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 MCCF-LIKE PROTEIN FROM STREPTOCOCCUS PNEUMONIAE
 
Authors :  B. Nocek, A. Tikhonov, K. Kwon, K. Severinov, W. F. Anderson, A. Joachim Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  20 Mar 12  (Deposition) - 09 May 12  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mccf, Csgid, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Serine Peptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, A. Tikhonov, K. Kwon, K. Severinov, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Mccf-Like Protein From Streptococcus Pneumoniae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MCCC FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SP_0182
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4

 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, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE13Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE7Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:204 , HOH A:514 , HOH A:542 , HOH A:585 , HOH A:822 , HIS B:187 , THR B:188BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREILE A:78 , GLY A:79 , PHE A:108 , SER A:109 , SER A:130 , GLU A:252 , HIS A:315 , HOH A:550BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREHIS A:22 , LEU A:138 , PHE A:175 , SER A:176 , PRO A:177 , HOH A:630 , HOH A:679BINDING SITE FOR RESIDUE GOL A 403
4AC4SOFTWAREARG A:30 , LEU A:34 , GLU A:141 , MSE A:142 , HOH A:662 , HOH A:755BINDING SITE FOR RESIDUE GOL A 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E94)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:317 -Pro A:318
2Thr B:317 -Pro B:318

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E94)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E94)

(-) Exons   (0, 0)

(no "Exon" information available for 4E94)

(-) 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:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh...........eeeehhhhhhhhhhhhhh....ee..hhhhhh.......hhhhhhhhhhhhhhh...ee....eee......hhhhh.....eee....eeee...eeeeeeeeeehhhhhhhhh.....hhhhhhhhh....hhhhhh..eeeee......hhhhhhhhhhhhhh.hhhhhh.eeeee.hhhhhhhhhhhhhhhhhh.....eeeee..........ee...eeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e94 A   1 mVSTIGIVSLSSGIIGEDFVKHEVDLGIQRLKDLGLNPIFLPHSLKGLDFIKDHPEARAEDLIHAFSDDSIDmILCAIGGDDTYRLLPYLFENDQLQKVIKQKIFLGFSDTTmNHLmLHKLGIKTFYGQSFLADICELDKEmLAYSLHYFKELIETGRISEIRPSDVWYEERTDFSPTALGTPRVSHTNTGFDLLQGSAQFEGKILGGCLESLYDIFDNSRYADSTELCQKYKLFPDLSDWEGKILLLETSEEKPKPEDFKKmLLTLKDTGIFAVINGLLVGKPmDETFHDDYKEALLDIIDSNIPIVYNLNVGHATPRAIVPFGVHAHVDAQEQVILFDYNK 343
                            |       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       320       330       340   
                            |                                                                      73-MSE                                 113-MSE                      142-MSE                                                                                                                  263-MSE               285-MSE                                                      
                            1-MSE                                                                                                             117-MSE                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh...........eeee..hhhhhhhhhhhh....ee...............hhhhhhhhhhhhhhh...ee....eee......hhhhh.....eee....eeee...eeeeeeeeeehhhhhhhhh.....hhhhhhhhh....hhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh.....eeeee..........ee...eeeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e94 B   2 VSTIGIVSLSSGIIGEDFVKHEVDLGIQRLKDLGLNPIFLPHSLKGLDFIKDHPEARAEDLIHAFSDDSIDmILCAIGGDDTYRLLPYLFENDQLQKVIKQKIFLGFSDTTmNHLmLHKLGIKTFYGQSFLADICELDKEmLAYSLHYFKELIETGRISEIRPSDVWYEERTDFSPTALGTPRVSHTNTGFDLLQGSAQFEGKILGGCLESLYDIFDNSRYADSTELCQKYKLFPDLSDWEGKILLLETSEEKPKPEDFKKmLLTLKDTGIFAVINGLLVGKPmDETFHDDYKEALLDIIDSNIPIVYNLNVGHATPRAIVPFGVHAHVDAQEQVILFDY 341
                                    11        21        31        41        51        61        71 |      81        91       101       111 |   | 121       131       141|      151       161       171       181       191       201       211       221       231       241       251       261 |     271       281   |   291       301       311       321       331       341
                                                                                                  73-MSE                                 113-MSE                      142-MSE                                                                                                                  263-MSE               285-MSE                                                    
                                                                                                                                             117-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 4E94)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E94)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E94)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4E94)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:317 - Pro A:318   [ RasMol ]  
    Thr B:317 - Pro B:318   [ RasMol ]  
 
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
  4e94
    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
  A0A0H2UN46_S | A0A0H2UN46
    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
  A0A0H2UN46_S | A0A0H2UN46
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A0H2UN46_S | A0A0H2UN46: 4eys

(-) Related Entries Specified in the PDB File

3gjz
3sr3 RELATED ID: CSGID-IDP91761 RELATED DB: TARGETTRACK
3tyx