4er1 4er2 4er4 4kup 4l6b 4lap 4lbt 4lhh 4lp9 4y35 4y36 4y37 4y38 4y39 4y3a 4y3d 4y3e 4y3f 4y3g 4y3h 4y3j 4y3l 4y3m 4y3n 4y3p 4y3q 4y3r 4y3s 4y3t 4y3w 4y3x 4y3y 4y3z 4y41 4y43 4y44 4y45 4y47 4y48 4y4a 4y4b 4y4d 4y4e 4y4g 4y4j 4y4t 4y4u 4y4w 4y4x 4y4z 4y50 4y51 4y53 4y54 4y56 4y57 4y58 4y5a 4y5b 4y5c 4y5e 4y5g 4y5k 4y5l 4y5m 4y5n 4y5p 4yck 4yct 4ycy 4yd3 4yd4 4yd5 4yd6 4yd7 4ze6 4zea 5dpz 5dq1 5dq2 5dq4 5dq5 5dr0 5dr1 5dr3 5dr4 5dr7 5dr8 5er1 5er2 5hco 5hct 5is4 5isj 5isk 5j25 5oyq 5oyr 5oys 5oyt 5oyu 5oyv 5oyw 5oyx 5oyy 5oyz 5oz0 5oz1 5oz2 5oz3 5oz4 5oz5 5oz6 5oz7 5oz8 5oz9 5oza 5ozb 5ozc 5ozd 5oze 5ozf 5ozg 5ozh 5ozi 5ozj 5ozk 5ozl 5ozm 5ozn 5ozo 5ozp 5ozq 5ozr 5ozs 5ozt 5ozu 5ozv 5ozw 5ozx 5ozy 5ozz 5p00 5p01 5p02 5p03 5p04 5p05 5p06 5p07 5p08 5p09 5p0a 5p0b 5p0c 5p0d 5p0e 5p0f 5p0g 5p0h 5p0i 5p0j 5p0k 5p0l 5p0m 5p0n 5p0o 5p0p 5p0q 5p0r 5p0s 5p0t 5p0u 5p0v 5p0w 5p0x 5p0y 5p0z 5p10 5p11 5p12 5p13 5p14 5p15 5p16 5p17 5p18 5p19 5p1a 5p1b 5p1c 5p1d 5p1e 5p1f 5p1g 5p1h 5p1i 5p1j 5p1k 5p1l 5p1m 5p1n 5p1o 5p1p 5p1q 5p1r 5p1s 5p1t 5p1u 5p1v 5p1w 5p1x 5p1y 5p1z 5p20 5p22 5p23 5p24 5p25 5p26 5p27 5p28 5p29 5p2a 5p2b 5p2c 5p2d 5p2f 5p2g 5p2h 5p2i 5p2j 5p2k 5p2l 5p2m 5p2n 5p2o 5p2q 5p2r 5p2s 5p2t 5p2u 5p2v 5p2w 5p2x 5p2y 5p2z 5p30 5p31 5p32 5p33 5p34 5p35 5p36 5p37 5p38 5p39 5p3a 5p3b 5p3c 5p3d 5p3e 5p3f 5p3g 5p3h 5p3i 5p3j 5p3k 5p3l 5p3m 5p3n 5p3o 5p3p 5p3q 5p3r 5p3s 5p3t 5p3u 5p3v 5p3w 5p3x 5p3y 5p3z 5p40 5p41 5p42 5p43 5p44 5p45 5p46 5p47 5p48 5p49 5p4a 5p4b 5p4c 5p4d 5p4e 5p4f 5p4g 5p4h 5p4i 5p4j 5p4k 5p4l 5p4m 5p4n 5p4o 5p4p 5p4q 5p4r 5p4s 5p4t 5p4u 5p4v 5p4w 5p4x 5p4y 5p4z 5p50 5p51 5p52 5p53 5p54 5p55 5p56 5p57 5p58 5p59 5p5a 5p5b 5p5c 5p5d 5p5e 5p5f 5p5g 5p5h 5p5i 5p5j 5p5k 5p5l 5p5m 5p5n 5p5o 5p5p 5p5q 5p5r 5p5s 5p5t 5p5u 5p5v 5p5w 5p5x 5p5y 5p5z 5p60 5p61 5p62 5p63 5p64 5p65 5p66 5p67 5p68 5p69 5p6a 5p6b 5p6c 5p6d 5p6e 5p6f 5p6g 5p6h 5p6i 5p6j 5p6k 5p6l 5p6m 5p6n 5p6o 5p6p 5p6q 5p6r 5p6s 5p6t 5p6u 5p6v 5p6w 5p6x 5p6y 5p6z 5p70 5p71 5p72 5p73 5p74 5p75 5p76 5p77 5p78 5p79 5p7a 5p7b 5p7c 5p7d 5p7e 5p7f 5p7g 5p7h 5p7i 5p7j 5p7k 5p7l 5p7m 5p7n 5p7o 5p7p 5p7q 5p7r 5p7s 5p7t 5p7u 5p7v 5p7w 5p7x 5p7y 5p7z 5p80 5p81 5p82 5p83 5p84 5p85 5p86 5p87 5p88 5p89 5p8a 5p8b 5p8c 5p8d 5p8e 5p8f 5p8g 5p8h 5p8i 5p8j 5p8k 5p8l 5p8m 5p8n 5p8o 5p8p 5p8q 5p8r 5p8s 5p8t 5p8u 5p8v

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5P2E)