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 :  EXTENSIVE COUNTER-ION INTERACTIONS WITH SUBTILISIN IN AQUEOUS MEDIUM, CS DERIVATIVE
 
Authors :  M. Cianci, J. Negroni, J. R. Helliwell, P. J. Halling
Date :  27 Aug 13  (Deposition) - 20 Aug 14  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Protease, Metal-Binding, Hydrolase, Soft X-Ray (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Cianci, J. Negroni, J. R. Helliwell, P. J. Halling
Extensive Counter-Ion Interactions Seen At The Surface Of Subtilisin In An Aqueous Medium
Rsc Adv 2014
PubMed: search  |  Reference-DOI: 10.1039/C4RA06448H

(-) Compounds

Molecule 1 - SUBTILISIN CARLSBERG
    Chains: A
    EC Number: 3.4.21.62
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 1402

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL6Ligand/IonCHLORIDE ION
3CS10Ligand/IonCESIUM ION
4NA1Ligand/IonSODIUM ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:2 , SER A:184 , ASN A:185BINDING SITE FOR RESIDUE CL A1276
02AC2SOFTWAREASN A:240 , GLN A:245BINDING SITE FOR RESIDUE CL A1277
03AC3SOFTWARELYS A:170BINDING SITE FOR RESIDUE CL A1291
04AC4SOFTWAREASN A:158BINDING SITE FOR RESIDUE CL A1278
05AC5SOFTWARESER A:99 , ASN A:248BINDING SITE FOR RESIDUE CL A1292
06AC6SOFTWAREALA A:194BINDING SITE FOR RESIDUE CL A1293
07AC7SOFTWAREALA A:37 , HIS A:39 , LEU A:42BINDING SITE FOR RESIDUE CS A1279
08AC8SOFTWAREGLY A:193 , ALA A:194 , LEU A:196 , SER A:260BINDING SITE FOR RESIDUE CS A1280
09AC9SOFTWAREGLY A:61 , SER A:98 , HOH A:2042BINDING SITE FOR RESIDUE CS A1281
10BC1SOFTWAREALA A:52 , TYR A:256 , HOH A:2025BINDING SITE FOR RESIDUE CS A1282
11BC2SOFTWARETYR A:143 , HOH A:2066BINDING SITE FOR RESIDUE CS A1283
12BC3SOFTWAREPRO A:239 , LEU A:241 , HOH A:2058 , HOH A:2068BINDING SITE FOR RESIDUE CS A1284
13BC4SOFTWAREALA A:1 , THR A:3 , GLY A:80 , HOH A:2001 , HOH A:2093BINDING SITE FOR RESIDUE CS A1285
14BC5SOFTWARESER A:156 , ASN A:158BINDING SITE FOR RESIDUE CS A1286
15BC6SOFTWAREGLY A:47BINDING SITE FOR RESIDUE CS A1287
16BC7SOFTWARESER A:159 , THR A:162BINDING SITE FOR RESIDUE CS A1288
17BC8SOFTWAREGLN A:2 , ASP A:41 , LEU A:75 , ASN A:77 , THR A:79 , VAL A:81BINDING SITE FOR RESIDUE CA A1289
18BC9SOFTWAREALA A:169 , TYR A:171 , VAL A:174 , HOH A:2078 , HOH A:2081BINDING SITE FOR RESIDUE NA A1290

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C3U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:167 -Pro A:168
2Pro A:210 -Thr A:211

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C3U)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.SUBT_BACLI133-144  1A:28-39
2SUBTILASE_HISPS00137 Serine proteases, subtilase family, histidine active site.SUBT_BACLI168-178  1A:64-74
3SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.SUBT_BACLI323-333  1A:219-229

(-) Exons   (0, 0)

(no "Exon" information available for 4C3U)

(-) 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:274
 aligned with SUBT_BACLI | P00780 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:274
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375    
           SUBT_BACLI   106 AQTVPYGIPLIKADKVQAQGFKGANVKVAVLDTGIQASHPDLNVVGGASFVAGEAYNTDGNGHGTHVAGTVAALDNTTGVLGVAPSVSLYAVKVLNSSGSGTYSGIVSGIEWATTNGMDVINMSLGGPSGSTAMKQAVDNAYARGVVVVAAAGNSGSSGNTNTIGYPAKYDSVIAVGAVDSNSNRASFSSVGAELEVMAPGAGVYSTYPTSTYATLNGTSMASPHVAGAAALILSKHPNLSASQVRNRLSSTATYLGSSFYYGKGLINVEAAAQ 379
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.......eeeeee...........eeeeee............hhhhhhhhhhhh..............eeeeee........hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhh..eeeee......................eeeeee.................eeee...eeeee...eeeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------SUBTILASE_AS-----------------------SUBTILASE_H------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c3u A   1 AQTVPYGIPLIKADKVQAQGFKGANVKVAVLDTGIQASHPDLNVVGGASFVAGEAYNTDGNGHGTHVAGTVAALDNTTGVLGVAPSVSLYAVKVLNSSGSGSYSGIVSGIEWATTNGMDVINMSLGGASGSTAMKQAVDNAYARGVVVVAAAGNSGNSGSTNTIGYPAKYDSVIAVGAVDSNSNRASFSSVGAELEVMAPGAGVYSTYPTNTYATLNGTSMASPHVAGAAALILSKHPNLSASQVRNRLSSTATYLGSSFYYGKGLINVEAAAQ 275
                                    10        20        30        40        50    ||  61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
                                                                                 55|                                                                                                                                                                                                                          
                                                                                  57
   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 4C3U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C3U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C3U)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SUBT_BACLI | P00780)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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 ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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
    Pro A:210 - Thr A:211   [ RasMol ]  
    Tyr A:167 - Pro A:168   [ 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 | 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
  4c3u
    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
  SUBT_BACLI | P00780
    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)
  3.4.21.62
    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
  SUBT_BACLI | P00780
    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
        SUBT_BACLI | P00780: 1af4 1av7 1avt 1be6 1be8 1bfk 1bfu 1c3l 1cse 1oyv 1r0r 1sbc 1sca 1scb 1scd 1scn 1sel 1vsb 1yu6 2sec 2wuv 2wuw 3unx 3vsb 4c3v

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4C3U)