Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE SUCCINOGLYCAN BIOSYNTHESIS PROTEIN. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET BCR135
 
Authors :  A. P. Kuzin, M. Abashidze, J. Seetharaman, H. Wang, L. Mao, K. Cunningham, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  14 Sep 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  X-Ray, Nesg, Bcr135, Succinoglycan Biosynthesis Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Unknown Function, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Kuzin, M. Su, J. Seetharaman, H. Wang, L. Mao, K. Cunningham, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt
Crystal Structure Of The Succinoglycan Biosynthesis Protein.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUCCINOGLYCAN BIOSYNTHESIS PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BC_3120
    Organism Scientific: BACILLUS CEREUS ATCC 14579
    Organism Taxid: 226900
    Strain: DSM 31

 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  (1, 16)

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2RAD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RAD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RAD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RAD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RAD)

(-) Exons   (0, 0)

(no "Exon" information available for 2RAD)

(-) 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:403
 aligned with Q81BN2_BACCR | Q81BN2 from UniProtKB/TrEMBL  Length:443

    Alignment length:403
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439   
         Q81BN2_BACCR    40 NQIAKWLEAHAKPLKTTNPTASLNDLKPLKNMVGSASIVGLGEATHGAHEVFTMKHRIVKYLVSEKGFTNLVLEEGWDRALELDRYVLTGKGNPSQHLTPVFKTKEMLDLLDWIRQYNANPKHKSKVRVIGMDIQSVNENVYNNIIEYIKANNSKLLPRVEEKIKGLIPVTKDMNTFESLTKEEKEKYVLDAKQISALLEENKSYLNGKSKEFAWIKQNARIIEQFTTMLATPPDKPADFYLKHDIAMYENAKWTEEHLGKTIVWGHNGHVSKTNMLSFIYPKVAGQHLAEYYGKRYVSIGTSVYEGQYNVKNSDGEFGPYGTLKSDDPNSYNYIFGQVKKDQFFIDLRKANGVTKTWLNEQHPIFAGITTEGPDIPKTVDISLGKAFDILVQIQKVSPSQVH 442
               SCOP domains d2rada1 A:40-442 Succinoglycan biosynthesis protein BC3120                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2radA01 A:40-103,A:303-442 EreA-like (biosynthetic domain)      2radA02 A:104-175 EreA-like; domain 2                                   2radA03 A:176-302 Biosynthetic Protein domain                                                                                  2radA01 A:40-103,A:303-442 EreA-like (biosynthetic domain)                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh.ee.........hhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhh......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhh...........hhhhhhhhhhh..eeeeeeeeeee...ee.....ee...........hhhhhh......eeeee.hhh.hhhhhhh...eeee............eeeehhhhhh.eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rad A  40 NQIAKWLEAHAKPLKTTNPTASLNDLKPLKNmVGSASIVGLGEATHGAHEVFTmKHRIVKYLVSEKGFTNLVLEEGWDRALELDRYVLTGKGNPSQHLTPVFKTKEmLDLLDWIRQYNANPKHKSKVRVIGmDIQSVNENVYNNIIEYIKANNSKLLPRVEEKIKGLIPVTKDmNTFESLTKEEKEKYVLDAKTISALLEENKSYLNGKSKEFAWIKQNARIIEQFTTmLATPPDKPADFYLKHDIAmYENAKWTEEHLGKTIVWGHNGHVSKTNmLSFIYPKVAGQHLAEYYGKRYVSIGTSVYEGQYNVKNSDGEFGPYGTLKSDDPNSYNYIFGQVKKDQFFIDLRKANGVTKTWLNEQHPIFAGITTEGPDIPKTVDISLGKAFDILVQIQKVSPSQVH 442
                                    49        59        69 |      79        89   |    99       109       119       129       139      |149       159       169 |     179       189       199       209   |   219       229       239       249       259       269       279       289       299       309     | 319       329       339       349       359       369       379       389       399       409       419       429       439   
                                                          71-MSE                93-MSE                                              146-MSE                  171-MSE                                   213-MSE                                                268-MSE            287-MSE                     315-MSE                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:405
 aligned with Q81BN2_BACCR | Q81BN2 from UniProtKB/TrEMBL  Length:443

