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(-) Description

Title :  HUMAN TNFA DIMER IN COMPLEX WITH THE SEMI-SYNTHETIC BICYCLIC PEPTIDE M21
 
Authors :  S. Luzi, Y. Kondo, E. Bernard, L. Stadler, G. Winter, P. Holliger
Date :  01 Jul 14  (Deposition) - 04 Feb 15  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Tumor Necrosis Factor-Alpha, Bicyclo Compounds, Peptides, Cytokine- Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Luzi, Y. Kondo, E. Bernard, L. K. Stadler, M. Vaysburd, G. Winter, P. Holliger
Subunit Disassembly And Inhibition Of Tnf Alpha By A Semi-Synthetic Bicyclic Peptide.
Protein Eng. Des. Sel. V. 28 45 2015
PubMed-ID: 25614525  |  Reference-DOI: 10.1093/PROTEIN/GZU055

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 77-233
    Gene: TNF, TNFA, TNFSF2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CACHECTIN,TNF-ALPHA,TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 2,TNF-A
 
Molecule 2 - ALA-CYS-PRO-PRO-CYS-LEU-TRP-GLN-VAL-LEU-CYS-GLY
    Chains: E, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synonym: PEPTIDE M21
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
138A2Ligand/Ion(2,4,6-TRIMETHYLBENZENE-1,3,5-TRIYL)TRIMETHANOL
2GOL6Ligand/IonGLYCEROL
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
138A1Ligand/Ion(2,4,6-TRIMETHYLBENZENE-1,3,5-TRIYL)TRIMETHANOL
2GOL4Ligand/IonGLYCEROL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
138A1Ligand/Ion(2,4,6-TRIMETHYLBENZENE-1,3,5-TRIYL)TRIMETHANOL
2GOL2Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:119 , PRO B:117 , ILE B:118 , TYR B:119binding site for residue GOL B 201
2AC2SOFTWARELEU B:26 , ALA B:134 , GLU B:135 , ILE B:136 , PRO B:139binding site for residue GOL B 202
3AC3SOFTWAREARG A:138 , TYR A:141 , ALA E:1 , CYS E:2binding site for residue GOL E 101
4AC4SOFTWAREGLY E:12binding site for residue GOL E 102
5AC5SOFTWAREPRO C:51binding site for residue GOL C 201
6AC6SOFTWAREPRO C:117 , ILE C:118 , TYR C:119 , TYR D:119binding site for residue GOL D 201
7AC7SOFTWARELEU A:57 , TYR A:119 , ARG A:138 , TYR A:141 , LEU A:157 , HIS B:15 , LEU B:57 , TYR B:59 , LEU B:120 , GLY B:148 , GLN B:149 , TYR B:151 , TYR C:87binding site for peptide chain E
8AC8SOFTWARETYR C:119 , LEU C:157 , HIS D:15 , LEU D:57 , TYR D:59 , SER D:147 , GLY D:148 , GLN D:149 , TYR D:151binding site for peptide chain F

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:69 -A:101
2B:69 -B:101
3C:69 -C:101
4D:69 -D:101

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4TWT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TWT)

(-) 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:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee.........ee......eee...eee..eee....eeeeeeeeeeeeee........eeeeeeee......eeeeeeeee..............eeeeeeeeeeeeee....eeeeee.hhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4twt A   8 PSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL 157
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157


Chain B from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....................eee..eee....eeeeeeeeeeeeee........eeeeeeee......eeeeeeeee.........eeeeeeeeeeeeee....eeeeee.hhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4twt B  10 DKPVAHVVANPQAEGQLQWLNRLLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL 157
                                    19        29 ||     43        53        63        73        83        93       103 ||    118       128       138       148         
                                                31|                                                                  105|                                              
                                                 36                                                                   111                                              


Chain C from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.........ee............eee..eee....eeeeeeeeeeeeee........eeeeeeee......eeeeeeeee........eeeeeeeeeeeeee....eeeeee.hhhhh........eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4twt C   9 SDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL 157
                                    18        28        38        48        58        68        78        88        98      |114       124       134       144       154   
                                                                                                                          105|                                             
                                                                                                                           112                                             


Chain D from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.........ee.....eee..eee....eeeeeeeeeeeee........eeeeeeee......eeeeeeeee......eeeeeeeeeeeee....eeeeee.hhhhh.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4twt D   9 SDKPVAHVVANPQAEGQLQWLNRNGVELRDNQLVVPSEGLYLIYSQVLFKGQGCSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRPWYEPIYLGGVFQLEKGDRLSAEINRPDYLFAESGQVYFGIIAL 157
                                    18        28  ||    45        55        65   ||   76        86        96      |115       125       135      |146       156 
                                                 31|                            69|                             103|                          142|             
                                                  39                             71                              113                           144             


Chain E from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ......hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 4twt E   1 ACPPCLWQVLCG  12
                                    10  


Chain F from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 4twt F   1 ACPPCLWQVLCG  12
                                    10
   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 4TWT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (147, 147)

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  4twt
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  TNFA_HUMAN | P01375
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 Related Entries

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UniProtKB/Swiss-Prot
        TNFA_HUMAN | P01375: 1a8m 1tnf 2az5 2e7a 2tun 2zjc 2zpx 3alq 3it8 3l9j 3wd5 4g3y 4tsv 4y6o 5mu8 5tsw

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