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 :  CRYSTAL STRUCTURE OF MILB COMPLEXED WITH CYTIDINE 5'-MONOPHOSPHATE
 
Authors :  M. D. Sikowitz, L. E. Cooper, T. P. Begley, P. A. Kaminski, S. E. Ealick
Date :  27 Feb 13  (Deposition) - 11 Sep 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cmp N-Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Sikowitz, L. E. Cooper, T. P. Begley, P. A. Kaminski, S. E. Ealick
Reversal Of The Substrate Specificity Of Cmp N-Glycosidase To Dcmp.
Biochemistry V. 52 4037 2013
PubMed-ID: 23659472  |  Reference-DOI: 10.1021/BI400316P

(-) Compounds

Molecule 1 - CMP/HYDROXYMETHYL CMP HYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MILB
    Organism Scientific: STREPTOMYCES RIMOFACIENS
    Organism Taxid: 504097

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1C5P2Ligand/IonCYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:17 , GLY A:19 , GLY A:20 , PRO A:21 , PHE A:22 , ARG A:23 , ALA A:58 , ARG A:61 , GLU A:62 , PHE A:68 , ASP A:78 , SER A:97 , PRO A:98 , GLY A:99 , THR A:100 , GLU A:103 , HOH A:313 , HOH A:333 , HOH A:394 , PHE B:126 , LEU B:127BINDING SITE FOR RESIDUE C5P A 201
2AC2SOFTWAREPHE A:126 , LEU A:127 , PHE B:17 , GLY B:19 , GLY B:20 , PRO B:21 , PHE B:22 , ARG B:23 , ALA B:58 , ARG B:61 , GLU B:62 , PHE B:68 , ALA B:74 , ASP B:78 , SER B:97 , PRO B:98 , GLY B:99 , THR B:100 , GLU B:103 , HOH B:320 , HOH B:322 , HOH B:331BINDING SITE FOR RESIDUE C5P B 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:94 -Pro A:95
2Val B:94 -Pro B:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JEM)

(-) 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:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhh.......hhhhhhhhhhhhhhhhh...eeeehhhhhhhhh...hhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhhh...eeeeee.....hhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jem A  12 AVGSVFLGGPFRQLVDPRTGVMSSGDQNVFSRLIEHFESRGTTVYNAHRREAWGAEFLSPAEATRLDHDEIKAADVFVAFPGVPASPGTHVEIGWASGMGKPMVLLLERDEDYAFLVTGLESQANVEILRFSGTEEIVERLDGAVARVLGRAGEPTV 168
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       


Chain B from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhh.......hhhhhhhhhhhhhhhhh...eeeehhhhhhhhh...hhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jem B  10 APAVGSVFLGGPFRQLVDPRTGVMSSGDQNVFSRLIEHFESRGTTVYNAHRREAWGAEFLSPAEATRLDHDEIKAADVFVAFPGVPASPGTHVEIGWASGMGKPMVLLLERDEDYAFLVTGLESQANVEILRFSGTEEIVERLDGAVARVLGR 162
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
   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 4JEM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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
    C5P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:94 - Pro A:95   [ RasMol ]  
    Val B:94 - Pro B:95   [ RasMol ]  
 

(-) 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
  4jem
    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
  B4Y381_9ACTN | B4Y381
    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
  B4Y381_9ACTN | B4Y381
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B4Y381_9ACTN | B4Y381: 4jel 4ohb 4ohr

(-) Related Entries Specified in the PDB File

4jel 4jen