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 ESTERASE B FROM LACTOBACILLUS RHAMNOSIS (HN001)
 
Authors :  M. D. Bennett, R. Holland, T. S. Loo, C. A. Smith, G. E. Norris, M. -L. Dela B. F. Anderson
Date :  09 Oct 13  (Deposition) - 15 Oct 14  (Release) - 15 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (4x)
Keywords :  Alpha/Beta Hydrolase Fold, Hydrolase, Esterase Acyltransferase, Hydrolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Bennett, B. F. Anderson, G. E. Norris, M. -L. Delabre, C. A. Smith
Crystal Structure Of Esterase B From Lactobacillus Rhamnosi (Hn001)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ESTERASE/LIPASE
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX_6P3_ESTB
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PGEX 6P3
    Gene: LC705_02872, LRH_10360
    Mutation: YES
    Organism Scientific: LACTOBACILLUS RHAMNOSUS
    Organism Taxid: 568704
    Strain: LC 705

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : X
Biological Unit 1 (4x): X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3IPA3Ligand/IonISOPROPYL ALCOHOL
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3IPA12Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS X:266 , TRP X:268 , HOH X:651 , HOH X:680BINDING SITE FOR RESIDUE IPA X 401
2AC2SOFTWAREARG X:86 , HOH X:561 , HOH X:699BINDING SITE FOR RESIDUE IPA X 402
3AC3SOFTWAREGLN X:132 , PRO X:288 , GLU X:289 , GLU X:292BINDING SITE FOR RESIDUE IPA X 403
4AC4SOFTWAREARG X:30 , TRP X:37BINDING SITE FOR RESIDUE CL X 404
5AC5SOFTWARETHR X:65 , GLU X:166 , HOH X:569 , HOH X:653 , HOH X:773BINDING SITE FOR RESIDUE CA X 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N5H)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu X:107 -Pro X:108

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N5H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N5H)

(-) Exons   (0, 0)

(no "Exon" information available for 4N5H)

(-) 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 X from PDB  Type:PROTEIN  Length:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.........eeeeeee.......eeeeeee............hhhhhhhhhhh..eeeee........hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhh.hhhhhhhhh.........eeeee....hhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhh..hhhhhh.......eeeeee....hhhhhhhhhhhhhhh...eeeeeehhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n5h X   1 MADEEAMLAKVQASWAQTAARDKARYADERVPEDVHWETEYRYEQSADPQQTLNLYYPAKRRNATMPTVIDIHGGGWFYGDRNLNRNYCRYLASQGYAVMGMGYRLLPDVDLRGQIQDIFASLRWLSHFGPQRGFDLDHVLLTGDSAGGHLASLVACIQQSAELQELFGVSRVNFNFTLVALVCPVAEPSKLPEAAGDMSDMAAFYLDKLSGGDQALVDHLNFSQVVKGLDLPPFMLIGGQNDSFYLQSQALLKVFDANHVTYTTKLWPASAGPHLKHVFNVQHWEWPESIETNLEMLRTFDALSKQQDQAEENE 315
                                    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       290       300       310
   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 4N5H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N5H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N5H)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4N5H)

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IPA  [ 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 ]
 
  Cis Peptide Bonds
    Leu X:107 - Pro X:108   [ 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
  4n5h
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4N5H)

(-) Related Entries Specified in the PDB File

4n5i