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
(-)Biological Unit 2
(-)Biological Unit 3
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN WITH UNKNOWN FUNCTION FROM DUF364 FAMILY (ZP_00559375.1) FROM DESULFITOBACTERIUM HAFNIENSE DCB-2 AT 2.01 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics, Joint Center For Struct Genomics (Jcsg)
Date :  22 Dec 09  (Deposition) - 02 Feb 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Rare Metals, Siderophores, Adenosyl Binding Site, Protein With Unknown Function From Duf364 Family, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Adenosyl Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Miller, L. Aravind, C. Bakolitsa, C. L. Rife, D. Carlton, P. Abdubek, T. Astakhova, H. L. Axelrod, H. J. Chiu, T. Clayton, M. C. Deller, L. Duan, J. Feuerhelm, J. C. Grant, G. W. Han, L. Jaroszewski, K. K. Jin, H. E. Klock, M. W. Knuth, P. Kozbial, S. S. Krishna, A. Kumar, D. Marciano, D. Mcmullan, A. T. Morse, E. Nigoghossian, L. Okach, R. Reyes, H. Van Den Bedem, D. Weekes, Q. Xu, K. O. Hodgson, J. Wooley, M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Structure Of The First Representative Of Pfam Family Pf0401 (Duf364) Reveals Enolase And Rossmann-Like Folds That Combine To Form A Unique Active Site With A Possible Role I Heavy-Metal Chelation.
Acta Crystallogr. , Sect. F V. 66 1167 2010
PubMed-ID: 20944207  |  Reference-DOI: 10.1107/S1744309110007517

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN FROM DUF364 FAMILY
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DHAF_4260
    Organism Scientific: DESULFITOBACTERIUM HAFNIENSE
    Organism Taxid: 272564
    Strain: DCB-2 / DSM 10664

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 24)

Asymmetric Unit (4, 24)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO6Ligand/Ion1,2-ETHANEDIOL
3IMD4Ligand/IonIMIDAZOLE
4MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3IMD2Ligand/IonIMIDAZOLE
4MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3IMD2Ligand/IonIMIDAZOLE
4MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (3, 22)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO6Ligand/Ion1,2-ETHANEDIOL
3IMD4Ligand/IonIMIDAZOLE
4MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:148 , TRP A:149 , IMD A:303 , HOH A:372 , HOH A:445BINDING SITE FOR RESIDUE CL A 301
02AC2SOFTWARETRP A:149 , LEU A:158 , THR A:174 , SER A:177 , ASP A:180 , THR A:182 , CL A:301 , HOH A:445BINDING SITE FOR RESIDUE IMD A 303
03AC3SOFTWAREPRO A:40 , ARG A:42 , TYR A:72 , ALA A:176 , ASP A:180 , HOH A:482BINDING SITE FOR RESIDUE IMD A 304
04AC4SOFTWAREGLY A:200 , SER A:218 , GLY A:219 , TYR A:241 , LYS A:246 , EDO A:311BINDING SITE FOR RESIDUE EDO A 307
05AC5SOFTWAREASP A:111 , PRO A:112 , LYS A:246 , EDO A:307 , HOH A:489BINDING SITE FOR RESIDUE EDO A 311
06AC6SOFTWAREGLU B:148 , TRP B:149 , IMD B:302 , EDO B:310 , HOH B:477BINDING SITE FOR RESIDUE CL B 301
07AC7SOFTWAREVAL B:128 , LEU B:158 , ALA B:176 , SER B:177 , ASP B:180 , THR B:182 , CL B:301 , HOH B:477BINDING SITE FOR RESIDUE IMD B 302
08AC8SOFTWAREPRO B:40 , ARG B:42 , GLU B:45 , TYR B:72 , ALA B:176BINDING SITE FOR RESIDUE IMD B 305
09AC9SOFTWAREGLU B:20 , ARG B:31 , ASN B:225 , ALA B:226 , PHE B:229BINDING SITE FOR RESIDUE EDO B 306
10BC1SOFTWAREGLN B:-1 , PHE B:-2 , MSE B:1 , TRP B:2BINDING SITE FOR RESIDUE EDO B 308
11BC2SOFTWAREASP B:15 , GLY B:154 , TYR B:156BINDING SITE FOR RESIDUE EDO B 309
12BC3SOFTWAREGLY B:129 , HIS B:130 , THR B:174 , CL B:301BINDING SITE FOR RESIDUE EDO B 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L5O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L5O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L5O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L5O)

(-) Exons   (0, 0)

(no "Exon" information available for 3L5O)

(-) 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:247
 aligned with B8FUJ5_DESHD | B8FUJ5 from UniProtKB/TrEMBL  Length:251

