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(-) Description

Title :  X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN IN COMPLEX WITH FAB
 
Authors :  A. Ruf, M. Stihle, J. Benz, R. Thoma, M. G. Rudolph
Date :  03 Mar 16  (Deposition) - 18 May 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym. Unit :  A,B,H,L,M,N
Biol. Unit 1:  A,B,M  (1x)
Biol. Unit 2:  H,L,N  (1x)
Keywords :  Dcx Domain, Ubiquitin-Like Fold, Microtubule Associated, Signaling Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Burger, M. Stihle, A. Sharma, P. Di Lello, J. Benz, B. D'Arcy, M. Debulpaep, D. Fry, W. Huber, T. Kremer, T. Laeremans, H. Matile, A. Ross, A. C. Rufer, G. Schoch, M. O. Steinmetz, J. Steyaert, M. G. Rudolph, R. Thoma, A. Ruf
Crystal Structures Of The Human Doublecortin C- And N-Terminal Domains In Complex With Specific Antibodies.
J. Biol. Chem. V. 291 16292 2016
PubMed-ID: 27226599  |  Reference-DOI: 10.1074/JBC.M116.726547

(-) Compounds

Molecule 1 - MAB 6H10 LIGHT CHAIN
    Chains: A, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LC
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - IGHG PROTEIN
    Chains: B, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: IGHG
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - NEURONAL MIGRATION PROTEIN DOUBLECORTIN
    Chains: M, N
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 133-221
    Gene: DCX, DBCN, LISX
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DOUBLIN,LISSENCEPHALIN-X,LIS-X

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABHLMN
Biological Unit 1 (1x): AB  M 
Biological Unit 2 (1x):   HL N

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2PCA2Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:33 , HIS B:35 , ARG B:50 , LYS B:100binding site for residue CL B 301
2AC2SOFTWARETYR H:33 , HIS H:35 , ARG H:50 , LYS H:100binding site for residue CL H 301

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:96
4B:142 -B:197
5H:22 -H:96
6H:142 -H:197
7L:23 -L:88
8L:134 -L:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Tyr A:94 -Pro A:95
2Tyr A:140 -Pro A:141
3Phe B:148 -Pro B:149
4Trp B:190 -Pro B:191
5Phe H:148 -Pro H:149
6Trp H:190 -Pro H:191
7Tyr L:94 -Pro L:95
8Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IKC)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ikc A   1 DIVMTQSQKLMSTSVGDRVSITCKASQIVDTAVAWYQQKPGQSPKPLIYLASNRHTGVPDRFTGSGSGTDFTLTINNVQSDDLADYFCLQHWNYPLTFGAGTKLELKGADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    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:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..........eeeee........eeeee..........eeeeeeeeeee.....eeeee...eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ikc B   1 xVQLQQSGADLVRPGASVKLSCTASGFDIKDDYVHWVKQRPEQGLEWIGRIDPANGATKYAPKFQDKATLTADTSSNTAYLQLSSLTSEDTAVYYCGRSKYFDSWGQGTTLTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPS 215
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       164       174       184       194       204       214 
                            1-PCA                                                                                                                                                      158|                                                    
                                                                                                                                                                                        163                                                    


Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee..........eeeee........eeeee..........eeeeeeeeeee.....eeee....hhhhheeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ikc H   1 xVQLQQSGADLVRPGASVKLSCTASGFDIKDDYVHWVKQRPEQGLEWIGRIDPANGATKYAPKFQDKATLTADTSSNTAYLQLSSLTSEDTAVYYCGRSKYFDSWGQGTTLTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPS 215
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     
                            1-PCA                                                                                                                                                                                                                  


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ikc L   1 DIVMTQSQKLMSTSVGDRVSITCKASQIVDTAVAWYQQKPGQSPKPLIYLASNRHTGVPDRFTGSGSGTDFTLTINNVQSDDLADYFCLQHWNYPLTFGAGTKLELKGADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       202       212 
                                                                                                                                                                                                                               198|            
                                                                                                                                                                                                                                201            


Chain M from PDB  Type:PROTEIN  Length:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee........eeeee......hhhhhhhhhhhhhh..........eeee........hhhhh....eeeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 5ikc M  51 AAKKVRFYRNGDRYFKGIVYAVSSDRFRSFDALLADLTRSLSDNINLPQGVRYIYTIDGSRKIGSMDELEEGESYVCSSDNFFKKVEYT 139
                                    60        70        80        90       100       110       120       130         


Chain N from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee........eeeee......hhhhhhhhhhhhh...........eeee........hhhhh....eeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 5ikc N  51 AAKKVRFYRNGDRYFKGIVYAVSSDRFRSFDALLADLTRSLSDNINLPQGVRYIYTIDGSRKIGSMDELEEGESYVCSSDNFFKKVEYTK 140
                                    60        70        80        90       100       110       120       130       140
   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 5IKC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DCX_HUMAN | O43602: 1mjd 2bqq 2xrp 4atu 5in7 5io9 5ioi 5ip4
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        Q569X1_MOUSE | Q569X1: 1mpa 2mpa

(-) Related Entries Specified in the PDB File

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