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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF GEBA250068378 FROM SULFUROSPIRILLUM DELEYIANUM
 
Authors :  Y. Kim, N. Marshall, G. Cobb, J. Eisen, C. Kerfeld, A. Joachimiak, Midwe For Structural Genomics (Mcsg)
Date :  19 Jun 10  (Deposition) - 18 Aug 10  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Geba Target, Bata-Fold, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, N. Marshall, G. Cobb, J. Eisen, C. Kerfeld, A. Joachimiak
Crystal Structure Of Geba250068378 From Sulfurospirillum Deleyianum
To Be Published 2010
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN GEBA250068378
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: SDEL_1248
    Organism Scientific: SULFUROSPIRILLUM DELEYIANUM
    Organism Taxid: 525898
    Strain: DSM 6946

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1ACY5Ligand/IonACETIC ACID
2GOL3Ligand/IonGLYCEROL
3MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2GOL2Ligand/IonGLYCEROL
3MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2GOL1Ligand/IonGLYCEROL
3MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:123 , TYR A:128 , HOH A:192BINDING SITE FOR RESIDUE ACY A 175
2AC2SOFTWARESER A:26 , TRP A:27 , SER A:136 , LEU A:137 , ASP A:138BINDING SITE FOR RESIDUE GOL A 176
3AC3SOFTWAREPRO A:1 , ASN A:2 , ILE A:4 , TYR A:29 , HOH A:195BINDING SITE FOR RESIDUE ACY A 177
4AC4SOFTWARELYS A:111 , HOH A:293BINDING SITE FOR RESIDUE ACY A 178
5AC5SOFTWAREASN A:116 , LEU A:117 , TYR A:118 , HOH A:265 , HOH A:277BINDING SITE FOR RESIDUE GOL A 179
6AC6SOFTWAREASN B:123 , TYR B:128 , HOH B:194BINDING SITE FOR RESIDUE ACY B 175
7AC7SOFTWAREGLN B:103 , ILE B:113 , LEU B:137 , ASP B:138 , TYR B:142BINDING SITE FOR RESIDUE ACY B 176
8AC8SOFTWAREASN B:58 , TYR B:60 , ASP B:91 , HOH B:205 , HOH B:227BINDING SITE FOR RESIDUE GOL B 177

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NKG)

(-) 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:170
 aligned with D1B2F0_SULD5 | D1B2F0 from UniProtKB/TrEMBL  Length:190

    Alignment length:170
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
         D1B2F0_SULD5    19 NPNPISIPIDLSQAGSVVEKEVKIEESWSYHLILQFAVHDRKEDGGLDGKRVWKFLGFNSYDPRDGKQVGYVDYRLAKSELGDLIDETYDCDGTVVPIKITIHQINQDNTKKLIADNLYMTKGNGSGAYTRDITTISLDKGKYIFRIENIEAFSEMIGRKVDFTIYINKR 188
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee......eeeeeeeee...eeeeeeeee.........hhhhhhhhhhhh..ee......eee..hhhhhhhhhhhhh..........eeeeeeeeee.....eeeeeeeeeee........eeeeeeeee..eeeeeeeee...hhhhh...eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nkg A   0 APNPISIPIDLSQAGSVVEKEVKIEESWSYHLILQFAVHDRKEDGGLDGKRVWKFLGFNSYDPRDGKQVGYVDYRLAKSELGDLIDETYDCDGTVVPIKITIHQINQDNTKKLIADNLYmTKGNGSGAYTRDITTISLDKGKYIFRIENIEAFSEmIGRKVDFTIYINKR 169
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149     | 159       169
                                                                                                                                                 119-MSE                             155-MSE          


Chain B from PDB  Type:PROTEIN  Length:170
 aligned with D1B2F0_SULD5 | D1B2F0 from UniProtKB/TrEMBL  Length:190

    Alignment length:170
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
         D1B2F0_SULD5    19 NPNPISIPIDLSQAGSVVEKEVKIEESWSYHLILQFAVHDRKEDGGLDGKRVWKFLGFNSYDPRDGKQVGYVDYRLAKSELGDLIDETYDCDGTVVPIKITIHQINQDNTKKLIADNLYMTKGNGSGAYTRDITTISLDKGKYIFRIENIEAFSEMIGRKVDFTIYINKR 188
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.......eeeeeeeee...eeeeeeeee...hhhhhhhhhhhhhhhhhh..ee......eee..hhhhhhhhhhhhh..........eeeeeeeeee.....eeeeeeeeeee........eeeeeeeee..eeeeeeeee...hhhhh...eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nkg B   0 APNPISIPIDLSQAGSVVEKEVKIEESWSYHLILQFAVHDRKEDGGLDGKRVWKFLGFNSYDPRDGKQVGYVDYRLAKSELGDLIDETYDCDGTVVPIKITIHQINQDNTKKLIADNLYmTKGNGSGAYTRDITTISLDKGKYIFRIENIEAFSEmIGRKVDFTIYINKR 169
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149     | 159       169
                                                                                                                                                 119-MSE                             155-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 3NKG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NKG)

(-) Gene Ontology  (0, 0)

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

 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
    ACY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nkg)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  3nkg
    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
  D1B2F0_SULD5 | D1B2F0
    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
  D1B2F0_SULD5 | D1B2F0
    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 3NKG)

(-) Related Entries Specified in the PDB File

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