    Alignment length:405
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437     
         Q81BN2_BACCR    38 NTNQIAKWLEAHAKPLKTTNPTASLNDLKPLKNMVGSASIVGLGEATHGAHEVFTMKHRIVKYLVSEKGFTNLVLEEGWDRALELDRYVLTGKGNPSQHLTPVFKTKEMLDLLDWIRQYNANPKHKSKVRVIGMDIQSVNENVYNNIIEYIKANNSKLLPRVEEKIKGLIPVTKDMNTFESLTKEEKEKYVLDAKQISALLEENKSYLNGKSKEFAWIKQNARIIEQFTTMLATPPDKPADFYLKHDIAMYENAKWTEEHLGKTIVWGHNGHVSKTNMLSFIYPKVAGQHLAEYYGKRYVSIGTSVYEGQYNVKNSDGEFGPYGTLKSDDPNSYNYIFGQVKKDQFFIDLRKANGVTKTWLNEQHPIFAGITTEGPDIPKTVDISLGKAFDILVQIQKVSPSQVH 442
               SCOP domains d2radb_ B: Succinoglycan biosynthesis protein BC3120                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2radB01 B:38-103,B:303-442 EreA-like (biosynthetic domain)        2radB02 B:104-175 EreA-like; domain 2                                   2radB03 B:176-302 Biosynthetic Protein domain                                                                                  2radB01 B:38-103,B:303-442 EreA-like (biosynthetic domain)                                                                                   CATH domains
           Pfam domains (1) -----------------------------------------------------------------------Erythro_esteras-2radB01 B:109-436                                                                                                                                                                                                                                                                                                       ------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------Erythro_esteras-2radB02 B:109-436                                                                                                                                                                                                                                                                                                       ------ Pfam domains (2)
         Sec.struct. author ......hhhhhh.eee.............hhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhh.......eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhh............hhhhhhhhhhh..eeeeeeeeeee...ee.....ee...........hhhhhhhhh...eeeee.hhh.hhhhhhhh..eeee............eeeehhhhhh.eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rad B  38 NTNQIAKWLEAHAKPLKTTNPTASLNDLKPLKNmVGSASIVGLGEATHGAHEVFTmKHRIVKYLVSEKGFTNLVLEEGWDRALELDRYVLTGKGNPSQHLTPVFKTKEmLDLLDWIRQYNANPKHKSKVRVIGmDIQSVNENVYNNIIEYIKANNSKLLPRVEEKIKGLIPVTKDmNTFESLTKEEKEKYVLDAKTISALLEENKSYLNGKSKEFAWIKQNARIIEQFTTmLATPPDKPADFYLKHDIAmYENAKWTEEHLGKTIVWGHNGHVSKTNmLSFIYPKVAGQHLAEYYGKRYVSIGTSVYEGQYNVKNSDGEFGPYGTLKSDDPNSYNYIFGQVKKDQFFIDLRKANGVTKTWLNEQHPIFAGITTEGPDIPKTVDISLGKAFDILVQIQKVSPSQVH 442
                                    47        57        67   |    77        87     |  97       107       117       127       137       147       157       167   |   177       187       197       207     | 217       227       237       247       257       267|      277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437     
                                                            71-MSE                93-MSE                                              146-MSE                  171-MSE                                   213-MSE                                                268-MSE            287-MSE                     315-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  (3, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q81BN2_BACCR | Q81BN2)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

 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 ]
 
  Sites
(no "Sites" information available for 2rad)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2rad)
 
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 | Biol. Unit 1 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
  2rad
    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
  Q81BN2_BACCR | Q81BN2
    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
  Q81BN2_BACCR | Q81BN2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q81BN2_BACCR | Q81BN2: 3b55

(-) Related Entries Specified in the PDB File

2qgm CRYSTAL STRUCTURE OF SUCCINOGLYCAN BIOSYNTHESIS PROTEIN (STRUCTURAL HOMOLOG)