Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PKNI KINASE DOMAIN, C20A_R136A DOUBLE MUTANT
 
Authors :  M. N. Lisa, T. Wagner, M. Alexandre, N. Barilone, B. Raynal, P. M. Alzari M. Bellinzoni
Date :  03 Oct 16  (Deposition) - 11 Jan 17  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.03
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tuberculosis, Kinase, Signalling, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. N. Lisa, T. Wagner, M. Alexandre, N. Barilone, B. Raynal, P. M. Alzari, M. Bellinzoni
The Crystal Structure Of Pkni From Mycobacterium Tuberculosis Shows An Inactive, Pseudokinase-Like Conformation.
Febs J. V. 284 602 2017
PubMed-ID: 28054744  |  Reference-DOI: 10.1111/FEBS.14003

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PKNI
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: PKNI, RV2914C, MTCY338.02C
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5M08)

(-) Sites  (0, 0)

(no "Site" information available for 5M08)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M08)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:105 -Pro A:106
2Phe B:105 -Pro B:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M08)

(-) Exons   (0, 0)

(no "Exon" information available for 5M08)

(-) 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:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee..eeeeeeeeee..eeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee....eeeeee...eeehhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh........hhh.eeee.....eee............hhhhhh.....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m08 A   1 MALASGVTFAGYTVVRMLGASAMGEVYLVQHPGFPGWQALKVLSPAMAADDEFRRRFQRETEVAARLFHPHILEVHDRGEFDGQLWIAMDYVDGIDATQHMADRFPAVLPVGEVLAIVTAVAGALDYAHQRGLLHADVNPANVVLTSQDQRILLADFGIASQPSYPAPELSAGADVDGRADQYALALTAIHLFAGAPPVDRQPPKLSAFRPDLARLDGVLSRALATAPADRFGSCREFADAMNEQAG 256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       153       163       173       183       193       203||     219       229       239       249       
                                                                                                                                                                             148|                                                 204|                                             
                                                                                                                                                                              152                                                  211                                             


Chain B from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee..eeeeeeeeee..eeeeeee.......eeeeeehhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee....eeeeee...eeehhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh........hhh.eeee.....eee............hhhhhh.....hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m08 B   1 MALASGVTFAGYTVVRMLGASAMGEVYLVQHPGFPGWQALKVLSPAMAADDEFRRRFQRETEVAARLFHPHILEVHDRGEFDGQLWIAMDYVDGIDATQHMADRFPAVLPVGEVLAIVTAVAGALDYAHQRGLLHADVNPANVVLTSQDQRILLADFGIASQPSYPAPELSAGADVDGRADQYALALTAIHLFAGAPPVDRSHTGPLQPPKLSAFRPDLARLDGVLSRALATAPADRFGSCREFADAMNEQAG 256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       153       163       173       183       193       203       213       223       233       243       253   
                                                                                                                                                                             148|                                                                                                        
                                                                                                                                                                              152
   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 5M08)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M08)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M08)

(-) Gene Ontology  (19, 19)

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
(no "Ligands, Modified Residues, Ions" information available for 5m08)
 
  Sites
(no "Sites" information available for 5m08)
 
  Cis Peptide Bonds
    Phe A:105 - Pro A:106   [ RasMol ]  
    Phe B:105 - Pro B:106   [ RasMol ]  
 
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 | Biol. Unit 1 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
  5m08
    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
  PKNI_MYCTU | P9WI69
    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)
  2.7.11.1
    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
  PKNI_MYCTU | P9WI69
    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
        PKNI_MYCTU | P9WI69: 5m06 5m07 5m09

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5M08)