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 :  THE CRYSTAL STRUCTURE OF IGE FC MUTANT - P333C
 
Authors :  B. Dhaliwal, M. O. Y. Pang, B. J. Sutton
Date :  07 Jul 16  (Deposition) - 15 Mar 17  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Immune System, Immunoglobulin Domain, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Dhaliwal, M. O. Y. Pang, A. H. Keeble, A. I. Taylor, L. K. James, H. J. Gould, J. M. Mcdonnell, A. J. Beavil, B. J. Sutton
The Crystal Structure Of Ige Fc Mutant - P333C
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - IG EPSILON CHAIN C REGION
    Chains: A
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Gene: IGHE
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - IG EPSILON CHAIN C REGION
    Chains: B
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Gene: IGHE
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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  (6, 19)

Asymmetric Unit (6, 19)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2GOL1Ligand/IonGLYCEROL
3MAN6Ligand/IonALPHA-D-MANNOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PG42Ligand/IonTETRAETHYLENE GLYCOL
6SO44Ligand/IonSULFATE ION
Biological Unit 1 (5, 10)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GOL-1Ligand/IonGLYCEROL
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PG42Ligand/IonTETRAETHYLENE GLYCOL
6SO43Ligand/IonSULFATE ION
Biological Unit 2 (5, 9)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GOL1Ligand/IonGLYCEROL
3MAN4Ligand/IonALPHA-D-MANNOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PG4-1Ligand/IonTETRAETHYLENE GLYCOL
6SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:323 , SER A:324 , ASP B:242 , GLY B:243 , TRP B:453 , PRO B:454binding site for residue SO4 A 606
2AC2SOFTWAREGLU A:270 , GLN A:273 , VAL A:274 , HOH A:706 , HOH A:713binding site for residue SO4 A 607
3AC3SOFTWARETHR A:493 , GLN A:494 , ARG A:496 , THR B:493 , GLN B:494 , ARG B:496binding site for residue SO4 A 608
4AC4SOFTWAREILE A:266 , VAL A:277 , SER A:280 , THR A:281 , ALA A:282 , SER A:295binding site for residue PG4 A 609
5AC5SOFTWAREASP A:271 , ARG A:525 , THR A:536 , VAL A:537 , GLN A:538binding site for residue PG4 A 610
6AC6SOFTWAREGLY B:406 , THR B:407 , ARG B:408 , ASP B:409binding site for residue GOL B 608
7AC7SOFTWAREHIS B:384 , ASN B:481 , GLU B:482 , GLU B:521 , ILE B:523binding site for residue SO4 B 609
8AC8SOFTWARETYR A:339 , LEU A:359 , VAL A:361 , ASP A:362 , GLN A:392 , ASN A:394 , THR A:396 , THR A:398 , GLN A:494 , HOH A:737 , ARG B:496binding site for Poly-Saccharide residues NAG A 601 through MAN A 605 bound to ASN A 394
9AC9SOFTWARETYR B:339 , SER B:344 , LEU B:359 , ASP B:362 , GLN B:392 , ASN B:394 , THR B:396 , THR B:398 , GLN B:494 , HOH B:724binding site for Poly-Saccharide residues NAG B 601 through MAN B 607 bound to ASN B 394

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:254 -A:312
2A:328 -B:241
3A:464 -A:524
4B:254 -B:312
5B:358 -B:418
6B:464 -B:524

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Met A:470 -Pro A:471
2Ser A:532 -Pro A:533
3Met B:470 -Pro B:471
4Ser B:532 -Pro B:533

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LGJ)

(-) 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:315
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..........eeeeeeeeeee....eeeeeee..ee.hhh.eeeeeeee..eeeeeeeeeeehhhhhh...eeeeeee..eeeeeee........eee...hhhhhhh....eeeeeeeee.......eeeeee...........eeee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeeee.........eeeeeeeeeee.....eeeeee..ee.hhh.eee...ee.....eeeeeeeeeehhhhhhh..eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lgj A  228 DFTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCACRGSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP  545
                                   237       247      |256       266       276       286       296       306       316       326  || ||340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540     
                                                   253A                                                                         329| ||                                                                                                                                                                                                                
                                                                                                                                 333 ||                                                                                                                                                                                                                
                                                                                                                                   335|                                                                                                                                                                                                                
                                                                                                                                    337                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..........eeeeeeeeeee....eeeeeee..eeehhh.eeeeee.eeeeeeeeeehhhhhh...eeeeeee..eeeeeee........eeee...hhhhhhh....eeeeeeeee......eeeeee.........eeeeee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeeee.........eeeeeeeeeee.....eeeeee..ee.hhh.eee...ee.....eeeeeeeeeehhhhhhh..eeeeee........eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lgj B  231 PPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTLASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNVSAYLSRPSPFDLFIRKSPTITCLVVDLAPKGTVQLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNPG  546
                                   240       250   |   259       269       279     ||293       303       313       323       336       346       356       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537         
                                                253A                             285|                                       332|                          365|                                                                                                                                                                                   
                                                                                  290                                        336                           367
   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 5LGJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

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
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ 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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Met A:470 - Pro A:471   [ RasMol ]  
    Met B:470 - Pro B:471   [ RasMol ]  
    Ser A:532 - Pro A:533   [ RasMol ]  
    Ser B:532 - Pro B:533   [ 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
  5lgj
    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
  IGHE_HUMAN | P01854
    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)
  (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
  IGHE_HUMAN | P01854
    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
        IGHE_HUMAN | P01854: 1f6a 1fp5 1g84 1ige 1o0v 2ige 2wqr 2y7q 3h9y 3h9z 3ha0 4ezm 4gko 4grg 4gt7 4j4p 4ki1 5anm 5hys 5lgk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LGJ)