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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF LIGHT MUTANT2 AND DCR3 COMPLEX
 
Authors :  W. Liu, J. B. Bonanno, C. Zhan, P. R. Kumar, R. Toro, S. G. Nathenson, S. C. Atoms-To-Animals: The Immune Function Network (Ifn), New Yor Structural Genomics Research Consortium (Nysgrc)
Date :  29 Apr 13  (Deposition) - 07 Aug 13  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.78
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Biol. Unit 2:  A,C  (3x)
Biol. Unit 3:  B,D  (3x)
Keywords :  Light, Dcr3, Tnf, Tnfr, Tnf14, Structural Genomics, Psi-Biology, New Hvem, N-Glycosylation, Membrane, Secreted Protein, Cytokine, Ifn, Jelly-Roll Fold, Bind Tnf Receptor Hvem And Ltbr, Ltbr, Protein Structure Initiative, Atoms-To-Animals: The Immune Function Network, New York Structural Genomics Research Consortium, Nysgrc, Immune System, Cytokine-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Liu, C. Zhan, H. Cheng, P. R. Kumar, J. B. Bonanno, S. G. Nathenson, S. C. Almo
Mechanistic Basis For Functional Promiscuity In The Tnf And Tnf Receptor Superfamilies: Structure Of The Light:Dcr3 Assembly.
Structure V. 22 1252 2014
PubMed-ID: 25087510  |  Reference-DOI: 10.1016/J.STR.2014.06.013

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 6B
    Chains: C, D
    Engineered: YES
    Expression System: DROSOPHILA
    Expression System Plasmid: PMT-BIP-HIS-V5
    Expression System Taxid: 7215
    Expression System Vector Type: PLASMID
    Fragment: 30-195
    Gene: TNFRSF6B, DCR3, TR6, UNQ186/PRO212
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DECOY RECEPTOR 3, DCR3, DECOY RECEPTOR FOR FAS LIGAND, M68
 
Molecule 2 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 14
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21-PHYS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: 83-240
    Gene: TNFSF14, HVEML, LIGHT, UNQ391/PRO726
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HERPES VIRUS ENTRY MEDIATOR LIGAND, HVEM-L, HERPESVIRUS ENTRY MEDIATOR LIGAND, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 14, MEMBRANE FORM, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 14, SOLUBLE FORM

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD
Biological Unit 2 (3x): A C 
Biological Unit 3 (3x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN1Ligand/IonALPHA-D-MANNOSE
3MG2Ligand/IonMAGNESIUM ION
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2MAN3Ligand/IonALPHA-D-MANNOSE
3MG-1Ligand/IonMAGNESIUM ION
4NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2MAN3Ligand/IonALPHA-D-MANNOSE
3MG-1Ligand/IonMAGNESIUM ION
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (1, 6)
No.NameCountTypeFull Name
1BMA-1Ligand/IonBETA-D-MANNOSE
2MAN-1Ligand/IonALPHA-D-MANNOSE
3MG-1Ligand/IonMAGNESIUM ION
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS C:132 , PRO C:133 , ALA C:136 , SER C:159 , SER C:161 , HOH C:401BINDING SITE FOR RESIDUE MG C 301
2AC2SOFTWARECYS D:132 , PRO D:133 , ALA D:136 , SER D:159 , SER D:161 , HOH D:403BINDING SITE FOR RESIDUE MG D 301
3AC3SOFTWAREASN C:173 , GLN D:80 , PHE D:81 , TRP D:82 , ARG D:103 , HIS D:106 , THR D:108 , HIS D:109BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 173 RESIDUES 302 TO 305
4AC4SOFTWARETRP C:82 , ASN D:173 , ALA D:176BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 173 RESIDUES 302 TO 303

(-) SS Bonds  (20, 20)

