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 :  HUMAN CD38 IN COMPLEX WITH NANOBODY MU375
 
Authors :  Q. Hao, H. Zhang
Date :  01 Dec 15  (Deposition) - 15 Jun 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cd38, Adp-Ribosyl Cyclase, Cyclic Adp-Ribose, X-Crystallography, Calcium Signaling, Nanobody, Mu375, Hydrolase-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Li, S. Qi, M. Unger, Y. N. Hou, Q. W. Deng, J. Liu, C. M. Lam, X. W. Wang, D. Xin, P. Zhang, F. Koch-Nolte, Q. Hao, H. Zhang, H. C. Lee, Y. J. Zhao
Immuno-Targeting The Multifunctional Cd38 Using Nanobody
Sci Rep V. 6 27055 2016
PubMed-ID: 27251573  |  Reference-DOI: 10.1038/SREP27055

(-) Compounds

Molecule 1 - ADP-RIBOSYL CYCLASE/CYCLIC ADP-RIBOSE HYDROLASE 1
    Chains: A
    EC Number: 3.2.2.6
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Common: PICHIA PASTORIS
    Expression System Plasmid: PPICZALPHA
    Expression System Strain: X33
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: ECTODOMAIN, UNP RESIDUES 46-300
    Gene: CD38
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CD38
 
Molecule 2 - NANOBODY MU375
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PHEN2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:125 , SER A:126 , ARG A:127 , SER A:220 , THR A:221 , PHE A:222 , HOH A:511 , HOH A:535 , HOH A:586binding site for residue SO4 A 401
2AC2SOFTWARELYS A:214 , ARG A:280 , PRO A:281 , ASP A:282 , LYS A:283binding site for residue SO4 A 402
3AC3SOFTWAREASP A:100 , ILE A:101 , THR A:102 , SER A:166 , ILE A:168 , ASN A:182 , HOH A:506 , HOH A:510 , HOH A:515 , HOH A:543binding site for residue GOL A 403

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:67 -A:82
2A:99 -A:180
3A:119 -A:201
4A:160 -A:173
5A:254 -A:275
6A:287 -A:296
7B:22 -B:99

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F21)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F21)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F21)

(-) Exons   (0, 0)

(no "Exon" information available for 5F21)

(-) 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:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhh.........eeee.hhhhhhhhhhhh....hhhhhhhhhhhh................ee.........hhhhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhh....eeeeeeeee....hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh..hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f21 A  49 TWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFDTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVEVHNLQPEKVQTLEAWVIHGSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSCTSEI 300
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238      |252       262       272       282       292        
                                                                                                                                                                                                                              245|                                                  
                                                                                                                                                                                                                               250                                                  


Chain B from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eee.....eeeeeeeehhhhhhh.eeeeee......eeeeee.....eee.......eeeeee..eeeeeeee...hhhhheeeeeee.............eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5f21 B   3 QLQESGGGSVQAGGSLTLSCTASGLLFRLASMGWYRQAPGKERELIATITVGGKTNYKDSVQGRFIITRDNTKSTVTLQMNRLKPEDTAVYYCNTASPAVGADTWGQGTRVTVS 120
                                    12        22        32        42        52        62        72||      86        96       106       116    
                                                                                                 73|                                          
                                                                                                  78
   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 5F21)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F21)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F21)

(-) Gene Ontology  (37, 37)

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
    GOL  [ 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
(no "Cis Peptide Bonds" information available for 5f21)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5f21
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CD38_HUMAN | P28907
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.2.6
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CD38_HUMAN | P28907
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CD38_HUMAN | P28907: 1yh3 1zvm 2ef1 2hct 2i65 2i66 2i67 2o3q 2o3r 2o3s 2o3t 2o3u 2pgj 2pgl 3dzf 3dzg 3dzh 3dzi 3dzj 3dzk 3f6y 3i9m 3i9n 3ofs 3raj 3rok 3rom 3rop 3roq 3u4h 3u4i 4cmh 4f45 4f46 4ogw 4tmf 4xjs 4xjt 5f1k 5f1o

(-) Related Entries Specified in the PDB File

5f1k HUMAN CD38 IN COMPLEX WITH NANOBODY MU1053
5f1o HUMAN CD38 IN COMPLEX WITH NANOBODY MU551