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(-) Description

Title :  QUASI-RACEMIC SNAKIN-1 IN P1 AFTER RADIATION DAMAGE
 
Authors :  H. Yeung, C. J. Squire, Y. Yosaatmadja, S. Panjikar, E. N. Baker, P. W. R. M. A. Brimble
Date :  09 Oct 15  (Deposition) - 18 May 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
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 :  Gasa/Snakin, Cysteine-Rich Antimicrobial Peptide, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yeung, C. J. Squire, Y. Yosaatmadja, S. Panjikar, G. Lopez, A. Molina, E. N. Baker, P. W. Harris, M. A. Brimble
Radiation Damage And Racemic Protein Crystallography Reveal The Unique Structure Of The Gasa/Snakin Protein Superfamily
Angew. Chem. Int. Ed. Engl. V. 55 7930 2016
PubMed-ID: 27145301  |  Reference-DOI: 10.1002/ANIE.201602719

(-) Compounds

Molecule 1 - SNAKIN-1
    Chains: A, C
    Engineered: YES
    Mutation: YES
    Organism Common: POTATO
    Organism Scientific: SOLANUM TUBEROSUM
    Organism Taxid: 4113
    Other Details: POTATO L- SNAKIN-1 CONTAINING SINGLE SUBSTITUTION OF P-IODOPHENYLALANINE FOR 25TYR
    Synonym: UNCHARACTERIZED PROTEIN
    Synthetic: YES
 
Molecule 2 - D- SNAKIN-1
    Chains: B, D
    Engineered: YES
    Organism Common: POTATO
    Organism Scientific: SOLANUM TUBEROSUM
    Organism Taxid: 4113
    Other Details: D- ENANTIOMER OF POTATO SNAKIN-1
    Synthetic: YES

 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  (19, 123)

