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

(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPSILIGASE (K60E/N143H/Y151H/D189K TRYPSIN) ORTHORHOMBIC FORM
 
Authors :  M. Schoepfel, C. Parthier, M. T. Stubbs
Date :  08 Nov 13  (Deposition) - 19 Feb 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.31
Chains :  Asym./Biol. Unit :  A
Keywords :  Trypsin, Serine Proteinase, Enzyme Design, Activation Domain, Zymogen, Peptide Ligation, Reverse Proteolysis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Liebscher, M. Schopfel, T. Aumuller, A. Sharkhuukhen, A. Pech, E. Hoss, C. Parthier, G. Jahreis, M. T. Stubbs, F. Bordusa
N-Terminal Protein Modification By Substrate-Activated Reverse Proteolysis.
Angew. Chem. Int. Ed. Engl. V. 53 3024 2014
PubMed-ID: 24520050  |  Reference-DOI: 10.1002/ANIE.201307736

(-) Compounds

Molecule 1 - CATIONIC TRYPSIN
    Chains: A
    EC Number: 3.4.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 24-246
    Mutation: YES
    Organism Common: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: BETA-TRYPSIN, ALPHA-TRYPSIN CHAIN 1, ALPHA-TRYPSIN CHAIN 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:70 , ASN A:72 , VAL A:75 , GLU A:80 , HOH A:404 , HOH A:418BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWAREGLU A:80 , GLN A:81 , PHE A:82 , HOH A:547BINDING SITE FOR RESIDUE GOL A 302

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:157
2A:42 -A:58
3A:128 -A:232
4A:136 -A:201
5A:168 -A:182
6A:191 -A:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NIW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NIW)

(-) 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:221
                                                                                                                                                                                                                                                              
               SCOP domains d4niwa_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeeee.........eeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4niw A   18 GGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYESGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGHTKSSGTSHPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKKSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN  245
                                    27      ||39        49        59       |70        80        90       100       110       120    || 132       142       152       162       172       182  |    190       200   ||  214  ||  |224       234       244 
                                           34|                            67|                                                     125|  ||                                                 184A 188A             204|     217|  |                        
                                            37                             69                                                      127  ||                                                                        209      219  |                        
                                                                                                                                      130|                                                                                   221A                        
                                                                                                                                       132
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4niw)
 

