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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SHARK TBC1D15 GAP DOMAIN
 
Authors :  Y. -N. Chen, W. Wang, D. Cheng, Y. Ge, X. Gu, X. E. Zhou, F. Ye, H. E. Xu, Z. Lv
Date :  05 Nov 16  (Deposition) - 22 Feb 17  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Shark (Chiloscyllium Plagiosum), Tbc1D15, Gap (Gtpase-Activating Protein), Gtpase, Protein Binding, Hydrolase Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. N. Chen, X. Gu, X. E. Zhou, W. Wang, D. Cheng, Y. Ge, F. Ye, H. E. Xu, Z. Lv
Crystal Structure Of Tbc1D15 Gtpase-Activating Protein (Gap Domain And Its Activity On Rab Gtpases.
Protein Sci. V. 26 834 2017
PubMed-ID: 28168758  |  Reference-DOI: 10.1002/PRO.3132

(-) Compounds

Molecule 1 - SHARK TBC1D15 GTPASE-ACTIVATING PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: TBC1D15 GAP DOMAIN
    Organism Common: SHARKS
    Organism Scientific: SQUALIMORPHII
    Organism Taxid: 118040

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 5TUB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TUB)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:576 -Pro A:577
2Leu B:576 -Pro B:577
3Leu C:576 -Pro C:577
4Leu D:576 -Pro D:577

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TUB)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh................hhhhhhhhh.......hhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tub A 317 FEVITRIDLGIRPEIQRGEPVSIERWSQCMDAEGKVLDPENVKKLIFRGGLCHAVRKLTWKFLLNYFPWDSSKEDRRLLIKRKTDEYFRMKLQWKSVSEEQEKRNTRLKDYKSLIEKDVNRTDRTNPFYEGHENPGLILLHDILMTYCMYDFDLGYIQGMSDLLSPILYVMENEVDAFWCFVAFIEQMHCNFEEQMQGMKTELSQLSTLLKLLDLGFWNYLESQESGYLYFCFRWLLIRFKREFNFQDTLRLWEVMWTGLPCQNFHLLICCAILDSEKQKIMENHYGFNEILKHINELSLKLDVEEVLCKAEAIYCQMMKCKDLPQAVGEILGLK 651
                                   326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646     


Chain B from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...............hhhhhhhh........hhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tub B 317 FEVITRIDLGIRPEIQRGEPVSIERWSQCMDAEGKVLDPENVKKLIFRGGLCHAVRKLTWKFLLNYFPWDSSKEDRRLLIKRKTDEYFRMKLQWKSVSEEQEKRNTRLKDYKSLIEKDVNRTDRTNPFYEGHENPGLILLHDILMTYCMYDFDLGYIQGMSDLLSPILYVMENEVDAFWCFVAFIEQMHCNFEEQMQGMKTELSQLSTLLKLLDLGFWNYLESQESGYLYFCFRWLLIRFKREFNFQDTLRLWEVMWTGLPCQNFHLLICCAILDSEKQKIMENHYGFNEILKHINELSLKLDVEEVLCKAEAIYCQMMKCKDLPQAVGEILGL 650
                                   326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646    


Chain C from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................hhhhhhhhh.......hhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5tub C 322 RIDLGIRPEIQRGEPVSIERWSQCMDAEGKVLDPENVKKLIFRGGLCHAVRKLTWKFLLNYFPWDSSKEDRRLLIKRKTDEYFRMKLQWKSVSEEQEKRNTRLKDYKSLIEKDVNRTDRTNPFYEGHENPGLILLHDILMTYCMYDFDLGYIQGMSDLLSPILYVMENEVDAFWCFVAFIEQMHCNFEEQMQGMKTELSQLSTLLKLLDLGFWNYLESQESGYLYFCFRWLLIRFKREFNFQDTLRLWEVMWTGLPCQNFHLLICCAILDSEKQKIMENHYGFNEILKHINELSLKLDVEEVLCKAEAIYCQMMKCKDLPQAVGEILGLK 651
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651


Chain D from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...............hhhhhhhhh.......hhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tub D 318 EVITRIDLGIRPEIQRGEPVSIERWSQCMDAEGKVLDPENVKKLIFRGGLCHAVRKLTWKFLLNYFPWDSSKEDRRLLIKRKTDEYFRMKLQWKSVSEEQEKRNTRLKDYKSLIEKDVNRTDRTNPFYEGHENPGLILLHDILMTYCMYDFDLGYIQGMSDLLSPILYVMENEVDAFWCFVAFIEQMHCNFEEQMQGMKTELSQLSTLLKLLDLGFWNYLESQESGYLYFCFRWLLIRFKREFNFQDTLRLWEVMWTGLPCQNFHLLICCAILDSEKQKIMENHYGFNEILKHINELSLKLDVEEVLCKAEAIYCQMMKCKDLPQAVGEILGL 650
                                   327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647
   Legend:   → Mismatch (orange background)
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  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 5TUB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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    (no "Gene Ontology" information available for 5TUB)

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  Cis Peptide Bonds
    Leu A:576 - Pro A:577   [ RasMol ]  
    Leu B:576 - Pro B:577   [ RasMol ]  
    Leu C:576 - Pro C:577   [ RasMol ]  
    Leu D:576 - Pro D:577   [ RasMol ]  
 
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5tuc