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 HTLV PROTEASE COMPLEXED WITH THE INHIBITOR KNI-10729
 
Authors :  T. Satoh, M. Li, J. Nguyen, Y. Kiso, A. Wlodawer, A. Gustchina
Date :  25 Jan 10  (Deposition) - 14 Jul 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (6x)
Keywords :  Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Satoh, M. Li, J. T. Nguyen, Y. Kiso, A. Gustchina, A. Wlodawer
Crystal Structures Of Inhibitor Complexes Of Human T-Cell Leukemia Virus (Htlv-1) Protease.
J. Mol. Biol. V. 401 626 2010
PubMed-ID: 20600105  |  Reference-DOI: 10.1016/J.JMB.2010.06.052

(-) Compounds

Molecule 1 - PROTEASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHTLVDELTA9
    Expression System Strain: ROSETTA2(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PRT
    Mutation: YES
    Organism Scientific: HUMAN T-LYMPHOTROPIC VIRUS 1
    Organism Taxid: 11908

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (6x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1E171Ligand/IonN-{(1S,2S)-1-BENZYL-3-[(4R)-5,5-DIMETHYL-4-{[(1R)-1,2,2-TRIMETHYLPROPYL]CARBAMOYL}-1,3-THIAZOLIDIN-3-YL]-2-HYDROXY-3-OXOPROPYL}-3-METHYL-N~2~-{(2S)-2-[(MORPHOLIN-4-YLACETYL)AMINO]-2-PHENYLACETYL}-L-VALINAMIDE
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1E171Ligand/IonN-{(1S,2S)-1-BENZYL-3-[(4R)-5,5-DIMETHYL-4-{[(1R)-1,2,2-TRIMETHYLPROPYL]CARBAMOYL}-1,3-THIAZOLIDIN-3-YL]-2-HYDROXY-3-OXOPROPYL}-3-METHYL-N~2~-{(2S)-2-[(MORPHOLIN-4-YLACETYL)AMINO]-2-PHENYLACETYL}-L-VALINAMIDE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1E176Ligand/IonN-{(1S,2S)-1-BENZYL-3-[(4R)-5,5-DIMETHYL-4-{[(1R)-1,2,2-TRIMETHYLPROPYL]CARBAMOYL}-1,3-THIAZOLIDIN-3-YL]-2-HYDROXY-3-OXOPROPYL}-3-METHYL-N~2~-{(2S)-2-[(MORPHOLIN-4-YLACETYL)AMINO]-2-PHENYLACETYL}-L-VALINAMIDE
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:65 , HIS A:66 , ASP B:65 , HIS B:66BINDING SITE FOR RESIDUE ZN A 117
2AC2SOFTWAREARG A:10 , ASP A:32 , GLY A:34 , ALA A:35 , MET A:37 , VAL A:56 , LEU A:57 , ALA A:59 , TRP A:98 , LEU B:30 , ASP B:32 , GLY B:34 , ASP B:36 , MET B:37 , VAL B:56 , LEU B:57 , GLY B:58 , ALA B:59 , HOH B:119BINDING SITE FOR RESIDUE E17 B 117

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LIX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LIX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LIX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LIX)

(-) Exons   (0, 0)

(no "Exon" information available for 3LIX)

(-) 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:116
 aligned with Q82134_9DELA | Q82134 from UniProtKB/TrEMBL  Length:125

    Alignment length:116
                                    10        20        30        40        50        60        70        80        90       100       110      
         Q82134_9DELA     1 PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVLPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP 116
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......eeeeeee......eeeeeee.......eee.hhh......eeeeee....eeeeeeee....eeee.......eee...eee.....eeehhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3lix A   1 PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVIPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with Q82134_9DELA | Q82134 from UniProtKB/TrEMBL  Length:125

    Alignment length:116
                                    10        20        30        40        50        60        70        80        90       100       110      
         Q82134_9DELA     1 PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVLPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP 116
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----RVP-3lixB01 B:6-114                                                                                          -- Pfam domains (1)
           Pfam domains (2) -----RVP-3lixB02 B:6-114                                                                                          -- Pfam domains (2)
         Sec.struct. author .eee.......eeeeeee......eeeeeee.......eee.hhh.....eee..eee..eee...eeee...eeee.......eee...eee......eehhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3lix B   1 PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVIPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP 116
                                    10        20        30        40        50        60        70        80        90       100       110
   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 3LIX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LIX)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Peptidase_AA (368)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q82134_9DELA | Q82134)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    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: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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

 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
    E17  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3lix)
 
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
  3lix
    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
  Q82134_9DELA | Q82134
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q82134_9DELA | Q82134
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q82134_9DELA | Q82134: 3lin 3liq 3lit 3liv 3liy 3wsj 4ydf

(-) Related Entries Specified in the PDB File

2b7f 3lin 3liq 3lit 3liv 3liy