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(-) Description

Title :  CRYSTAL STRUCTURE OF MOR04357, A NEUTRALIZING ANTI-HUMAN GM-CSF ANTIBODY FAB FRAGMENT IN COMPLEX WITH HUMAN GM-CSF
 
Authors :  R. Eylenstein, D. Weinfurtner, S. Steidl, J. Boettcher, M. Augustin
Date :  25 Jun 15  (Deposition) - 14 Oct 15  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B,H,L,M,N
Biol. Unit 1:  A,H,L  (1x)
Biol. Unit 2:  B,M,N  (1x)
Keywords :  Gm-Csf, Affinity Maturation, Phage Display, Cytokine, Antibody, Proteros Biostructures Gmbh, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Eylenstein, D. Weinfurtner, S. Hartle, R. Strohner, J. Bottcher, M. Augustin, R. Ostendorp, S. Steidl
Molecular Basis Of In Vitro Affinity Maturation And Functional Evolution Of A Neutralizing Anti-Human Gm-Csf Antibody.
Mabs V. 8 176 2016
PubMed-ID: 26406987  |  Reference-DOI: 10.1080/19420862.2015.1099774

(-) Compounds

Molecule 1 - GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 18-144
    GeneCSF2, GMCSF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGM-CSF,COLONY-STIMULATING FACTOR,CSF,MOLGRAMOSTIN, SARGRAMOSTIM
 
Molecule 2 - IMMUNGLOBULIN G1 FAB FRAGMENT, HEAVY CHAIN
    ChainsH, M
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - IMMUNGLOBULIN G1 FAB FRAGMENT, LIGHT CHAIN
    ChainsL, N
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABHLMN
Biological Unit 1 (1x)A HL  
Biological Unit 2 (1x) B  MN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
2PG61Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
3PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
2PG61Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
3PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
2PG6-1Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
3PGE-1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:9 , ALA H:56 , THR H:57binding site for residue PGE H 301
2AC2SOFTWAREGLY H:42 , LYS H:43 , GLY H:44 , GLY L:100binding site for residue PGE H 302
3AC3SOFTWAREPRO L:40 , GLY L:41binding site for residue PEG L 301
4AC4SOFTWAREGLY H:42 , PRO L:8 , ASP L:85 , GLY L:100 , GLY L:101 , LYS L:103 , LEU L:104 , THR L:105binding site for residue PG6 L 302
5AC5SOFTWARELYS M:43 , GLY M:44 , GLY N:100binding site for residue PEG M 301
6AC6SOFTWAREPRO N:40 , GLY N:41 , ASP N:85binding site for residue PEG N 301

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:54 -A:96
2A:88 -A:121
3B:54 -B:96
4B:88 -B:121
5H:22 -H:92
6H:140 -H:196
7L:23 -L:88
8L:134 -L:193
9M:22 -M:92
10M:140 -M:196
11N:23 -N:88
12N:134 -N:193

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Tyr L:140 -Pro L:141
4Phe M:146 -Pro M:147
5Glu M:148 -Pro M:149
6Tyr N:140 -Pro N:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C7X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C7X)

(-) Exons   (0, 0)

(no "Exon" information available for 5C7X)

(-) 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:115
                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh..hhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeehhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                5c7x A    9 STQPWEHVNAIQEARRLLNLSRTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIPFDCWEP  124
                                    18        28 ||     39        49        59        69        79        89        99       109       119     
                                                30|                                                                                            
                                                 32                                                                                            

Chain B from PDB  Type:PROTEIN  Length:116
                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh...hhhhhheeee...........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..........eeeehhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                5c7x B    9 STQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIPFDCWEP  124
                                    18        28        38        48        58        68        78        88        98       108       118      

Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee........eee.......eeeeee....eeeeee...hhhhheeeeeee..........eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhhh...eeeeehhhheee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5c7x H    1 QVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWMNWVRQAPGKGLEWVSGIENKYAGGATYYAASVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGFGTDFWGQGTLVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |||   57        67        77     |||84        94   ||  106       116       126 ||    140       150       160       170       180       190       200       210    
                                                                              52A||                            82A||              98|                        128|                                                                                 
                                                                               52B|                             82B|              101                         133                                                                                 
                                                                                52C                              82C                                                                                                                              

Chain L from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee.........eeee.......ee.............eeeeee..eeeeee...hhhhh.eeeeeee....eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5c7x L    1 DIELTQPPSVSVAPGQTARISCSGDSIGKKYAYWYQQKPGQAPVLVIYKKRPSGIPERFSGSNSGNTATLTISGTQAEDEADYYCSAWGDKGMVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  208
                                    11        21        31        41        51  ||    63        73        83        93       103   |   112       122       132       142       152       162       172       182       192       202      
                                    9|                                         54|                                              106A                                                                                                      
                                    11                                          57                                                                                                                                                        

Chain M from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee........eee.......eeeeee....eeeeee...hhhhheeeeeee.....ee....eeee........eeeee......eeeeeeeeeee.................eee...ee.....eeeeeeeeee.hhhh....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5c7x M    1 QVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWMNWVRQAPGKGLEWVSGIENKYAGGATYYAASVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGFGTDFWGQGTLVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50  |||   57        67        77     |||84        94   ||  106       116       126 ||    140       150       160       170       180       190       200       210   
                                                                              52A||                            82A||              98|                        128|                                                                                
                                                                               52B|                             82B|              101                         133                                                                                
                                                                                52C                              82C                                                                                                                             

Chain N from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee.........eeeee......ee........eeeee...eeeeee...hhhhh.eeeeeeee..eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5c7x N    1 DIELTQPPSVSVAPGQTARISCSGDSIGKKYAYWYQQKPGQAPVLVIYKKRERFSGSNSGNTATLTISGTQAEDEADYYCSAWGDKGMVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  208
                                    11        21        31        41        51||      68        78        88        98       107       117       127       137       147       157       167       177       187       197       207 
                                    9|                                       52|                                           106A                                                                                                      
                                    11                                        60                                                                                                                                                     

   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 5C7X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C7X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C7X)

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CSF2_HUMAN | P041411csg 2gmf 4nkq 4rs1 5d70 5d71 5d72

(-) Related Entries Specified in the PDB File

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