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
(-)Biological Unit 4
(-)Biological Unit 5
(-)Biological Unit 6
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)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)
Image Biological Unit 6
Biological Unit 6  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PAS DOMAIN OF RHA05790
 
Authors :  C. Chang, X. Xu, H. Cui, A. Savchenko, A. Edwards, A. Joachimiak, Midwes For Structural Genomics (Mcsg)
Date :  05 Dec 08  (Deposition) - 20 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Pas Domain, Uncharacterized Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, X. Xu, H. Cui, A. Savchenko, A. Edwards, A. Joachimiak
Crystal Structure Of Pas Domain Of Rha05790
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN RHA05790
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET DERIVATIVE
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RHA1_RO04714
    Organism Scientific: RHODOCOCCUS SP. RHA1
    Organism Taxid: 101510
    Strain: STRAIN RHA1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
13PB6Ligand/Ion(3R)-3-(PHOSPHONOOXY)BUTANOIC ACID
2MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
13PB1Ligand/Ion(3R)-3-(PHOSPHONOOXY)BUTANOIC ACID
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
13PB1Ligand/Ion(3R)-3-(PHOSPHONOOXY)BUTANOIC ACID
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
13PB1Ligand/Ion(3R)-3-(PHOSPHONOOXY)BUTANOIC ACID
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
13PB1Ligand/Ion(3R)-3-(PHOSPHONOOXY)BUTANOIC ACID
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (2, 3)
No.NameCountTypeFull Name
13PB1Ligand/Ion(3R)-3-(PHOSPHONOOXY)BUTANOIC ACID
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 6 (2, 3)
No.NameCountTypeFull Name
13PB1Ligand/Ion(3R)-3-(PHOSPHONOOXY)BUTANOIC ACID
2MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:147 , HIS A:150 , VAL A:151 , TYR A:174 , SER A:195 , LEU A:196 , TYR A:197 , ILE A:203 , VAL A:216BINDING SITE FOR RESIDUE 3PB A 301
2AC2SOFTWAREMSE B:132 , CYS B:147 , HIS B:150 , VAL B:151 , TYR B:174 , SER B:195 , LEU B:196 , TYR B:197 , ILE B:203BINDING SITE FOR RESIDUE 3PB B 301
3AC3SOFTWAREHIS C:150 , VAL C:151 , TYR C:174 , SER C:195 , LEU C:196 , TYR C:197 , ILE C:203 , VAL C:216 , PHE C:218BINDING SITE FOR RESIDUE 3PB C 301
4AC4SOFTWAREHIS D:150 , VAL D:151 , TYR D:174 , SER D:195 , LEU D:196 , TYR D:197 , ILE D:203 , VAL D:216BINDING SITE FOR RESIDUE 3PB D 301
5AC5SOFTWAREMSE E:132 , HIS E:150 , VAL E:151 , TYR E:174 , SER E:195 , LEU E:196 , TYR E:197 , ILE E:203 , VAL E:216BINDING SITE FOR RESIDUE 3PB E 301
6AC6SOFTWAREHIS F:150 , VAL F:151 , TYR F:174 , SER F:195 , LEU F:196 , TYR F:197 , ILE F:203 , VAL F:216BINDING SITE FOR RESIDUE 3PB F 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FG8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FG8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FG8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FG8)

(-) Exons   (0, 0)

(no "Exon" information available for 3FG8)

(-) 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:106
 aligned with Q0S7I6_RHOJR | Q0S7I6 from UniProtKB/TrEMBL  Length:399

    Alignment length:110
                                   124       134       144       154       164       174       184       194       204       214       224
         Q0S7I6_RHOJR   115 GRDAQLAALLDRVGLGFMALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYSPGMTIEVTAAADSGALVVHFRDVTAE 224
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fg8    A00 A:119-224  [code=3.30.450.20, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....----.......eeeee.....eeeehhhhhhhhh.hhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhh..eeeeee.......eeeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3fg8 A 119 GREN----LYFQGGLGFmALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYSPGmTIEVTAAADSGALVVHFRDVTAE 224
                               |   124       134       144       154       164       174       184       194      |204       214       224
                             122  123      132-MSE                                                              201-MSE                   


Chain B from PDB  Type:PROTEIN  Length:105
 aligned with Q0S7I6_RHOJR | Q0S7I6 from UniProtKB/TrEMBL  Length:399

