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(-)Asym./Biol. Unit
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(-) Description

Title :  HUMAN CD38 IN COMPLEX WITH NANOBODY MU551
 
Authors :  H. Zhang, Q. Hao
Date :  30 Nov 15  (Deposition) - 15 Jun 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cd38, Adp-Ribosyl Cyclase, Cyclic Adp-Ribose, X-Crystallography, Calcium Signaling, Nanobody, Mu551, 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 MU551
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHEN2
    Expression System Taxid: 562
    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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5F1O)

(-) Sites  (0, 0)

(no "Site" information available for 5F1O)

(-) 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:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F1O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F1O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F1O)

(-) Exons   (0, 0)

(no "Exon" information available for 5F1O)

(-) 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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhh........eeee.hhhhhhhhhhhh....hhhhhhhhhhhh................ee.........hhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhhhhhhh.....eeeeeeeee........hhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f1o A  49 TWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFDTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVEVHNLQPEKVQTLEAWVIHGSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEC 296
                                    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|                                       292|
                                                                                                                                                                                                                               250                                        296


Chain B from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeee....eeeeeeeee.hhh.eeeeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee.....hhhhhhh....ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f1o B   1 DVQLQESGGGLVQAGHSLRLSCVGSGSRFDNYAMGWFRQAPGKEREFVAAISWSSGTTRYLDTVKGRFTISRDNAKSTVYLQMNSLKPEDTAVYYCAARYQPRYYDSGDMDGYEYDNWGQGTQVTVSS 128
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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 5F1O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F1O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F1O)

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5f1o)
 

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 Databases and Analysis Tools

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  5f1o
    Family and Domain Information: ProDom | SYSTERS
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    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
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Access by UniProt ID/Accession number
  CD38_HUMAN | P28907
    Comparative Protein Structure Models: ModBase
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  3.2.2.6
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(-) Analysis Tools

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  CD38_HUMAN | P28907
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 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 5f21

(-) Related Entries Specified in the PDB File

5f1k HUMAN CD38 IN COMPLEX WITH NANOBODY MU1053
5f21 HUMAN CD38 IN COMPLEX WITH NANOBODY MU375