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(-) Description

Title :  STRUCTURE OF THE TRANSFORMING GROWTH FACTOR-BETA NEUTRALIZING ANTIBODY GC-1008
 
Authors :  C. Gruetter, M. G. Gruetter
Date :  26 Sep 08  (Deposition) - 02 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cytokine Neutralizing Antibody, Fab Fragment, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Wilkinson, R. Turner, S. Podichetty, D. Finch, M. Mccourt, S. Loning, L. Jermutus
A Cytokine-Neutralizing Antibody As A Structural Mimetic Of 2 Receptor Interactions
Proc. Natl. Acad. Sci. Usa V. 105 20251 2008
PubMed-ID: 19073914  |  Reference-DOI: 10.1073/PNAS.0807200106

(-) Compounds

Molecule 1 - GC-1008 FAB LIGHT CHAIN
    Chains: A, C
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Strain: NS0
    Expression System Taxid: 10090
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - GC-1008 FAB HEAVY CHAIN
    Chains: B, D
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Strain: NS0
    Expression System Taxid: 10090
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:165 , GLU A:166 , GLN A:167 , ASP A:168 , HOH A:335 , HOH A:336 , HOH A:356 , HIS B:171BINDING SITE FOR RESIDUE GOL A 216
2AC2SOFTWARESER A:163 , SER A:177 , SER A:178 , THR A:179 , PHE B:173 , PRO B:174 , SER B:184 , LEU B:185 , SER B:186 , HOH B:347BINDING SITE FOR RESIDUE GOL B 226
3AC3SOFTWAREVAL B:2 , THR B:28 , PHE B:29BINDING SITE FOR RESIDUE GOL B 227
4AC4SOFTWAREGLU C:166 , GLN C:167 , ASP C:168 , HOH C:235 , HOH C:274 , HOH C:317 , HIS D:171BINDING SITE FOR RESIDUE GOL C 216
5AC5SOFTWARESER C:163 , SER C:177 , SER C:178 , THR C:179 , PHE D:173 , PRO D:174 , SER D:184 , LEU D:185 , SER D:186 , HOH D:429BINDING SITE FOR RESIDUE GOL D 226
6AC6SOFTWAREVAL D:2 , THR D:28 , PHE D:29BINDING SITE FOR RESIDUE GOL D 227

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:23 -A:89
2A:135 -A:195
3A:215 -B:134
4B:22 -B:96
5B:147 -B:203
6C:23 -C:89
7C:135 -C:195
8C:215 -D:134
9D:22 -D:96
10D:147 -D:203

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Ser A:95 -Pro A:96
3Tyr A:141 -Pro A:142
4Phe B:153 -Pro B:154
5Glu B:155 -Pro B:156
6Ser C:7 -Pro C:8
7Ser C:95 -Pro C:96
8Tyr C:141 -Pro C:142
9Phe D:153 -Pro D:154
10Glu D:155 -Pro D:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EO0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EO0)

(-) Exons   (0, 0)

(no "Exon" information available for 3EO0)

(-) 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:215
                                                                                                                                                                                                                                                       
               SCOP domains d3eo0a1 A:1-108 automated matches                                                                           d3eo0a2 A:109-215 automated matches                                                                         SCOP domains
               CATH domains 3eo0A01 A:1-109 Immunoglobulins                                                                              3eo0A02 A:110-213 Immunoglobulins                                                                       -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eo0 A   1 ETVLTQSPGTLSLSPGERATLSCRASQSLGSSYLAWYQQKPGQAPRLLIYGASSRAPGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYADSPITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3eo0B01 B:1-120 Immunoglobulins                                                                                         3eo0B02 B:121-220 Immunoglobulins                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee......eeeeeee....eeee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eo0 B   1 QVQLVQSGAEVKKPGSSVKVSCKASGYTFSSNVISWVRQAPGQGLEWMGGVIPIVDIANYAQRFKGRVTITADESTSTTYMELSSLRSEDTAVYYCASTLGLVLDAMDYWGQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVEP 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220


Chain C from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d3eo0c1 C:1-108 automated matches                                                                           d3eo0c2 C:109-215 automated matches                                                                         SCOP domains
               CATH domains 3eo0C01 C:1-109 Immunoglobulins                                                                              3eo0C02 C:110-213 Immunoglobulins                                                                       -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eo0 C   1 ETVLTQSPGTLSLSPGERATLSCRASQSLGSSYLAWYQQKPGQAPRLLIYGASSRAPGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYADSPITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain D from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3eo0D01 D:1-120 Immunoglobulins                                                                                         3eo0D02 D:121-220 Immunoglobulins                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee......eeeeeee....eeee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eo0 D   1 QVQLVQSGAEVKKPGSSVKVSCKASGYTFSSNVISWVRQAPGQGLEWMGGVIPIVDIANYAQRFKGRVTITADESTSTTYMELSSLRSEDTAVYYCASTLGLVLDAMDYWGQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVEP 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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  (2, 4)

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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Mus musculus. Organism_taxid: 10090. (7)
1a3eo0A02A:110-213
1b3eo0A01A:1-109
1c3eo0C01C:1-109
1d3eo0C02C:110-213
1e3eo0B02B:121-220
1f3eo0D02D:121-220
1g3eo0B01B:1-120
1h3eo0D01D:1-120

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EO0)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3EO0)

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 Related Entries

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

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        Q6PYX1_HUMAN | Q6PYX1: 3c2s 4j12
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(-) Related Entries Specified in the PDB File

3eo1