Asymmetric Unit
No.Residues
1A:154 -A:187
2B:154 -B:187
3C:49 -C:62
4C:52 -C:70
5C:73 -C:88
6C:91 -C:105
7C:95 -C:113
8C:115 -C:126
9C:132 -C:150
10C:153 -C:168
11C:174 -C:193
12D:49 -D:62
13D:52 -D:70
14D:73 -D:88
15D:91 -D:105
16D:95 -D:113
17D:115 -D:126
18D:132 -D:150
19D:153 -D:168
20D:174 -D:193

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:220 -Asp A:221
2Leu B:220 -Asp B:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KGG)

(-) 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:141
                                                                                                                                                                             
               SCOP domains d4kgga_ A: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......................eee.eeee..eeee...eeeeeeeeeeeeee.......eeeeeeee.......eeeeeeee.....eeeeeeeeeeeeee....eeeeeeehhhhh........eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgg A  92 VNPAAHLTGANSSLTGSGGPLLWETQLGLAFLRGLSYHDGALVVTKAGYYYIYSKVQLGGVGCPLASTITHGLYKRTPRYPEELELLVSQQSPCGSNWFDSSFLGGVVHLEAGEEVVVRVLDERLVRLRDGTRSYFGAFMV 240
                                   101       111       121       131       141       151    || 163       173       183    || 199       209       219       229       239 
                                                                                          156|                          188|                                             
                                                                                           159                           195                                             


Chain B from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains d4kggb_ B: automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......................eee.eeee..eeee...eeeeeeeeeeeeee.....eeeeeeee.......eeeeeeee.....eeeeeeeeeeeeee....eeeeeeehhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgg B  92 VNPAAHLTGANSSLTGSGGPLLWETQLGLAFLRGLSYHDGALVVTKAGYYYIYSKVQLGGVGCASTITHGLYKRTPRYPEELELLVSQQSPCGSNWFDSSFLGGVVHLEAGEEVVVRVLDERLVRLRDGTRSYFGAFMV 240
                                   101       111       121       131       141       151  ||   165       175       185  ||   201       211       221       231         
                                                                                        154|                          188|                                             
                                                                                         159                           195                                             


Chain C from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeee.....eeeee........eeee....ee..........ee........eeeee........eeee...eeee..eeee.......eeeee........eeee....ee..........ee..........eee........ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgg C  33 TPTYPWRDAETGERLVCAQCPPGTFVQRPCRRDSPTTCGPCPPRHYTQFWNYLERCRYCNVLCGEREEEARACHATHNRACRCRTGFFAHAGFCLEHASCPPGAGVIAPGTPSQNTQCQPCPPGTFSASSSSSEQCQPHRNCTALGLALNVPGSSSHDTLCTSTG 197
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     


Chain D from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeee.....eeeee........eeee....ee..........ee........eeeee........eeee...eeee..eeee.......eeeee........eeee....ee..........ee...hhhhh.eeee........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgg D  33 TPTYPWRDAETGERLVCAQCPPGTFVQRPCRRDSPTTCGPCPPRHYTQFWNYLERCRYCNVLCGEREEEARACHATHNRACRCRTGFFAHAGFCLEHASCPPGAGVIAPGTPSQNTQCQPCPPGTFSASSSSSEQCQPHRNCTALGLALNVPGSSSHDTLCTS 195
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192
   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  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (35, 41)

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 ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ 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
    Leu A:220 - Asp A:221   [ RasMol ]  
    Leu B:220 - Asp B:221   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 ](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
  4kgg
    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
  TNF14_HUMAN | O43557
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TNF6B_HUMAN | O95407
    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
  TNF14_HUMAN | O43557
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TNF6B_HUMAN | O95407
    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
        TNF14_HUMAN | O43557: 4en0 4j6g 4kg8 4kgq 4rsu
        TNF6B_HUMAN | O95407: 3k51 3mhd 3mi8 4j6g 4kgq 4msv 5l36

(-) Related Entries Specified in the PDB File

3k51
3mhd
3mi8
4en0
4j6g RELATED ID: NYSGRC-011104 RELATED DB: TARGETTRACK RELATED ID: NYSGRC-011073 RELATED DB: TARGETTRACK