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(-) Description

Title :  YEAST DELTA-COP-I MU-HOMOLOGY DOMAIN
 
Authors :  R. J. Suckling, P. R. Evans, D. J. Owen
Date :  14 Oct 15  (Deposition) - 11 Nov 15  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  G  (1x)
Biol. Unit 8:  H  (1x)
Keywords :  Structural Protein, Cop-I, Vesicle Coat Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. J. Suckling, P. P. Poon, S. M. Travis, I. V. Majoul, F. M. Hughson, P. R. Evans, R. Duden, D. J. Owen
Structural Basis For The Binding Of Tryptophan-Based Motifs By Delta-Cop.
Proc. Natl. Acad. Sci. Usa V. 112 14242 2015
PubMed-ID: 26578768  |  Reference-DOI: 10.1073/PNAS.1506186112

(-) Compounds

Molecule 1 - COATOMER SUBUNIT DELTA
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: MU-HOMOLOGY DOMAIN, RESIDUES 282-546
    Gene: RET2, H834_YJM1574F00127
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: DELTA-COAT PROTEIN, DELTA-COP, RET2P

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A       
Biological Unit 2 (1x):  B      
Biological Unit 3 (1x):   C     
Biological Unit 4 (1x):    D    
Biological Unit 5 (1x):     E   
Biological Unit 6 (1x):      F  
Biological Unit 7 (1x):       G 
Biological Unit 8 (1x):        H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/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
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 7 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 8 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:518 , HOH A:2055 , HOH A:2056 , HOH A:2058 , ASP B:525BINDING SITE FOR RESIDUE CA A 601
2AC2SOFTWAREASP B:444 , ILE B:445 , HOH B:2040 , HOH B:2041 , ASP C:324 , ASP C:326BINDING SITE FOR RESIDUE CA B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FK0)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Tyr A:494 -Pro A:495
2Tyr B:494 -Pro B:495
3Tyr C:494 -Pro C:495
4Tyr D:494 -Pro D:495
5Tyr E:494 -Pro E:495
6Tyr F:494 -Pro F:495
7Tyr G:494 -Pro G:495
8Tyr H:494 -Pro H:495

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FK0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FK0)

(-) Exons   (0, 0)

(no "Exon" information available for 5FK0)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeee.....eeeeeeeeeeeeee.......eeeee.......hhhhh.ee....hhhhhhhhhee...............eeeeeeeeee.........eeeeeeeee.....eeeeeeeeee.....eeeeeeee........ee..........eeee......eeeeeeee....eeeeeeeee..hhhhhh.eeee.eeee............eeeeee......ee..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fk0 A 284 DVPENNGILISIKEVINAEFSRDGTIHSSELKGVLELRINDHDLSHSNLKLADSIDVRDKSFQFKTHPNIDKQSFLSTKLISLRDKSKAFPANDQSLGVLRWRKVAPAEDDSLIPLTLTTWVSPSESQQGFDVIIEYESVLETELADVIFTIPVFPQEPVDINTESSTCSDAEVVNMDQEMGTSIKISKIAANDAGALAFTIEAPYEDALYPMTVSFQESTRDKLAKSFTGMAIQSVVMANDHDQELPYDVITSLKSDEYLVQ 546
                                   293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543   


Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeee.....eeeeeeeeeeeeee.......eeeee.......hhhhh.ee....hhhhhhhhhee...............eeeeeeeeee.........eeeeeeeee.....eeeeeeeeee.....eeeeeeee........ee.........eeeee......eeeeeeee....eeeeeeeee..hhhhhh.eeee.eeee............eeeeee..........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fk0 B 284 DVPENNGILISIKEVINAEFSRDGTIHSSELKGVLELRINDHDLSHSNLKLADSIDVRDKSFQFKTHPNIDKQSFLSTKLISLRDKSKAFPANDQSLGVLRWRKVAPAEDDSLIPLTLTTWVSPSESQQGFDVIIEYESVLETELADVIFTIPVFPQEPVDINTESSTCSDAEVVNMDQEMGTSIKISKIAANDAGALAFTIEAPYEDALYPMTVSFQESTRDKLAKSFTGMAIQSVVMANDHDQELPYDVITSLKSDEYLVQ 546
                                   293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543   


Chain C from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeee.....eeeeeeeeeeeeee.......eeeee.......hhhhh.ee....hhhhhhhhhee...............eeeeeeeeee.........eeeeeeeee.....eeeeeeeeee.....eeeeeeee........ee..........eeee......eeeeeeee....eeeeeeeee..hhhhhh.eeee.eeee............eeeeee..........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fk0 C 284 DVPENNGILISIKEVINAEFSRDGTIHSSELKGVLELRINDHDLSHSNLKLADSIDVRDKSFQFKTHPNIDKQSFLSTKLISLRDKSKAFPANDQSLGVLRWRKVAPAEDDSLIPLTLTTWVSPSESQQGFDVIIEYESVLETELADVIFTIPVFPQEPVDINTESSTCSDAEVVNMDQEMGTSIKISKIAANDAGALAFTIEAPYEDALYPMTVSFQESTRDKLAKSFTGMAIQSVVMANDHDQELPYDVITSLKSDEYLVQ 546
                                   293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543   