(-) 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 | Asym./Biol. Unit - 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
  4niw
    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
  TRY1_BOVIN | P00760
    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)
  3.4.21.4
    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
  TRY1_BOVIN | P00760
    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
        TRY1_BOVIN | P00760: 1aq7 1auj 1az8 1bju 1bjv 1btp 1btw 1btx 1bty 1btz 1c1n 1c1o 1c1p 1c1q 1c1r 1c1s 1c1t 1c2d 1c2e 1c2f 1c2g 1c2h 1c2i 1c2j 1c2k 1c2l 1c2m 1c5p 1c5q 1c5r 1c5s 1c5t 1c5u 1c5v 1c9t 1ce5 1cu7 1cu8 1cu9 1d6r 1eb2 1ejm 1ezx 1f0t 1f0u 1f2s 1g36 1g3b 1g3c 1g3d 1g3e 1g9i 1gbt 1ghz 1gi0 1gi1 1gi2 1gi3 1gi4 1gi5 1gi6 1gj6 1hj9 1j8a 1jir 1jrs 1jrt 1k1i 1k1j 1k1l 1k1m 1k1n 1k1o 1k1p 1lqe 1max 1may 1mts 1mtu 1mtv 1mtw 1n6x 1n6y 1nc6 1ntp 1o2h 1o2i 1o2j 1o2k 1o2l 1o2m 1o2n 1o2o 1o2p 1o2q 1o2r 1o2s 1o2t 1o2u 1o2v 1o2w 1o2x 1o2y 1o2z 1o30 1o31 1o32 1o33 1o34 1o35 1o36 1o37 1o38 1o39 1o3a 1o3b 1o3c 1o3d 1o3e 1o3f 1o3g 1o3h 1o3i 1o3j 1o3k 1o3l 1o3m 1o3n 1o3o 1oph 1ox1 1oyq 1p2i 1p2j 1p2k 1ppc 1ppe 1pph 1qa0 1qb1 1qb6 1qb9 1qbn 1qbo 1qcp 1ql7 1ql8 1rxp 1s0q 1s0r 1sbw 1sfi 1smf 1tab 1taw 1tgb 1tgc 1tgn 1tgs 1tgt 1tio 1tld 1tng 1tnh 1tni 1tnj 1tnk 1tnl 1tpa 1tpo 1tpp 1tps 1tx7 1tx8 1tyn 1utn 1uto 1utp 1utq 1v2j 1v2k 1v2l 1v2m 1v2n 1v2o 1v2p 1v2q 1v2r 1v2s 1v2t 1v2u 1v2v 1v2w 1xuf 1xug 1xuh 1xui 1xuj 1xuk 1y3u 1y3v 1y3w 1y3x 1y3y 1y59 1y5a 1y5b 1y5u 1yp9 1yyy 1zr0 1zzz 2a7h 2age 2agg 2agi 2ah4 2ayw 2blv 2blw 2btc 2by5 2by6 2by7 2by8 2by9 2bya 2bza 2cmy 2d8w 2f3c 2fi3 2fi4 2fi5 2ftl 2ftm 2fx4 2fx6 2g55 2g5n 2g5v 2g81 2g8t 2iln 2j9n 2o9q 2otv 2oxs 2plx 2ptc 2ptn 2qn5 2qyi 2tga 2tgd 2tgp 2tgt 2tio 2tld 2tpi 2uuy 2xtt 2zdk 2zdl 2zdm 2zdn 2zfs 2zft 2zhd 2zq1 2zq2 3a7t 3a7v 3a7w 3a7x 3a7y 3a7z 3a80 3a81 3a82 3a83 3a84 3a85 3a86 3a87 3a88 3a89 3a8a 3a8b 3a8c 3a8d 3aas 3aau 3aav 3ati 3atk 3atl 3atm 3btd 3bte 3btf 3btg 3bth 3btk 3btm 3btq 3btt 3btw 3d65 3e8l 3gy2 3gy3 3gy4 3gy5 3gy6 3gy7 3gy8 3i29 3iti 3ljj 3ljo 3m35 3m7q 3mfj 3mi4 3nk8 3nkk 3otj 3plb 3plk 3plp 3pm3 3pmj 3ptb 3ptn 3pwb 3pwc 3pyh 3q00 3qk1 3rdz 3ru4 3rxa 3rxb 3rxc 3rxd 3rxe 3rxf 3rxg 3rxh 3rxi 3rxj 3rxk 3rxl 3rxm 3rxo 3rxp 3rxq 3rxr 3rxs 3rxt 3rxu 3rxv 3t25 3t26 3t27 3t28 3t29 3tpi 3unq 3unr 3uns 3uop 3upe 3uqo 3uqv 3uuz 3uwi 3uy9 3v0x 3v12 3v13 3veq 3vpk 4ab8 4ab9 4aba 4abb 4abd 4abe 4abf 4abg 4abh 4abi 4abj 4aoq 4aor 4b1t 4b2a 4b2b 4b2c 4gux 4hgc 4i8g 4i8h 4i8j 4i8k 4i8l 4j2y 4kts 4ktu 4mtb 4ncy 4niv 4nix 4niy 4tpi 4tpy 4u2w 4xoj 4y0y 4y0z 4y10 4y11 4yta 5eg4 5f6m 5fxl 5gib 5gxp 5jyi 5k7r 5lgo 5lh8 5mn1 5mna 5mnb 5mnc 5mnx 5mny 5mon 5moo 5ptp 5t3h

(-) Related Entries Specified in the PDB File

4niv 4nix 4niy