Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN FC AT 1.80 A
 
Authors :  J. M. M. Caaveiro, M. Kiyoshi, K. Tsumoto
Date :  15 Aug 14  (Deposition) - 29 Apr 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Human Fc Asymmetry Dynamics Immune Molecule, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kiyoshi, J. M. M. Caaveiro, T. Kawai, S. Tashiro, T. Ide, Y. Asaoka, K. Hatayama, K. Tsumoto
Structural Basis For Binding Of Human Igg1 To Its High-Affinity Human Receptor Fc Gamma Ri
Nat Commun V. 6 6866 2015
PubMed-ID: 25925696  |  Reference-DOI: 10.1038/NCOMMS7866

(-) Compounds

Molecule 1 - IG GAMMA-1 CHAIN C REGION
    Chains: A, B
    Engineered: YES
    Fragment: UNP RESIDUES 107-329
    Gene: IGHG1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THE PROTEIN IS COMMERCIALLY PURCHASED FROM ROCHE.

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3GOL1Ligand/IonGLYCEROL
4MAN4Ligand/IonALPHA-D-MANNOSE
5NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:362 , ASN A:390 , LYS A:409 , LYS B:370 , ASP B:399 , SER B:400 , ASP B:401binding site for residue GOL B 509
2AC2SOFTWAREPHE A:241 , PHE A:243 , THR A:260 , VAL A:264 , ASP A:265 , GLN A:295 , ASN A:297 , THR A:299 , ARG A:301 , HOH A:603 , HOH A:612 , HOH A:637 , MAN B:506 , HOH B:617 , HOH B:639binding site for Poly-Saccharide residues NAG A 501 through NAG A 507 bound to ASN A 297
3AC3SOFTWAREASN A:384 , BMA A:503 , MAN A:506 , HOH A:612 , HOH A:637 , PHE B:241 , PHE B:243 , LYS B:246 , THR B:260 , VAL B:264 , ASP B:265 , GLU B:272 , GLN B:295 , ASN B:297 , THR B:299 , ARG B:301 , HOH B:613 , HOH B:617 , HOH B:639 , HOH B:651 , HOH B:653 , HOH B:654 , HOH B:713 , HOH B:717 , HOH B:729 , HOH B:731 , HOH B:742 , HOH B:746 , HOH B:750binding site for Poly-Saccharide residues NAG B 501 through FUC B 508 bound to ASN B 297

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:261 -A:321
2A:367 -A:425
3B:261 -B:321
4B:367 -B:425

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:373 -Pro A:374
2Tyr B:373 -Pro B:374

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W4N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W4N)

(-) Exons   (0, 0)

(no "Exon" information available for 4W4N)

(-) Sequences/Alignments

Asymmetric/Biological 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:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhh.....eeeeeeeee.......eeeeee..eee...ee...ee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee..eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w4n A 238 PSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL 443
                                   247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437      


Chain B from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhh.....eeeeeeeee.......eeeeee..eee...ee...ee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhhhheeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w4n B 237 GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL 443
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436
   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 4W4N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W4N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W4N)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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 ]
    FUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:373 - Pro A:374   [ RasMol ]  
    Tyr B:373 - Pro B:374   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  4w4n
    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
  IGHG1_HUMAN | P01857
    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
  IGHG1_HUMAN | P01857
    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
        IGHG1_HUMAN | P01857: 1aj7 1aqk 1axs 1bey 1d5b 1d5i 1d6v 1dfb 1dn2 1e4k 1fc1 1fc2 1fcc 1gaf 1h3t 1h3u 1h3v 1h3w 1h3x 1h3y 1hkl 1hzh 1i7z 1l6x 1n7m 1op3 1oqo 1oqx 1pg7 1t83 1t89 1vge 2dts 2gj7 2i5y 2iwg 2j6e 2jb5 2jb6 2o5x 2o5y 2o5z 2osl 2qad 2ql1 2qqk 2qql 2qqn 2qr0 2r56 2rcj 2rcs 2vxq 2wah 3agv 3ave 3ay4 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3c2s 3cfj 3cfk 3csy 3d0l 3d0v 3d6g 3d85 3dj9 3dnk 3do3 3dro 3drq 3dvg 3dvn 3eyf 3eyo 3eyq 3fjt 3mcl 3o11 3ry6 3s7g 3sgj 3sgk 3tv3 3twc 3tyg 3u0w 3u7w 3u7y 3v7m 3v8c 3v95 3wjj 3wjl 3wkn 3wn5 4acp 4b7i 4bm7 4bsv 4bsw 4byh 4cdh 4d9q 4d9r 4dag 4dz8 4eow 4hix 4j12 4ku1 4lld 4llm 4llq 4n0u 4nqs 4nqt 4nqu 4nwt 4nwu 4o4y 4o51 4q6y 4q74 4q7d 4w4o 4wi2 4wi3 4wi4 4wi5 4wi6 4wi7 4wi8 4wi9 4x4m 4x98 4x99 4xmp 4xny 4xnz 4xxd 4zne 5bw7 5c7k 5d4q 5d6d 5di8 5dj0 5dj2 5dj6 5dj8 5dja 5djc 5djd 5djx 5djy 5djz 5dk0 5dk2 5dvk 5dvl 5dvm 5dvn 5dvo 5gsq 5hsf 5hy9 5hye 5hyf 5hyi 5iq7 5iq9 5iw3 5iw6 5jih 5jii 5jik 5k33 5k8d 5kwg 5m3v 5v43 5v4e

(-) Related Entries Specified in the PDB File

4w4o