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 N-TERMINAL 618-RESIDUE FRAGMENT OF LEPB FROM LEGIONELLA PNEUMOPHILA
 
Authors :  L. Hu, Q. Yao, Y. Zhu, F. Shao
Date :  26 Mar 13  (Deposition) - 08 May 13  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.16
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  New Gap Fold, Gtpase-Accelerating Protein, Rab1, Hydrolase Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Yu, L. Hu, Q. Yao, Y. Zhu, N. Dong, D. -C. Wang, F. Shao
Structural Analyses Of Legionella Lepb Reveal A New Gap Fol That Catalytically Mimics Eukaryotic Rasgap
Cell Res. V. 23 775 2013
PubMed-ID: 23588383  |  Reference-DOI: 10.1038/CR.2013.54

(-) Compounds

Molecule 1 - EFFECTOR PROTEIN B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Fragment: N-TERMINAL FRAGMENT, UNP RESIDUES 1-618
    Gene: LEPB
    Organism Scientific: LEGIONELLA PNEUMOPHILA
    Organism Taxid: 446
    Synonym: GTPASE-ACTIVATING PROTEIN

 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, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2GOL5Ligand/IonGLYCEROL
3MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2GOL1Ligand/IonGLYCEROL
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1FLC-1Ligand/IonCITRATE ANION
2GOL4Ligand/IonGLYCEROL
3MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:195BINDING SITE FOR RESIDUE GOL A 701
2AC2SOFTWAREASN A:366 , LEU A:367 , LEU A:368 , PHE A:440 , LYS A:485BINDING SITE FOR RESIDUE FLC A 702
3AC3SOFTWAREGLU B:165 , GLU B:167BINDING SITE FOR RESIDUE GOL B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JW1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:183 -Phe A:184
2Gly B:410 -Gly B:411

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JW1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JW1)

(-) Exons   (0, 0)

(no "Exon" information available for 4JW1)

(-) 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:515
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eee.....eeeee...hhhhhhhhhhhhhhhhhhhhh......hhhhh...eeee.....eeeeee...eeehhhhh......hhhhhhhhhhhh.........eeee....eee....................................hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhh.........hhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhhh.........................hhhhhhhhhh..............hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jw1 A  10 VRFAGFYKDNDGGKFFIKKPGDPRELFTELFAGLLLKEFmKRGLIDESYFPSLICADVIQFEDKSYGLIQPLVSFDELHKVIGQNKYFGLSmALmFSLLLGAHSVHSGNIVVLNGEEKEKSKQFGRIDWGDRYFAHPNNNDNLYAKDYFLNYKKINGLFPAmAEKARQLQSKLNPELLVKIVTSALKNIPADLIDEKTKIQLAAYmCmDSFKEATFGTEGNCKDFAIAmATLLENRLGKIAVLKLKPLTLLmTSSTSFSETINQWADILKTTDmEKFSFDSNPINLLELVKQFNLYVDELAITCEANNVWLFALYDNSGGEAIHGHAFVPYYKESIVLRRLFTVDPNTFNLSRFAAFEGPCQLYCKEHKDSAWVKIQTLLTLGNGIINTLKIIKQAQAFGIDEAVTENLKALKEQFIAFQLAEADIKEPNKESEFFYPIDEKALAKmNGYQLATICLEELNSPKPSPLIERILSNKKFWKRINSAFESGVFKGRTDDPAGKIAKIREWHQLLQIS 617
                               ||   31        41        51        61        71        81        91       101  ||   138 |  |  148       158       168       178||     190 || || 214       224 |     234       244       254       264     | 274       284       294       304   ||  331 |     341       351   |   361       371       381       391|      411       421       431       441       451       461       471       481       491       501       511       532       542      |552       562       572       582       592       602       612     
                              13|                                 61-MSE                                    104|     140-MSE                                179|       192| ||             226-MSE                                     270-MSE                293-MSE        308|      |                   355-MSE                             391|                                                                                                                  519|               549-MSE                                                                
                               26                                                                            132        143-MSE                              182        194 ||                                                           272-MSE                              326      |                                                        402                                                                                                                   531                                                                                      
                                                                                                                                                                          196|                                                                                                       333-MSE                                                                                                                                                                                                                                                                   
                                                                                                                                                                           210                                                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................................ee........hhhhhhhhhhhhhhh..ee.....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhh.....ee..ee.....hhhhhhhhhhh..........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.................hhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhh.........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jw1 B  48 FTELFAGLLHKVIGHSVHSGNIVVLEKEKSKQFRGWKDYFLNYKILKNIPADLKPLTLLmTSSTSFSETINQWADILKTKFSFDSNPINLLELVKQFNLYVDELAITCEANNVWAENLFALYDNSGGEAIHGHAFVPYYKESIVLRRLFTVDPNTFNLSRFAAFEGPCQLYCKEHKDSAWVKIQTLLTLGNGIINTLKIIKQAQAFGIDEAVTENLKALKEQFIAFQLAADIKLPNKESEFFYPIDEKALAKmNGYQLATICLEELNSPKPSPLIERILSNKKFWKRINSAFESGVFKGRTDDPAGKIAKIREWHQLLQ 615
                                   100   ||  156    || 169  || ||213   ||| 254  ||   333       343       357       367       377       387    |||404       414       424       434       444       454       464       474       484       494       504       515  ||   536       546  |    556       566       576       586       596       606         
                                   56| 104|       161|    172| ||    217||    257|     |                352|                                392||                                                                                                             513|  ||                549-MSE                                                              
                                   100  151        165     200 ||     219|     327     |                 357                                 394|                                                                                                              515  ||                                                                                     
                                                             202|      250           333-MSE                                                  401                                                                                                                 518|                                                                                     
                                                              210                                                                                                                                                                                                  530
   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 4JW1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JW1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JW1)

(-) Gene Ontology  (2, 2)

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
    FLC  [ 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 ]
 
  Cis Peptide Bonds
    Gly B:410 - Gly B:411   [ RasMol ]  
    Tyr A:183 - Phe A:184   [ 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
  4jw1
    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
  Q6X1Y7_LEGPN | Q6X1Y7
    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
  Q6X1Y7_LEGPN | Q6X1Y7
    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 4JW1)

(-) Related Entries Specified in the PDB File

4jvs