    Alignment length:254
                               1                                                                                                                                                                                                                                                          
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247    
         B8FUJ5_DESHD     - ---MWEIYDAMINGIPEDFLVDELVCGTTHSVIRSGNGVGLGPNRPFETRMPMLTQNLLGLPLRVAAGCVKSWNYVEASIGLAAINAYYNNPQVAREHGVIFSDAKRVEDRMNDPFIMSQNEVKGKKVGVVGHFPHLESLLEPICDLSILEWSPEEGDYPLPASEFILPECDYVYITCASVVDKTLPRLLELSRNARRITLVGPGTPLAPVLFEHGLQELSGFMVKDNARAFRIVAGAEKVKIYSAGQKVTIKK 251
               SCOP domains d3l5oa_ A: Hypothetical protein Dhaf_3308                                                                                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh........eeee...eeeeee..eeeeee.......hhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......-------.hhhhhh.......eeeee....hhhhhhh...eeeeee.......ee..hhhhhhhhh.eeeeehhhhhh.hhhhhhhhh....eeeee......hhhhhhh...eeeeeee.hhhhhhhhhh.....hhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l5o A  -2 FQGmWEIYDAmINGIPEDFLVDELVCGTTHSVIRSGNGVGLGPNRPFETRmPmLTQNLLGLPLRVAAGCVKSWNYVEASIGLAAINAYYNNPQVAREHGVIFSDA-------NDPFImSQNEVKGKKVGVVGHFPHLESLLEPICDLSILEWSPEEGDYPLPASEFILPECDYVYITCASVVDKTLPRLLELSRNARRITLVGPGTPLAPVLFEHGLQELSGFmVKDNARAFRIVAGAEKVKIYSAGQKVTIKK 251
                               |     7|       17        27        37        47| |     57        67        77        87        97    |    -  |    117       127       137       147       157       167       177       187       197       207       217   |   227       237       247    
                               |      8-MSE                                  48-MSE                                               102     110    |                                                                                                       221-MSE                          
                               1-MSE                                           50-MSE                                                          115-MSE                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:244
 aligned with B8FUJ5_DESHD | B8FUJ5 from UniProtKB/TrEMBL  Length:251

    Alignment length:256
                                 1                                                                                                                                                                                                                                                          
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245      
         B8FUJ5_DESHD     - -----MWEIYDAMINGIPEDFLVDELVCGTTHSVIRSGNGVGLGPNRPFETRMPMLTQNLLGLPLRVAAGCVKSWNYVEASIGLAAINAYYNNPQVAREHGVIFSDAKRVEDRMNDPFIMSQNEVKGKKVGVVGHFPHLESLLEPICDLSILEWSPEEGDYPLPASEFILPECDYVYITCASVVDKTLPRLLELSRNARRITLVGPGTPLAPVLFEHGLQELSGFMVKDNARAFRIVAGAEKVKIYSAGQKVTIKK 251
               SCOP domains d3l5ob_ B: Hypothetical protein Dhaf_3308                                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------DUF4213-3l5oB03 B:4-87                                                              ---------------------------DUF364-3l5oB01 B:115-251                                                                                                                  Pfam domains (1)
           Pfam domains (2) --------DUF4213-3l5oB04 B:4-87                                                              ---------------------------DUF364-3l5oB02 B:115-251                                                                                                                  Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhh.........eeee...eeeeee..eeeeee.......hhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......------------hhhhh....eeeee..hhhhhhhhhhhheeeeee.......ee..hhhhhhhhh.eeeeehhhhhh.hhhhhhhhh....eeeee......hhhhhhh...eeeeeee.hhhhhhhhhh.....hhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l5o B  -4 LYFQGmWEIYDAmINGIPEDFLVDELVCGTTHSVIRSGNGVGLGPNRPFETRmPmLTQNLLGLPLRVAAGCVKSWNYVEASIGLAAINAYYNNPQVAREHGVIFSDA------------mSQNEVKGKKVGVVGHFPHLESLLEPICDLSILEWSPEEGDYPLPASEFILPECDYVYITCASVVDKTLPRLLELSRNARRITLVGPGTPLAPVLFEHGLQELSGFmVKDNARAFRIVAGAEKVKIYSAGQKVTIKK 251
                                 |   5  |     15        25        35        45  | |   55        65        75        85        95      |  -       115       125       135       145       155       165       175       185       195       205       215     | 225       235       245      
                                 1-MSE  8-MSE                                  48-MSE                                               102          115-MSE                                                                                                   221-MSE                          
                                                                                 50-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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L5O)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: DUF364] (2)
(-)
Clan: no clan defined [family: DUF4213] (2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3L5O)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IMD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3l5o)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 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
  3l5o
    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
  B8FUJ5_DESHD | B8FUJ5
    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
  B8FUJ5_DESHD | B8FUJ5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3L5O)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3L5O)