Asymmetric Unit (19, 123)
No.NameCountTypeFull Name
1DAL4Mod. Amino AcidD-ALANINE
2DAR6Mod. Amino AcidD-ARGININE
3DAS6Mod. Amino AcidD-ASPARTIC ACID
4DCY24Mod. Amino AcidD-CYSTEINE
5DGL6Mod. Amino AcidD-GLUTAMIC ACID
6DHI2Mod. Amino AcidD-HISTIDINE
7DIL2Mod. Amino AcidD-ISOLEUCINE
8DLE6Mod. Amino AcidD-LEUCINE
9DLY22Mod. Amino AcidD-LYSINE
10DPN2Mod. Amino AcidD-PHENYLALANINE
11DPR6Mod. Amino AcidD-PROLINE
12DSG6Mod. Amino AcidD-ASPARAGINE
13DSN12Mod. Amino AcidD-SERINE
14DTH2Mod. Amino AcidD-THREONINE
15DTY6Mod. Amino AcidD-TYROSINE
16DVA2Mod. Amino AcidD-VALINE
17EDO3Ligand/Ion1,2-ETHANEDIOL
18FMT4Ligand/IonFORMIC ACID
19PHI2Mod. Amino AcidIODO-PHENYLALANINE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1DAL-1Mod. Amino AcidD-ALANINE
2DAR-1Mod. Amino AcidD-ARGININE
3DAS-1Mod. Amino AcidD-ASPARTIC ACID
4DCY-1Mod. Amino AcidD-CYSTEINE
5DGL-1Mod. Amino AcidD-GLUTAMIC ACID
6DHI-1Mod. Amino AcidD-HISTIDINE
7DIL-1Mod. Amino AcidD-ISOLEUCINE
8DLE-1Mod. Amino AcidD-LEUCINE
9DLY-1Mod. Amino AcidD-LYSINE
10DPN-1Mod. Amino AcidD-PHENYLALANINE
11DPR-1Mod. Amino AcidD-PROLINE
12DSG-1Mod. Amino AcidD-ASPARAGINE
13DSN-1Mod. Amino AcidD-SERINE
14DTH-1Mod. Amino AcidD-THREONINE
15DTY-1Mod. Amino AcidD-TYROSINE
16DVA-1Mod. Amino AcidD-VALINE
17EDO2Ligand/Ion1,2-ETHANEDIOL
18FMT1Ligand/IonFORMIC ACID
19PHI1Mod. Amino AcidIODO-PHENYLALANINE
Biological Unit 2 (17, 58)
No.NameCountTypeFull Name
1DAL2Mod. Amino AcidD-ALANINE
2DAR3Mod. Amino AcidD-ARGININE
3DAS3Mod. Amino AcidD-ASPARTIC ACID
4DCY12Mod. Amino AcidD-CYSTEINE
5DGL3Mod. Amino AcidD-GLUTAMIC ACID
6DHI1Mod. Amino AcidD-HISTIDINE
7DIL1Mod. Amino AcidD-ISOLEUCINE
8DLE3Mod. Amino AcidD-LEUCINE
9DLY11Mod. Amino AcidD-LYSINE
10DPN1Mod. Amino AcidD-PHENYLALANINE
11DPR3Mod. Amino AcidD-PROLINE
12DSG3Mod. Amino AcidD-ASPARAGINE
13DSN6Mod. Amino AcidD-SERINE
14DTH1Mod. Amino AcidD-THREONINE
15DTY3Mod. Amino AcidD-TYROSINE
16DVA1Mod. Amino AcidD-VALINE
17EDO-1Ligand/Ion1,2-ETHANEDIOL
18FMT1Ligand/IonFORMIC ACID
19PHI-1Mod. Amino AcidIODO-PHENYLALANINE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1DAL-1Mod. Amino AcidD-ALANINE
2DAR-1Mod. Amino AcidD-ARGININE
3DAS-1Mod. Amino AcidD-ASPARTIC ACID
4DCY-1Mod. Amino AcidD-CYSTEINE
5DGL-1Mod. Amino AcidD-GLUTAMIC ACID
6DHI-1Mod. Amino AcidD-HISTIDINE
7DIL-1Mod. Amino AcidD-ISOLEUCINE
8DLE-1Mod. Amino AcidD-LEUCINE
9DLY-1Mod. Amino AcidD-LYSINE
10DPN-1Mod. Amino AcidD-PHENYLALANINE
11DPR-1Mod. Amino AcidD-PROLINE
12DSG-1Mod. Amino AcidD-ASPARAGINE
13DSN-1Mod. Amino AcidD-SERINE
14DTH-1Mod. Amino AcidD-THREONINE
15DTY-1Mod. Amino AcidD-TYROSINE
16DVA-1Mod. Amino AcidD-VALINE
17EDO-1Ligand/Ion1,2-ETHANEDIOL
18FMT1Ligand/IonFORMIC ACID
19PHI1Mod. Amino AcidIODO-PHENYLALANINE
Biological Unit 4 (18, 59)
No.NameCountTypeFull Name
1DAL2Mod. Amino AcidD-ALANINE
2DAR3Mod. Amino AcidD-ARGININE
3DAS3Mod. Amino AcidD-ASPARTIC ACID
4DCY12Mod. Amino AcidD-CYSTEINE
5DGL3Mod. Amino AcidD-GLUTAMIC ACID
6DHI1Mod. Amino AcidD-HISTIDINE
7DIL1Mod. Amino AcidD-ISOLEUCINE
8DLE3Mod. Amino AcidD-LEUCINE
9DLY11Mod. Amino AcidD-LYSINE
10DPN1Mod. Amino AcidD-PHENYLALANINE
11DPR3Mod. Amino AcidD-PROLINE
12DSG3Mod. Amino AcidD-ASPARAGINE
13DSN6Mod. Amino AcidD-SERINE
14DTH1Mod. Amino AcidD-THREONINE
15DTY3Mod. Amino AcidD-TYROSINE
16DVA1Mod. Amino AcidD-VALINE
17EDO1Ligand/Ion1,2-ETHANEDIOL
18FMT1Ligand/IonFORMIC ACID
19PHI-1Mod. Amino AcidIODO-PHENYLALANINE

(-) Sites  (0, 0)

(no "Site" information available for 5E5T)

(-) SS Bonds  (24, 24)

Asymmetric Unit
No.Residues
1A:5 -A:30
2A:9 -A:26
3A:13 -A:22
4A:29 -A:62
5A:33 -A:49
6A:35 -A:47
7B:5 -B:30
8B:9 -B:26
9B:13 -B:22
10B:29 -B:62
11B:33 -B:49
12B:35 -B:47
13C:5 -C:30
14C:9 -C:26
15C:13 -C:22
16C:29 -C:62
17C:33 -C:49
18C:35 -C:47
19D:5 -D:30
20D:9 -D:26
21D:13 -D:22
22D:29 -D:62
23D:33 -D:49
24D:35 -D:47

