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(-) Description

Title :  CRYSTAL STRUCTURE OF DEG5
 
Authors :  W. Gong, W. Sun, H. Fan, F. Gao, L. Liu
Date :  10 Dec 12  (Deposition) - 01 May 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  C  (1x)
Keywords :  Bets-Barrel, Endopeptidase, Calcium Binding, Chloroplast, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Sun, F. Gao, H. Fan, X. Shan, R. Sun, L. Liu, W. Gong
The Structures Of Arabidopsis Deg5 And Deg8 Reveal New Insights Into Htra Proteases
Acta Crystallogr. , Sect. D V. 69 830 2013
PubMed-ID: 23633592  |  Reference-DOI: 10.1107/S0907444913002023

(-) Compounds

Molecule 1 - PROTEASE DO-LIKE 5, CHLOROPLASTIC
    Chains: A, B, C
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DEGP5, HHOA, AT4G18370, F28J12.30
    Mutation: YES
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (1x): A  
Biological Unit 3 (1x):  B 
Biological Unit 4 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:82 , LEU A:84 , GLU A:89 , GLU B:86 , GLU B:89 , HOH B:513BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREGLU A:87 , GLU B:87 , HOH B:538 , GLU C:87 , HOH C:543BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREASP A:260 , HOH A:521 , HOH A:522 , ASP B:260 , HOH B:519 , HOH B:520 , ASP C:260 , HOH C:501BINDING SITE FOR RESIDUE CA A 403
4AC4SOFTWAREGLU A:86 , GLU A:89 , GLU B:82 , LEU B:84 , GLU B:89BINDING SITE FOR RESIDUE CA B 401
5AC5SOFTWAREGLU C:82 , LEU C:84 , GLU C:86 , GLU C:89BINDING SITE FOR RESIDUE CA C 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IC5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IC5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IC5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IC5)

(-) Exons   (0, 0)

(no "Exon" information available for 4IC5)

(-) 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:210
                                                                                                                                                                                                                                                  
               SCOP domains d4ic5a_ A: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh..eeeeee....eeeeeee.....eeee.hhhhhhhhhh.......eeeee.....eeeee.eeeeeehhhheeeee.......................eeeeee.......eeeeeeeeee...............eee....hhhhh..eee.....eeeee.....eeeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ic5 A  82 EELEEEEERNVNLFQKTSPSVVYIEAIELEGTGSGFVWDKLGHIVTNYHVIAKLATDQFGLQRCKVSLVDAKGTRFSKEGKIVGLDPDNDLAVLKIETEGRELNPVVLGTSNDLRVGQSCFAIGNPYGYENTLTIGVVSGLGREIPSPNGKSISEAIQTDADINSGNAGGPLLDSYGHTIGVNTATFVNFAIPIDTVVRTVPYLIVYGTA 318
                                    91       101       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278      |298       308       318
                                                      110|                                                                                                                                                          285|                      
                                                       128                                                                                                                                                           296                      


Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains d4ic5b_ B: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh..eeeee......eeeeee.....eeee.hhhhhhhhhh.......eeeee.....eeeee.eeeeeehhhheeeee.......................eeeeee.......eeeeeeeeee...............eee....hhhhh..eee.....eeeee.....eeeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ic5 B  82 EELEEEEERNVNLFQKTSPSVVYIEAIELEGTGSGFVWDKLGHIVTNYHVIAKLATDQFGLQRCKVSLVDAKGTRFSKEGKIVGLDPDNDLAVLKIETEGRELNPVVLGTSNDLRVGQSCFAIGNPYGYENTLTIGVVSGLGREIPSPNGKSISEAIQTDADINSGNAGGPLLDSYGHTIGVNTATFVNFAIPIDTVVRTVPYLIVYGTA 318
                                    91       101       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278      |298       308       318
                                                      110|                                                                                                                                                          285|                      
                                                       128                                                                                                                                                           296                      


Chain C from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains d4ic5c_ C: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh..eeeee.....eeeeee.....eeeee...hhhhhhh.......eeeee.....eeeee.eeeeee....eeeee.......................eeeeee.......eeeeeeeeee...............eee...........eee.....eeeee.....eeeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ic5 C  82 EELEEEEERNVNLFQKTSPSVVYIEAIELGTGSGFVWDKLGHIVTNYHVIAKLATDQFGLQRCKVSLVDAKGTRFSKEGKIVGLDPDNDLAVLKIETEGRELNPVVLGTSNDLRVGQSCFAIGNPYGYENTLTIGVVSGLGREIPSPNGKSISEAIQTDADINSGNAGGPLLDSYGHTIGVNTATFVNFAIPIDTVVRTVPYLIVYGTA 318
                                    91       101       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279     ||299       309         
                                                      110|                                                                                                                                                         285|                      
                                                       129                                                                                                                                                          296
   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  (1, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IC5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IC5)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4ic5