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(-) Description

Title :  SNOW FLEA ANTIFREEZE PROTEIN QUASI-RACEMATE
 
Authors :  B. L. Pentelute, Kent S. B. H. , Z. P. Gates, V. Tereshko, A. A. Kossiakoff, J. Kurutz, J. Dashnau, J. M. Vaderkooi
Date :  17 Dec 07  (Deposition) - 23 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Quasi-Racemate, Sfafp, Mirror Image Proteins, Racemic Protein Crystallography, Antifreeze Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. L. Pentelute, Z. P. Gates, V. Tereshko, J. L. Dashnau, J. M. Vanderkooi, A. A. Kossiakoff, S. B. Kent
X-Ray Structure Of Snow Flea Antifreeze Protein Determined By Racemic Crystallization Of Synthetic Protein Enantiomers
J. Am. Chem. Soc. V. 130 9695 2008
PubMed-ID: 18598029  |  Reference-DOI: 10.1021/JA8013538
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 6.5 KDA GLYCINE-RICH ANTIFREEZE PROTEIN
    Chains: A, B
    Engineered: YES
    Other Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED AND IS NATURALLY FOUND IN HYPOGASTRURA HARVEYI.
    Synthetic: YES
 
Molecule 2 - 6.5 KDA GLYCINE-RICH ANTIFREEZE PROTEIN
    Chains: C, D
    Engineered: YES
    Other Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED AND IS NATURALLY FOUND IN HYPOGASTRURA HARVEYI.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (13, 91)

Asymmetric Unit (13, 91)
No.NameCountTypeFull Name
1DAL22Mod. Amino AcidD-ALANINE
2DAR2Mod. Amino AcidD-ARGININE
3DAS6Mod. Amino AcidD-ASPARTIC ACID
4DCY8Mod. Amino AcidD-CYSTEINE
5DHI4Mod. Amino AcidD-HISTIDINE
6DLY6Mod. Amino AcidD-LYSINE
7DPR12Mod. Amino AcidD-PROLINE
8DSG8Mod. Amino AcidD-ASPARAGINE
9DSN6Mod. Amino AcidD-SERINE
10DTH6Mod. Amino AcidD-THREONINE
11DVA8Mod. Amino AcidD-VALINE
12SYS2Mod. Amino Acid3-[(2-AMINO-2-OXOETHYL)SELANYL]-L-ALANINE
13UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (12, 45)
No.NameCountTypeFull Name
1DAL11Mod. Amino AcidD-ALANINE
2DAR1Mod. Amino AcidD-ARGININE
3DAS3Mod. Amino AcidD-ASPARTIC ACID
4DCY4Mod. Amino AcidD-CYSTEINE
5DHI2Mod. Amino AcidD-HISTIDINE
6DLY3Mod. Amino AcidD-LYSINE
7DPR6Mod. Amino AcidD-PROLINE
8DSG4Mod. Amino AcidD-ASPARAGINE
9DSN3Mod. Amino AcidD-SERINE
10DTH3Mod. Amino AcidD-THREONINE
11DVA4Mod. Amino AcidD-VALINE
12SYS1Mod. Amino Acid3-[(2-AMINO-2-OXOETHYL)SELANYL]-L-ALANINE
13UNL-1Ligand/IonUNKNOWN LIGAND
Biological Unit 2 (13, 46)
No.NameCountTypeFull Name
1DAL11Mod. Amino AcidD-ALANINE
2DAR1Mod. Amino AcidD-ARGININE
3DAS3Mod. Amino AcidD-ASPARTIC ACID
4DCY4Mod. Amino AcidD-CYSTEINE
5DHI2Mod. Amino AcidD-HISTIDINE
6DLY3Mod. Amino AcidD-LYSINE
7DPR6Mod. Amino AcidD-PROLINE
8DSG4Mod. Amino AcidD-ASPARAGINE
9DSN3Mod. Amino AcidD-SERINE
10DTH3Mod. Amino AcidD-THREONINE
11DVA4Mod. Amino AcidD-VALINE
12SYS1Mod. Amino Acid3-[(2-AMINO-2-OXOETHYL)SELANYL]-L-ALANINE
13UNL1Ligand/IonUNKNOWN LIGAND

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:12 , CYS A:13 , PRO A:14 , THR A:16 , HOH A:1065 , HOH A:1110 , GLY B:56 , HOH B:2072 , GLY D:25 , HOH D:4033BINDING SITE FOR RESIDUE UNL B 5014