Chain D from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeee.....eeeeeeeeeeeeee.hhhhhheeeee.......hhhhh.ee....hhhhhhhhhee...............eeeeeeeeee.........eeeeeeeee.....eeeeeeeeee.....eeeeeeee........ee..........eeee......eeeeeeee....eeeeeeeee..hhhhhh.eeee...ee............eeeeee......ee..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fk0 D 284 DVPENNGILISIKEVINAEFSRDGTIHSSELKGVLELRINDHDLSHSNLKLADSIDVRDKSFQFKTHPNIDKQSFLSTKLISLRDKSKAFPANDQSLGVLRWRKVAPAEDDSLIPLTLTTWVSPSESQQGFDVIIEYESVLETELADVIFTIPVFPQEPVDINTESSTCSDAEVVNMDQEMGTSIKISKIAANDAGALAFTIEAPYEDALYPMTVSFQESTRDKLAKSFTGMAIQSVVMANDHDQELPYDVITSLKSDEYLVQ 546
                                   293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543   


Chain E from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeee.....eeeeeeeeeeeeee.......eeeee.......hhhhh.ee....hhhhhhhhhee...............eeeeeeeeee.........eeeeeeeee.....eeeeeeeeee.....eeeeeeee........ee..........eeee......eeeeeeee....eeeeeeeee..hhhhhh.eeee.eeee............eeeeee..........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fk0 E 284 DVPENNGILISIKEVINAEFSRDGTIHSSELKGVLELRINDHDLSHSNLKLADSIDVRDKSFQFKTHPNIDKQSFLSTKLISLRDKSKAFPANDQSLGVLRWRKVAPAEDDSLIPLTLTTWVSPSESQQGFDVIIEYESVLETELADVIFTIPVFPQEPVDINTESSTCSDAEVVNMDQEMGTSIKISKIAANDAGALAFTIEAPYEDALYPMTVSFQESTRDKLAKSFTGMAIQSVVMANDHDQELPYDVITSLKSDEYLVQ 546
                                   293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543   


Chain F from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeee.....eeeeeeeeeeeeee.hhhhhheeeee.......hhhhh.ee....hhhhhhhhhee...............eeeeeeeeee.........eeeeeeeee.....eeeeeeeeee.....eeeeeeee........ee..........eeee......eeeeeeee....eeeeeeeee..hhhhhh.eeee.eeee............eeeeee..........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fk0 F 284 DVPENNGILISIKEVINAEFSRDGTIHSSELKGVLELRINDHDLSHSNLKLADSIDVRDKSFQFKTHPNIDKQSFLSTKLISLRDKSKAFPANDQSLGVLRWRKVAPAEDDSLIPLTLTTWVSPSESQQGFDVIIEYESVLETELADVIFTIPVFPQEPVDINTESSTCSDAEVVNMDQEMGTSIKISKIAANDAGALAFTIEAPYEDALYPMTVSFQESTRDKLAKSFTGMAIQSVVMANDHDQELPYDVITSLKSDEYLVQ 546
                                   293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543   


Chain G from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeee.....eeeeeeeeeeeeee.......eeeee.......hhhhh.ee....hhhhhhhhhee...............eeeeeeeeee.........eeeeeeeee.....eeeeeeeeee.....eeeeeeee........ee..........eeee......eeeeeeee....eeeeeeeee..hhhhhh.eeee.eeee............eeeeee..........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fk0 G 284 DVPENNGILISIKEVINAEFSRDGTIHSSELKGVLELRINDHDLSHSNLKLADSIDVRDKSFQFKTHPNIDKQSFLSTKLISLRDKSKAFPANDQSLGVLRWRKVAPAEDDSLIPLTLTTWVSPSESQQGFDVIIEYESVLETELADVIFTIPVFPQEPVDINTESSTCSDAEVVNMDQEMGTSIKISKIAANDAGALAFTIEAPYEDALYPMTVSFQESTRDKLAKSFTGMAIQSVVMANDHDQELPYDVITSLKSDEYLVQ 546
                                   293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543   


Chain H from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeee.....eeeeeeeeeeeeee.......eeeee.......hhhhh.ee....hhhhhhhhhee...............eeeeeeeeee.........eeeeeeeee.....eeeeeeeeee.....eeeeeeee........ee..........eeee......eeeeeeee....eeeeeeeee..hhhhhh.eeee...ee............eeeeee..........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fk0 H 284 DVPENNGILISIKEVINAEFSRDGTIHSSELKGVLELRINDHDLSHSNLKLADSIDVRDKSFQFKTHPNIDKQSFLSTKLISLRDKSKAFPANDQSLGVLRWRKVAPAEDDSLIPLTLTTWVSPSESQQGFDVIIEYESVLETELADVIFTIPVFPQEPVDINTESSTCSDAEVVNMDQEMGTSIKISKIAANDAGALAFTIEAPYEDALYPMTVSFQESTRDKLAKSFTGMAIQSVVMANDHDQELPYDVITSLKSDEYLVQ 546
                                   293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543
   Legend:   → Mismatch (orange background)
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    → 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 5FK0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FK0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FK0)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        COPD_YEAST | P43621: 5fjw 5fjx 5fjz

(-) Related Entries Specified in the PDB File

5fjw YEAST DELTA-COP-I MU-HOMOLOGY DOMAIN COMPLEXED WITH DSL1 WXWXSEM PEPTIDE
5fjx YEAST DELTA-COP-I MU-HOMOLOGY DOMAIN COMPLEXED WITH GCS1 WXXF PEPTIDE
5fjz YEAST DELTA-COP-I MU-HOMOLOGY DOMAIN COMPLEXED WITH DSL1 WXWXV PEPTIDE