    Alignment length:145
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219     
         Q0S7I6_RHOJR    80 RSTRYILTRSIDVTTDASGAPVELTGVVIELGHVAGRDAQLAALLDRVGLGFMALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYSPGMTIEVTAAADSGALVVHFRDVTAE 224
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fg8B00                                         B:120-224  [code=3.30.450.20, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........----------------------------------------..eeeee.....eeeehhhhhhhhh.hhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhh..eeeeee.......eeeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fg8 B 120 RENLYFQG----------------------------------------GLGFmALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYSPGmTIEVTAAADSGALVVHFRDVTAE 224
                                   | -         -         -         -       129  |    139       149       159       169       179       189       199 |     209       219     
                                 127                                      128   |                                                                  201-MSE                   
                                                                              132-MSE                                                                                        


Chain C from PDB  Type:PROTEIN  Length:105
 aligned with Q0S7I6_RHOJR | Q0S7I6 from UniProtKB/TrEMBL  Length:399

    Alignment length:109
                                   123       133       143       153       163       173       183       193       203       213         
         Q0S7I6_RHOJR   114 AGRDAQLAALLDRVGLGFMALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYSPGMTIEVTAAADSGALVVHFRDVT 222
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fg8C    00 C:118-222  [code=3.30.450.20, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....----.......eeeee.....eeeehhhhhhhhh.hhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhh..eeeeee.......eeeeeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 3fg8 C 118 SGREN----LYFQGGLGFmALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYSPGmTIEVTAAADSGALVVHFRDVT 222
                                |  123       133       143       153       163       173       183       193       203       213         
                              122  123      132-MSE                                                              201-MSE                 


Chain D from PDB  Type:PROTEIN  Length:106
 aligned with Q0S7I6_RHOJR | Q0S7I6 from UniProtKB/TrEMBL  Length:399

    Alignment length:110
                                   124       134       144       154       164       174       184       194       204       214       224
         Q0S7I6_RHOJR   115 GRDAQLAALLDRVGLGFMALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYSPGMTIEVTAAADSGALVVHFRDVTAE 224
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fg8    D00 D:119-224  [code=3.30.450.20, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....----.......eeeee.....eeeehhhhhhhhh.hhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhh..eeeeee.......eeeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3fg8 D 119 GREN----LYFQGGLGFmALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYSPGmTIEVTAAADSGALVVHFRDVTAE 224
                               |   124       134       144       154       164       174       184       194      |204       214       224
                             122  123      132-MSE                                                              201-MSE                   


Chain E from PDB  Type:PROTEIN  Length:105
 aligned with Q0S7I6_RHOJR | Q0S7I6 from UniProtKB/TrEMBL  Length:399

    Alignment length:109
                                   124       134       144       154       164       174       184       194       204       214         
         Q0S7I6_RHOJR   115 GRDAQLAALLDRVGLGFMALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYSPGMTIEVTAAADSGALVVHFRDVTA 223
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fg8    E00 E:119-223  [code=3.30.450.20, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....----.......eeeee.....eeeehhhhhhhhh.hhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhh..eeeeee.......eeeeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 3fg8 E 119 GREN----LYFQGGLGFmALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYSPGmTIEVTAAADSGALVVHFRDVTA 223
                               |   124       134       144       154       164       174       184       194      |204       214         
                             122  123      132-MSE                                                              201-MSE                  


Chain F from PDB  Type:PROTEIN  Length:105
 aligned with Q0S7I6_RHOJR | Q0S7I6 from UniProtKB/TrEMBL  Length:399

    Alignment length:145
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219     
         Q0S7I6_RHOJR    80 RSTRYILTRSIDVTTDASGAPVELTGVVIELGHVAGRDAQLAALLDRVGLGFMALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYSPGMTIEVTAAADSGALVVHFRDVTAE 224
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fg8F00                                         F:120-224  [code=3.30.450.20, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........----------------------------------------..eeeee.....eeeehhhhhhhhh.hhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhh..eeeeee.......eeeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fg8 F 120 RENLYFQG----------------------------------------GLGFmALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYSPGmTIEVTAAADSGALVVHFRDVTAE 224
                                   | -         -         -         -       129  |    139       149       159       169       179       189       199 |     209       219     
                                 127                                      128   |                                                                  201-MSE                   
                                                                              132-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 3FG8)

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FG8)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3FG8)

 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
    3PB  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3fg8)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]
    Biological Unit 6  [ 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 | Biol. Unit 4 PNG format | Biol. Unit 5 PNG format | Biol. Unit 6 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
  3fg8
    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
  Q0S7I6_RHOJR | Q0S7I6
    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
  Q0S7I6_RHOJR | Q0S7I6
    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 3FG8)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3FG8)