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(-) Description

Title :  CRYSTAL STRUCTURE OF TNF-ALPHA IN COMPLEX WITH INFLIXIMAB FAB FRAGMENT
 
Authors :  S. Y. Liang, J. X. Dai, Y. J. Guo, Z. Y. Lou
Date :  15 Jul 12  (Deposition) - 27 Mar 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  C,H,L
Biol. Unit 1:  C,H,L  (3x)
Biol. Unit 2:  C,H,L  (1x)
Keywords :  Tnf, Infliximab, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Y. Liang, J. X. Dai, S. Hou, L. Su, D. Zhang, H. Guo, S. Hu, H. Wang, Z. Rao, Y. J. Guo, Z. Y. Lou
Structural Basis For Treating Tumor Necrosis Factor Alpha (Tnfalpha)-Associated Diseases With The Therapeutic Antibod Infliximab
J. Biol. Chem. V. 288 13799 2013
PubMed-ID: 23504311  |  Reference-DOI: 10.1074/JBC.M112.433961

(-) Compounds

Molecule 1 - INFLIXIMAB FAB L
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - INFLIXIMAB FAB H
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - TUMOR NECROSIS FACTOR
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: TUMOR NECROSIS FACTOR, SOLUBLE FORM
    Gene: TNFA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TNF-ALPHA

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : CHL
Biological Unit 1 (3x): CHL
Biological Unit 2 (1x): CHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4G3Y)

(-) Sites  (0, 0)

(no "Site" information available for 4G3Y)

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1C:69 -C:101
2H:22 -H:98
3H:147 -H:203
4L:23 -L:88
5L:134 -L:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Trp L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Glu H:1 -Val H:2
5Gly H:140 -Gly H:141
6Phe H:153 -Pro H:154
7Glu H:155 -Pro H:156
8Cys C:101 -Gln C:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G3Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G3Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4G3Y)

(-) 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 C from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains d4g3yc_ C: Tumor necrosis factor (TNF)                                                                                                               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
                 4g3y C  10 DKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL 157
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149        


Chain H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh...eeeeeeehhhheee..ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g3y H   1 EVKLEESGGGLVQPGGSMKLSCVASGFIFSNHWMNWVRQSPEKGLEWVAEIRSKSINSATHYAESVKGRFTISRDDSKSAVYLQMTDLRTEDTGVYYCSRNYYGSTYDYWGQGTTLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d4g3yl1 L:1-107 automated matches                                                                          d4g3yl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....ee..eee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g3y L   1 DILLTQSPAILSVSPGERVSFSCRASQFVGSSIHWYQQRTNGSPRLLIKYASESMSGIPSRFSGSGSGTDFTLSINTVESEDIADYYCQQSHSWPFTFGSGTNLEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (3, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G3Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G3Y)

(-) Gene Ontology  (147, 147)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Cys C:101 - Gln C:102   [ RasMol ]  
    Glu H:1 - Val H:2   [ RasMol ]  
    Glu H:155 - Pro H:156   [ RasMol ]  
    Gly H:140 - Gly H:141   [ RasMol ]  
    Phe H:153 - Pro H:154   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp L:94 - Pro L:95   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 
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  4g3y
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  TNFA_HUMAN | P01375
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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

(-) Related Entries Specified in the PDB File

4g3z