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 :  HUMAN TRANSKETOLASE IN COVALENT COMPLEX WITH DONOR KETOSE D-XYLULOSE-5-PHOSPHATE, CRYSTAL 2
 
Authors :  P. Neumann, S. Luedtke, R. Ficner, K. Tittmann
Date :  28 May 13  (Deposition) - 21 Aug 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.97
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Thiamin Diphosphate, Enzyme Catalysis, Pentose Phosphate Pathway, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ludtke, P. Neumann, K. M. Erixon, F. Leeper, R. Kluger, R. Ficner, K. Tittmann
Sub-Angstrom-Resolution Crystallography Reveals Physical Distortions That Enhance Reactivity Of A Covalent Enzymatic Intermediate.
Nat Chem V. 5 762 2013
PubMed-ID: 23965678  |  Reference-DOI: 10.1038/NCHEM.1728

(-) Compounds

Molecule 1 - TRANSKETOLASE
    Chains: A
    EC Number: 2.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TKT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TK

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric Unit (5, 17)
No.NameCountTypeFull Name
1DX52Ligand/IonD-XYLITOL-5-PHOSPHATE
2EDO12Ligand/Ion1,2-ETHANEDIOL
3MG1Ligand/IonMAGNESIUM ION
4NA1Ligand/IonSODIUM ION
5TDP1Ligand/IonTHIAMIN DIPHOSPHATE
Biological Unit 1 (3, 30)
No.NameCountTypeFull Name
1DX54Ligand/IonD-XYLITOL-5-PHOSPHATE
2EDO24Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION
5TDP2Ligand/IonTHIAMIN DIPHOSPHATE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:155 , ASN A:185 , LEU A:187 , TDP A:1015 , HOH A:7001BINDING SITE FOR RESIDUE MG A 1001
02AC2SOFTWAREPRO A:63 , ASN A:68 , ASP A:69 , ARG A:70 , PHE A:71 , ARG A:379 , HOH A:7186 , HOH A:7847BINDING SITE FOR RESIDUE EDO A 1002
03AC3SOFTWARETYR A:564 , ALA A:588 , ASN A:590 , HOH A:7051 , HOH A:7055 , HOH A:7126 , HOH A:7247BINDING SITE FOR RESIDUE EDO A 1003
04AC4SOFTWAREPHE A:71 , VAL A:72 , LEU A:73 , LEU A:82 , PHE A:117 , HOH A:7040 , HOH A:7056 , HOH A:7068BINDING SITE FOR RESIDUE EDO A 1004
05AC5SOFTWAREASP A:155 , GLY A:156 , LEU A:158 , SER A:159 , TRP A:164 , PRO A:194 , LEU A:195 , TYR A:202 , ARG A:205 , EDO A:1012 , HOH A:7467 , HOH A:7960 , HOH A:7961BINDING SITE FOR RESIDUE EDO A 1005
06AC6SOFTWARELEU A:92 , LEU A:107 , GLN A:115 , HOH A:7110 , HOH A:7124 , HOH A:7174 , HOH A:7920BINDING SITE FOR RESIDUE EDO A 1006
07AC7SOFTWAREGLN A:10 , ASN A:590 , ARG A:591 , HOH A:7260BINDING SITE FOR RESIDUE EDO A 1007
08AC8SOFTWARETYR A:137 , TYR A:141 , TYR A:173 , HOH A:7409 , HOH A:7610 , HOH A:7914BINDING SITE FOR RESIDUE EDO A 1008
09AC9SOFTWAREALA A:33 , ARG A:101 , GLU A:423 , LYS A:597 , HOH A:7103 , HOH A:7586 , HOH A:7742 , HOH A:7934BINDING SITE FOR RESIDUE EDO A 1009
10BC1SOFTWAREARG A:21 , SER A:25 , ALA A:84 , GLU A:88 , GLU A:94 , LEU A:97 , LYS A:283 , HOH A:7177 , HOH A:7472 , HOH A:7672BINDING SITE FOR RESIDUE EDO A 1010
11BC2SOFTWAREPHE A:142 , ASP A:333 , ARG A:358 , HOH A:7406 , HOH A:7539 , HOH A:7700 , HOH A:7894BINDING SITE FOR RESIDUE EDO A 1011
12BC3SOFTWARELEU A:158 , SER A:159 , TRP A:164 , GLU A:165 , ALA A:168 , PHE A:209 , EDO A:1005 , EDO A:1014 , HOH A:7961BINDING SITE FOR RESIDUE EDO A 1012
13BC4SOFTWAREASN A:411 , ALA A:461 , THR A:464 , CYS A:468 , HOH A:7070 , HOH A:7081BINDING SITE FOR RESIDUE NA A 1013
14BC5SOFTWARESER A:159 , GLU A:165 , ALA A:168 , EDO A:1012 , HOH A:7467 , HOH A:7715BINDING SITE FOR RESIDUE EDO A 1014
15BC6SOFTWARESER A:40 , LYS A:75 , HIS A:77 , GLY A:123 , SER A:124 , LEU A:125 , GLY A:154 , ASP A:155 , GLY A:156 , GLU A:157 , GLU A:160 , ASN A:185 , LEU A:187 , GLY A:188 , GLN A:189 , LYS A:244 , HIS A:258 , ASP A:341 , ILE A:364 , GLU A:366 , PHE A:392 , ARG A:395 , GLN A:428 , MG A:1001 , DX5 A:1016 , HOH A:7001BINDING SITE FOR RESIDUE TDP A 1015
16BC7SOFTWAREHIS A:37 , HIS A:77 , HIS A:110 , GLN A:189 , HIS A:258 , SER A:345 , PHE A:389 , HIS A:416 , ASP A:424 , GLN A:428 , ARG A:474 , TDP A:1015 , DX5 A:1017 , HOH A:7053 , HOH A:7095 , HOH A:7108 , HOH A:7246 , HOH A:7263 , HOH A:7299BINDING SITE FOR RESIDUE DX5 A 1016
17BC8SOFTWAREHIS A:37 , GLN A:189 , HIS A:258 , ARG A:318 , SER A:345 , HIS A:416 , ASP A:424 , ARG A:474 , DX5 A:1016 , HOH A:7108 , HOH A:7246 , HOH A:7263 , HOH A:7272 , HOH A:7299BINDING SITE FOR RESIDUE DX5 A 1017

