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 :  PYRIDOXAL KINASE OF ENTAMOEBA HISTOLYTICA WITH ADP
 
Authors :  K. F. Tarique, S. Devi, S. A. Abdul Rehman, S. Gourinath
Date :  13 Jan 15  (Deposition) - 28 Jan 15  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyridoxal 5'-Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. F. Tarique, S. Devi, S. A. Abdul Rehman, S. Gourinath
Pyridoxal Kinase From Entamoeba Histolytica
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PYRIDOXAL KINASE
    Chains: A, B
    EC Number: 2.7.1.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: EHI_126090
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 5759

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG4Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:116 , ASN A:143 , THR A:179 , SER A:180 , ILE A:187 , ILE A:206 , PRO A:207 , ARG A:208 , ILE A:209 , GLY A:211 , VAL A:216 , GLY A:217 , ILE A:242 , LEU A:245 , GLN A:246 , LEU A:249 , MG A:303 , HOH A:421 , HOH A:428 , HOH A:454 , HOH A:471 , HOH A:480 , HOH A:531 , HOH A:542 , HOH A:543 , HOH A:554BINDING SITE FOR RESIDUE ADP A 301
2AC2SOFTWAREASP A:111 , THR A:141 , HOH A:401 , HOH A:402 , HOH A:550 , HOH A:554BINDING SITE FOR RESIDUE MG A 302
3AC3SOFTWAREASP A:116 , ADP A:301 , HOH A:421 , HOH A:480BINDING SITE FOR RESIDUE MG A 303
4AC4SOFTWAREASP B:111 , THR B:141 , HOH B:490 , HOH B:545 , HOH B:548 , HOH B:551BINDING SITE FOR RESIDUE MG B 301
5AC5SOFTWAREASP B:116 , ASN B:143 , THR B:179 , SER B:180 , ILE B:187 , ARG B:208 , ILE B:209 , GLY B:211 , PHE B:213 , VAL B:216 , GLY B:217 , LEU B:245 , GLN B:246 , LEU B:249 , MG B:303 , HOH B:401 , HOH B:402 , HOH B:417 , HOH B:445 , HOH B:449 , HOH B:452 , HOH B:548BINDING SITE FOR RESIDUE ADP B 302
6AC6SOFTWAREASP B:116 , ADP B:302 , HOH B:401 , HOH B:402 , HOH B:449BINDING SITE FOR RESIDUE MG B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S1H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4S1H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S1H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S1H)

(-) Exons   (0, 0)

(no "Exon" information available for 4S1H)

(-) 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:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.......hhhhhhhhhhhhh...eeeee.eee..........eee.hhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhhh.....eeee....ee..ee..hhhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee........eeeeee.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...........hhhhh.........ee...hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s1h A   1 MTNKVLTISSYVCSGFVGNRCGMIILDSFQIQSIFVLTTHLANHTGYPVVGGSGVLLNDFISIMDSLEVNHLDKDIEFLVTGYFPSSDLVYETINRVKRIKDNKKVYFLCDPILGDNGKMYTKSEVQDSMKELIKYADIITPNATELSFLTGLEVNSVSEAIKACHILHEQGIPVILVTSIKEGNDIILLCSFKDTLNNKNFTIKIPRIEGDFTGVGDTLTYILLSWIIKGIPLEHAVNRAISTLQTILRNTVGTAEINIINCIPYLKGTEESFTITYILEHHHHHH 287
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       


Chain B from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.......hhhhhhhhhhhhh...eeeee.eee..........eee.hhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhhh.....eeee....ee..ee....hhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee........eeeeee.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...........hhhhh.........ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s1h B   1 MTNKVLTISSYVCSGFVGNRCGMIILDSFQIQSIFVLTTHLANHTGYPVVGGSGVLLNDFISIMDSLEVNHLDKDIEFLVTGYFPSSDLVYETINRVKRIKDNKKVYFLCDPILGDNGKMYTKSEVQDSMKELIKYADIITPNATELSFLTGLEVNSVSEAIKACHILHEQGIPVILVTSIKEGNDIILLCSFKDTLNNKNFTIKIPRIEGDFTGVGDTLTYILLSWIIKGIPLEHAVNRAISTLQTILRNTVGTAEINIINCIPYLKGTEESFTITYI 279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   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 4S1H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S1H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S1H)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4s1h)
 

(-) 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
  4s1h
    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
  C4LVZ4_ENTHI | C4LVZ4
    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)
  2.7.1.35
    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
  C4LVZ4_ENTHI | C4LVZ4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        C4LVZ4_ENTHI | C4LVZ4: 4s1i 4s1m

(-) Related Entries Specified in the PDB File

4s1i