Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MOR04302, 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 :  13 Aug 15  (Deposition) - 14 Oct 15  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,H,L
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
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    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
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - IMMUNGLOBULIN G1 FAB FRAGMENT, LIGHT CHAIN
    ChainsL
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO H:126 , SER H:127 , SER H:128 , THR H:135 , ALA H:137binding site for residue PEG H 301
2AC2SOFTWAREASP L:1 , ILE L:2 , LYS L:31 , GLY L:92 , ASP L:93binding site for residue SO4 L 301
3AC3SOFTWAREGLU L:83 , VAL L:106 , GLY L:107 , GLN L:108 , TYR L:140 , LYS L:166 , HOH L:428binding site for residue SO4 L 302

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:96
2A:88 -A:121
3H:22 -H:92
4H:140 -H:196
5L:23 -L:88
6L:134 -L:193

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D71)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D71)

(-) Exons   (0, 0)

(no "Exon" information available for 5D71)

(-) Sequences/Alignments

Asymmetric/Biological 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:114
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.........eeeee..........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.........eeeeehhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                5d71 A    9 STQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIPFDCW  122
                                    18        28        38        48        58        68        78        88        98       108       118    

Chain H from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               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.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5d71 H    1 QVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWMNWVRQAPGKGLEWVSGISYSGSETYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGFGTDFWGQGTLVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96 ||    108       118       128|      142       152       162       172       182       192       202       212 
                                                                              52A                            82A||              98|                        128|                                                                                
                                                                                                              82B|              101                         133                                                                                
                                                                                                               82C                                                                                                                             

Chain L from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeee.....eeeeee..hhhhh..eeeee......ee....eeeeee..eeeeee...hhhhheeeeeeeee..eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5d71 L    1 DIELTQPPSVSVAPGQTARISCSGDSIGKKYAYWYQQKPGQAPVLVIERFSGSNSGNTATLTISGTQAEDEADYYCSAWGDKGMVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                    11        21        31        41      ||62        72        82        92       102    |  111       121       131       141       151       161       171       181       191       201        
                                    9|                                   48|                                           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 5D71)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D71)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D71)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5d71
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CSF2_HUMAN | P04141
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CSF2_HUMAN | P04141
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CSF2_HUMAN | P041411csg 2gmf 4nkq 4rs1 5c7x 5d70 5d72

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5D71)