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 :  CRYSTAL STRUCTURE OF THE MRSD-PROTEIN A FUSION PROTEIN
 
Authors :  S. J. Youn, N. Y. Kwon, J. H. Lee, J. H. Kim, H. Lee, J. O. Lee
Date :  17 Nov 16  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.74
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Synthetic Protein, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Youn, N. Y. Kwon, J. H. Lee, J. H. Kim, J. Choi, H. Lee, J. O. Lee
Construction Of Novel Repeat Proteins With Rigid And Predictable Structures Using A Shared Helix Method.
Sci Rep V. 7 2595 2017
PubMed-ID: 28572639  |  Reference-DOI: 10.1038/S41598-017-02803-Z

(-) Compounds

Molecule 1 - MERSACIDIN DECARBOXYLASE,IMMUNOGLOBULIN G-BINDING PROTEIN A
    Chains: A, B, C, D
    EC Number: 4.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-184,223-269
    Gene: MRSD, SPA
    Mutation: YES
    Organism Scientific: BACILLUS SP. (STRAIN HIL-Y85/54728), STAPHYLOCOCCUS AUREUS
    Organism Taxid: 69002, 1280
    Strain: HIL-Y85/54728
    Synonym: MERSACIDIN-MODIFYING ENZYME MRSD,IGG-BINDING PROTEIN A, STAPHYLOCOCCAL PROTEIN A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1FAD12Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:17 , SER A:18 , THR A:43 , LYS A:44 , THR A:45 , ASP A:48 , THR A:91 , ALA A:92 , ASN A:93 , ASN A:105 , ASN A:123 , MET A:124 , MET A:128 , TYR B:57 , FAD B:301 , ALA C:103 , MET C:104 , THR C:109 , FAD C:301binding site for residue FAD A 301
2AC2SOFTWARETYR A:57 , GLU A:65 , ALA A:103 , MET A:104 , THR A:109 , FAD A:301 , CYS B:16 , GLY B:17 , THR B:43 , LYS B:44 , THR B:45 , THR B:91 , ALA B:92 , ASN B:93 , ASN B:105 , ASN B:123 , MET B:124binding site for residue FAD B 301
3AC3SOFTWAREFAD A:301 , ALA B:103 , MET B:104 , THR B:109 , CYS C:16 , GLY C:17 , SER C:18 , THR C:43 , THR C:45 , THR C:91 , ALA C:92 , ASN C:93 , ASN C:105 , ASN C:123 , MET C:124 , MET C:128 , TYR D:57binding site for residue FAD C 301
4AC4SOFTWARETYR C:57 , GLY D:17 , SER D:18 , THR D:43 , LYS D:44 , THR D:45 , LEU D:49 , THR D:91 , ALA D:92 , ASN D:93 , ALA D:103 , MET D:104 , ASN D:105 , THR D:109 , ASN D:123 , MET D:124 , MET D:128binding site for residue FAD D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H75)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ile A:88 -Pro A:89
2Ala A:156 -Phe A:157
3Ile B:88 -Pro B:89
4Ile C:88 -Pro C:89
5Ile D:88 -Pro D:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H75)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H75)

(-) Exons   (0, 0)

(no "Exon" information available for 5H75)

(-) 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:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhh.eee....hhhhh.eeeeeeehhhhhhhhhh....hhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhh..ee...eeee..........eeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h75 A   8 DKKLLIGICGSISSVGISSYLLYFKSFFKEIRVVMTKTAEDLIPAHTVSYFCDHVYSEHEIGRWADIYCIIPATANILGQTANGVAMNLVATTVLAHPHNTIFFPNMNDLMWNKTVVSRNIEQLRKDGHIVIEPVEIMAFEIATGTRKPNRGLITPDKALLAIEQGFAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQA 229
                                    17        27        37        47        57        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227  
                                                                                     66|                                                                                                                                                        
                                                                                      77                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh...eee....hhhhh.eeeeeeehhhhhhhhhh....hhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhh..ee..........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h75 B   7 KDKKLLIGICGSISSVGISSYLLYFKSFFKEIRVVMTKTAEDLIPAHTVSYFCDHVYSEHEIGRWADIYCIIPATANILGQTANGVAMNLVATTVLAHPHNTIFFPNMNDLMWNKTVVSRNIEQLRKDGHIVIEPVEIRGLITPDKALLAIEQGFAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQA 229
                                    16        26        36        46        56        66|       86        96       106       116       126       136       146       169       179       189       199       209       219       229
                                                                                      66|                                                                          154|                                                             
                                                                                       77                                                                           168                                                             


Chain C from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh...eee....hhhhh.eeeeeeehhhhhhhhhh....hhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhh..ee..........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h75 C   5 ILKDKKLLIGICGSISSVGISSYLLYFKSFFKEIRVVMTKTAEDLIPAHTVSYFCDHVYSEHEIGRWADIYCIIPATANILGQTANGVAMNLVATTVLAHPHNTIFFPNMNDLMWNKTVVSRNIEQLRKDGHIVIEPVEIRGLITPDKALLAIEQGFAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQA 229
                                    14        24        34        44        54        64 ||     84        94       104       114       124       134       144       154|      177       187       197       207       217       227  
                                                                                        66|                                                                          154|                                                             
                                                                                         77                                                                           168                                                             


Chain D from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhh.eee.....hhhhhh.eeeeeeehhhhhhhhhh....hhhhhhhhhh...eeeee.eehhhhhhhhhhhhhhhhhhh..ee...eeeeeee....eeeeeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h75 D  -3 GGGSMSISILKDKKLLIGICGSISSVGISSYLLYFKSFFKEIRVVMTKTAEDLIPAHTVSYFCDHVYSEHHVEIGRWADIYCIIPATANILGQTANGVAMNLVATTVLAHPHNTIFFPNMNDLMWNKTVVSRNIEQLRKDGHIVIEPVEIMAFEIATGTRKPNRGLITPDKALLAIEQGFAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQA 229
                                     6        16        26        36        46        56        66|       84        94       104       114       124       134       144       154       164       174       184       194       204       214       224     
                                                                                                66|                                                                                                                                                          
                                                                                                 75
   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 5H75)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H75)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H75)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

 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
    FAD  [ 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
    Ala A:156 - Phe A:157   [ RasMol ]  
    Ile A:88 - Pro A:89   [ RasMol ]  
    Ile B:88 - Pro B:89   [ RasMol ]  
    Ile C:88 - Pro C:89   [ RasMol ]  
    Ile D:88 - Pro D:89   [ 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
  5h75
    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
  MRSD_BACSY | Q9RC23
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SPA_STAAU | P38507
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.1.1.-
    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
  MRSD_BACSY | Q9RC23
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SPA_STAAU | P38507
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MRSD_BACSY | Q9RC23: 1p3y
        SPA_STAAU | P38507: 1bdc 1bdd 1edi 1edj 1edk 1edl 1fc2 1h0t 1lp1 1q2n 1ss1 2jwd 2m5a 2spz 3mzw 4npd 4npe 4npf 4wwi 4y4y 4y5z 4zmd 4znc 5cbn 5cbo 5coc 5ewx 5h76 5h77 5h79 5h7a 5h7b 5h7c 5h7d 5x3f 5xby

(-) Related Entries Specified in the PDB File

5h76 5h77 5h78 5h79 5h7a 5h7b 5h7c 5h7d