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly D:1 -Dsn D:2

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E5T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E5T)

(-) Exons   (0, 0)

(no "Exon" information available for 5E5T)

(-) 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:63
                                                                                              
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh....hhhhhhhhhhhhhhhhh........hhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  5e5t A  1 GSNFCDSKCKLRCSKAGLADRCLKxCGICCEECKCVPSGTYGNKHECPCYRDKKNSKGKSKCP 63
                                    10        20    |   30        40        50        60   
                                                   25-PHI                                  


Chain B from PDB  Type:PROTEIN  Length:63
                                                                                              
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh....hhhhhhhhhhhhhhhhh........hhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  5e5t B  1 GxxxxxxxxxxxxxxxGxxxxxxxxxGxxxxxxxxxxxGxxGxxxxxxxxxxxxxxxGxxxxx 63
                             |||||||10|||||| |20|||||| |30||||||||40| ||||||50||||||| 60|||
                             2-DSN|||11-DLE| ||21-DAR| ||31-DGL||| 41-DTY||||51-DAR|| |61-DLY
                              3-DSG|||12-DAR |||22-DCY |||32-DGL|| | 43-DSG|||52-DAS| ||62-DCY
                               4-DPN|| 13-DCY||| 23-DLE||| 33-DCY| |  44-DLY|| 53-DLY || 63-DPR
                                5-DCY|  14-DSN||  24-DLY||  34-DLY |   45-DHI|  54-DLY||   
                                 6-DAS   15-DLY|   25-DTY|   35-DCY|    46-DGL   55-DSG|   
                                  7-DSN   16-DAL    26-DCY    36-DVA     47-DCY   56-DSN   
                                   8-DLY    18-DLE    28-DIL   37-DPR     48-DPR   57-DLY  
                                    9-DCY    19-DAL    29-DCY   38-DSN     49-DCY    59-DLY
                                    10-DLY    20-DAS    30-DCY    40-DTH    50-DTY    60-DSN


Chain C from PDB  Type:PROTEIN  Length:62
                                                                                             
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh....hhhhhhhhhhhhhhhhh........hhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  5e5t C  2 SNFCDSKCKLRCSKAGLADRCLKxCGICCEECKCVPSGTYGNKHECPCYRDKKNSKGKSKCP 63
                                    11        21   |    31        41        51        61  
                                                  25-PHI                                  


Chain D from PDB  Type:PROTEIN  Length:63
                                                                                              
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh....hhhhhhhhhhhhhhhhh........hhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  5e5t D  1 GxxxxxxxxxxxxxxxGxxxxxxxxxGxxxxxxxxxxxGxxGxxxxxxxxxxxxxxxGxxxxx 63
                             |||||||10|||||| |20|||||| |30||||||||40| ||||||50||||||| 60|||
                             2-DSN|||11-DLE| ||21-DAR| ||31-DGL||| 41-DTY||||51-DAR|| |61-DLY
                              3-DSG|||12-DAR |||22-DCY |||32-DGL|| | 43-DSG|||52-DAS| ||62-DCY
                               4-DPN|| 13-DCY||| 23-DLE||| 33-DCY| |  44-DLY|| 53-DLY || 63-DPR
                                5-DCY|  14-DSN||  24-DLY||  34-DLY |   45-DHI|  54-DLY||   
                                 6-DAS   15-DLY|   25-DTY|   35-DCY|    46-DGL   55-DSG|   
                                  7-DSN   16-DAL    26-DCY    36-DVA     47-DCY   56-DSN   
                                   8-DLY    18-DLE    28-DIL   37-DPR     48-DPR   57-DLY  
                                    9-DCY    19-DAL    29-DCY   38-DSN     49-DCY    59-DLY
                                    10-DLY    20-DAS    30-DCY    40-DTH    50-DTY    60-DSN
   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 5E5T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E5T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E5T)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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  5e5t
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  SNAK1_SOLTU | Q948Z4
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 Related Entries

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

UniProtKB/Swiss-Prot
        B6E1W5_SOLTU | B6E1W5: 5e5q 5e5y
        SNAK1_SOLTU | Q948Z4: 5e5q 5e5y

(-) Related Entries Specified in the PDB File

5e5q 5E5Q CONTAINS THE THE CRYSTAL STRUCTURE OF THE TRUE RACEMIC PROTEIN.
5e5y