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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE LON-LIKE PROTEASE MTALONC IN COMPLEX WITH BORTEZOMIB
 
Authors :  C. I. Chang, C. I. Kuo, K. F. Huang
Date :  30 Jun 12  (Deposition) - 26 Jun 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Lon Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Liao, K. Ihara, C. I. Kuo, K. F. Huang, S. Wakatsuki, S. H. Wu, C. I. Chang
Structures Of An Atp-Independent Lon-Like Protease And Its Complexes With Covalent Inhibitors
Acta Crystallogr. , Sect. D V. 69 1395 2013
PubMed-ID: 23897463  |  Reference-DOI: 10.1107/S0907444913008214

(-) Compounds

Molecule 1 - TTC1975 PEPTIDASE
    Chains: A
    EC Number: 3.4.21.53
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: MEIOTHERMUS TAIWANENSIS
    Organism Taxid: 172827
    Synonym: LON-LIKE PROTEASE MTALONC

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1BO21Ligand/IonN-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1BO26Ligand/IonN-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
2PO46Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:503 , VAL A:504 , VAL A:576 , SER A:577 , ILE A:578 , GLU A:579 , GLY A:580 , ASP A:581 , SER A:582 , ALA A:583 , LYS A:625 , HOH A:938 , HOH A:1223 , HOH A:1241BINDING SITE FOR RESIDUE BO2 A 801
2AC2SOFTWARESER A:56 , LEU A:57 , GLY A:58 , LYS A:59 , HIS A:60 , HOH A:933 , HOH A:981 , HOH A:1023 , HOH A:1040 , HOH A:1174BINDING SITE FOR RESIDUE PO4 A 802

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:229 -Ala A:230
2Thr A:262 -Pro A:263
3Ala A:508 -Pro A:509

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FWD)

(-) 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:587
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh......................hhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhh.........eeeee....eeeeee........hhhhhhh.........................eeee.........eee....hhhhhhhee.......hhh.ee.hhhhhh...eeeeehhhhhhh.hhhhhhhhhhhh.............ee.......eeeeee..hhhhhhhhhhhhhhheeeeee...eee.hhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee.eeeeeee.......eeeeeeeeeeee...eeeehhhhh...hhhhhhhhhhhhhhhhhhh.......eeeeeee...........hhhhhhhhhhhhhhh.eee..eee..ee.....ee...hhhhhhhhhhhhhhhh......eeeee.hhhhhh..hhhhhhhhhh...eeeee.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fwd A   1 MRLSYEALEWRTPIENSTEPVSLPPPPPFFGQERAREALELAIRGGFHAYLVGPPSLGKHEALLAYLSTQSVETPPDLLYVPLSERKVAVLTLPSGQEIHLAEAVEGLQRFPQARAEALRRYAETGEPQWRPNLLTSSSSGTPPPIVYEPYATAPRLFGRLDYLVWSTNVSLIRPGAVHRAQGGYLILDALSLKREGTWEAFKRALRNGQVEPVTEPAPAGLEVEPFPIQMQVILVGTPEAFEGLEEDPAFSELFRIRAEFSPTLPASPENCTALGGWLLAQGFQLTQGGLTRLYDEARRMAEQRDRMDARLVEIRALAEEAAVLGGGLLTAESVEQAIAAREHRSFLSEEEFLRAVQEGVIRLRTTGRAVGEVNSLVVVEAAPYWGRPARLTARAAPGRDHLISIDREAGLGGQIFHKAVLTLAGYLRSRYIEHGSLPVTISLAFEQNYVSIEGDSAGLAELVAALSAIGNLPLRQDLAVTGAVDQTGKVLAVGAINAKVEGFFRVCKALGLSGTQGVILPEANLANLTLRAEVLEAVRAGQFHIYAVETAEQALEILAGARMEGFRGLQEKIRAGLEAFARLEEG 712
                                    10        20        30        40        50        60        70        80        90       100       220     ||232|      250       260       270       280    || 294       304       314       324       334      |345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       
                                                                                                                                     108|    226|  ||    244|                                 285|                                                341|                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                      219     229  ||     249                                  290                                                 343                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                 232|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                  237
   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 4FWD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

 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
    BO2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:508 - Pro A:509   [ RasMol ]  
    Glu A:229 - Ala A:230   [ RasMol ]  
    Thr A:262 - Pro A:263   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  4fwd
    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
  C9DRU9_9DEIN | C9DRU9
    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)
  3.4.21.53
    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
  C9DRU9_9DEIN | C9DRU9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        C9DRU9_9DEIN | C9DRU9: 4fw9 4fwg 4fwh 4fwv

(-) Related Entries Specified in the PDB File

4fw9 4fwg 4fwh