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:538 -Pro A:539

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KXW)

(-) 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:621
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...............eeee.hhhhhhhhhhhhhhh...hhhhhhhh..........................hhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhh....eeeeeee.............hhhhhhhhhhhh..eeeeee..hhhhhhhhhh......eeeeee.....................hhhhhhhhhhhhhh.....................................eeehhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhhh...eeeeee..hhhhh..hhhhh..hhhhhhhh....eee...hhhhhhhhhhhhhh...eeeee....eee..............eeee....eeeeee..hhhhhhhhhhhhhhhh...eeeeee..eee..hhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhh.....eeeeeee.......hhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kxw A   2 ESYHKPDQQKLQALKDTANRLRISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMRYKSQDPRNPHNDRFVLSKGHAAPILYAVWAEAGFLAEAELLNLRKISSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTGKYFDKASYRVYCLLGDGELSEGSVWEAMAFASIYKLDNLVAILDINRLGQSDPAPLQHQMDIYQKRCEAFGWHAIIVDGHSVEELCKAFGQAKHQPTAIIAKTFKGRGITGVEDKESWHGKPLPKNMAEQIIQEIYSQIQSKKKILATPPQEDAPSVDIANIRMPSLPSYKVGDKIATRKAYGQALAKLGHASDRIIALDGDTKNSTFSEIFKKEHPDRFIECYIAEQNMVSIAVGCATRNRTVPFCSTFAAFFTRAFDQIRMAAISESNINLCGSHCGVSIGEDGPSQMALEDLAMFRSVPTSTVFYPSDGVATEKAVELAANTKGICFIRTSRPENAIIYNNNEDFQVGQAKVVLKSKDDQVTVIGAGVTLHEALAAAELLKKEKINIRVLDPFTIKPLDRKLILDSARATKGRILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNRVPRSGKPAELLKMFGIDRDAIAQAVRGLITK 622
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621
   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 4KXW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

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
    DX5  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TDP  [ 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 ]
 
  Cis Peptide Bonds
    Lys A:538 - Pro A:539   [ 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
  4kxw
    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
  TKT_HUMAN | P29401
    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)
  2.2.1.1
    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
  TKT_HUMAN | P29401
    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
        TKT_HUMAN | P29401: 3mos 3ooy 4kxu 4kxv 4kxx 4kxy

(-) Related Entries Specified in the PDB File

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