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 :  ENSEMBLE REFINEMENT OF PLU4264 PROTEIN FROM PHOTORHABDUS LUMINESCENS
 
Authors :  F. Wang, K. Michalska, H. Li, R. Jedrzejczak, G. Babnigg, C. A. Bingman, R. Yennamalli, S. Weerth, M. D. Miller, M. G. Thomas, A. Joachimiak, G. N. Phillips Jr. , Enzyme Discovery For Natural Product Biosy (Natpro), Midwest Center For Structural Genomics (Mcsg)
Date :  07 Apr 14  (Deposition) - 07 May 14  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B  (20x)
Biol. Unit 1:  A,B  (1x)
Keywords :  Structural Genomics, Protein Structure Initiative, Enzyme Discovery For Natural Product Biosynthesis, Natpro, Midwest Center For Structural Genomics, Mcsg, Cupin, Unknown Function, Psi-Biology (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. S. Weerth, K. Michalska, C. A. Bingman, R. M. Yennamalli, H. Li, R. Jedrzejczak, F. Wang, G. Babnigg, A. Joachimiak, M. G. Thomas, G. N. Phillips
Structure Of A Cupin Protein Plu4264 From Photorhabdus Luminescens Subsp. Laumondii Tto1 At 1. 35 Angstrom Resolution.
Proteins V. 83 383 2015
PubMed-ID: 25354690  |  Reference-DOI: 10.1002/PROT.24705

(-) Compounds

Molecule 1 - PLU4264 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PLU4264
    Organism Scientific: PHOTORHABDUS LUMINESCENS SUBSP. LAUMONDII
    Organism Taxid: 243265
    Strain: TT01

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit (20x): AB
Biological Unit 1 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2NA1Ligand/IonSODIUM ION
3NI2Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:50 , HIS A:52 , GLU A:56 , HIS A:90 , HOH A:334BINDING SITE FOR RESIDUE NI A 201
2AC2SOFTWAREHOH A:381 , ASP B:11BINDING SITE FOR RESIDUE NA A 202
3AC3SOFTWAREHIS B:50 , HIS B:52 , GLU B:56 , HIS B:90BINDING SITE FOR RESIDUE NI B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q29)

(-) Cis Peptide Bonds  (2, 40)

Asymmetric Unit
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Leu A:25 -Pro A:26
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Leu B:25 -Pro B:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q29)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q29)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q29)

(-) 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:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..hhhhheee..eeeee...........eeeeeee...ee........eeeeeeee.eeeeee..eeeeee...eeee.....eeeee.....eeeeeeeehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q29 A   2 mNIIRKmDWDSmVHEYDLDGSRLLPWEGLNTPFGGAWCIVRPETKSFRHSHNEYELFIVIQGNAIIRINDEDFPVTKGDLIIIPLDSEHHVINNNQEDFHFYTIWWDKESTLNFLTRLEQD 122
                            |     | 11 |      21        31        41        51        61        71        81        91       101       111       121 
                            |     8-MSE|                                                                                                             
                            2-MSE     13-MSE                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.......eee..eeeee...........eeeeeee...ee........eeeeeeee.eeeeee..eeeeee...eeee.....eeeee.....eeeeeeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4q29 B   2 mNIIRKmDWDSmVHEYDLDGSRLLPWEGLNTPFGGAWCIVRPETKSFRHSHNEYELFIVIQGNAIIRINDEDFPVTKGDLIIIPLDSEHHVINNNQEDFHFYTIWWDKESTLNFLTRLEQ 121
                            |     | 11 |      21        31        41        51        61        71        81        91       101       111       121
                            2-MSE 8-MSE|                                                                                                            
                                      13-MSE
   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 4Q29)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q29)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q29)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4Q29)

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:25 - Pro A:26   [ RasMol ]  
    Leu B:25 - Pro B:26   [ 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
  4q29
    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
  Q7MZL9_PHOLL | Q7MZL9
    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
  Q7MZL9_PHOLL | Q7MZL9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q7MZL9_PHOLL | Q7MZL9: 4mv2

(-) Related Entries Specified in the PDB File

4mv2 REGULAR CRYSTAL STRUCTURE OF PLU4264 PROTEIN FROM PHOTORHABDUS LUMINESCENS RELATED ID: NATPRO-GO.119869 RELATED DB: TARGETTRACK RELATED ID: MCSG-APC109028 RELATED DB: TARGETTRACK