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:1 -A:28
2A:13 -A:43
3B:1 -B:28
4B:13 -B:43

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Cys A:13 -Pro A:14
2Thr A:70 -Pro A:71
3Cys B:13 -Pro B:14
4Thr B:70 -Pro B:71

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BOG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BOG)

(-) Exons   (0, 0)

(no "Exon" information available for 3BOG)

(-) 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:81
 aligned with Q38PT6_9HEXA | Q38PT6 from UniProtKB/TrEMBL  Length:103

    Alignment length:81
                                    32        42        52        62        72        82        92       102 
         Q38PT6_9HEXA    23 CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP 103
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................................................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 3bog A   1 CKGADGAHGVcGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP  81
                                    10|       20        30        40        50        60        70        80 
                                     11-SYS                                                                  


Chain B from PDB  Type:PROTEIN  Length:81
 aligned with Q38PT6_9HEXA | Q38PT6 from UniProtKB/TrEMBL  Length:103

    Alignment length:81
                                    32        42        52        62        72        82        92       102 
         Q38PT6_9HEXA    23 CKGADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP 103
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................................................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 3bog B   1 CKGADGAHGVcGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP  81
                                    10|       20        30        40        50        60        70        80 
                                     11-SYS                                                                  


Chain C from PDB  Type:PROTEIN  Length:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................................................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 3bog C   1 xxGxxGxxGxxGxxGxxGxxGxxGGxGxxGGxGGxGGxGxxGxxGGxGGxGGxxGGxGxGGxGGxGGxGxxxGxxGxxGxx  81
                            || || ||10| || || 20 ||  | |30 |  |  |40| ||  | 50  ||  | 60 |  |  |70|| || ||80|
                            1-DCY || || 14-DPR|| ||  | 29-DAS |  | || ||  |  |  54-DSN|  |  |  | ||| 75-DAS||
                             2-DLY|| || | 16-DTH ||  | |  32-DHI | || ||  |  |  |  57-DTH|  |  | ||| | 77-DAL
                               4-DAL || |  17-DAL||  | |     35-DSG|| ||  |  |  |    59-DVA |  | ||| |  78-DPR
                                5-DAS|| |    19-DAL  | |        38-DSG||  |  |  |       62-DAR | ||| |    80-DAL
                                  7-DAL |     20-DAL | |          40-DSG  |  |  |          65-DLY||| |     81-DPR
                                   8-DHI|       22-DSN |           41-DPR |  |  |             68-DSN |       
                                    10-DVA       23-DVA|             43-DCY  |  |               70-DTH       
                                     11-DSG         26-DPR            44-DAL |  |                71-DPR      
                                       13-DCY         28-DCY             47-DVA |                 72-DLY     


Chain D from PDB  Type:PROTEIN  Length:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................................................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 3bog D   1 xxGxxGxxGxxGxxGxxGxxGxxGGxGxxGGxGGxGGxGxxGxxGGxGGxGGxxGGxGxGGxGGxGGxGxxxGxxGxxGxx  81
                            || || ||10| || || 20 ||  | |30 |  |  |40| ||  | 50  ||  | 60 |  |  |70|| || ||80|
                            || || || || 14-DPR|| ||  | 29-DAS |  | || ||  |  |  54-DSN|  |  |  | ||| 75-DAS||
                            1-DCY || || | 16-DTH ||  | |  32-DHI | || ||  |  |  |  57-DTH|  |  | ||| | 77-DAL
                             2-DLY|| || |  17-DAL||  | |     35-DSG|| ||  |  |  |    59-DVA |  | ||| |  78-DPR
                               4-DAL || |    19-DAL  | |        38-DSG||  |  |  |       62-DAR | ||| |    80-DAL
                                5-DAS|| |     20-DAL | |          40-DSG  |  |  |          65-DLY||| |     81-DPR
                                  7-DAL |       22-DSN |           41-DPR |  |  |             68-DSN |       
                                   8-DHI|        23-DVA|             43-DCY  |  |               70-DTH       
                                    10-DVA          26-DPR            44-DAL |  |                71-DPR      
                                     11-DSG           28-DCY             47-DVA |                 72-DLY
   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 3BOG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3BOG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BOG)

(-) Gene Ontology  (0, 0)

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2pne 3boi