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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDECHETOXIN FROM PSEUDECHIS AUSTRALIS
 
Authors :  N. Suzuki, Y. Yamazaki, Z. Fujimoto, T. Morita, H. Mizuno
Date :  25 Jan 06  (Deposition) - 30 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
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 :  Crisp, Snake Venom, Cng Channel, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Suzuki, Y. Yamazaki, R. L. Brown, Z. Fujimoto, T. Morita, H. Mizuno
Structures Of Pseudechetoxin And Pseudecin, Two Snake-Venom Cysteine-Rich Secretory Proteins That Target Cyclic Nucleotide-Gated Ion Channels: Implications For Movement Of The C-Terminal Cysteine-Rich Domain
Acta Crystallogr. , Sect. D V. 64 1034 2008
PubMed-ID: 18931410  |  Reference-DOI: 10.1107/S0907444908023512

(-) Compounds

Molecule 1 - PSEUDECHETOXIN
    ChainsA, B, C, D
    Organism CommonMULGA SNAKE
    Organism ScientificPSEUDECHIS AUSTRALIS
    Organism Taxid8670
    SynonymPSTX, CHANNEL BLOCKER
    TissueVENOM

 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  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1FMT6Ligand/IonFORMIC ACID
2GOL1Ligand/IonGLYCEROL
3NA4Ligand/IonSODIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL-1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2GOL-1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2GOL-1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:73 , GLN A:74 , SER A:128 , HOH A:528 , HOH A:742 , HOH B:418BINDING SITE FOR RESIDUE NA A 301
02AC2SOFTWARESER B:73 , GLN B:74 , SER B:128 , FMT B:309 , HOH B:585BINDING SITE FOR RESIDUE NA B 302
03AC3SOFTWARESER C:73 , GLN C:74 , SER C:128 , HOH C:530BINDING SITE FOR RESIDUE NA C 303
04AC4SOFTWAREHOH C:496 , SER D:73 , GLN D:74 , SER D:128 , HOH D:532 , HOH D:597BINDING SITE FOR RESIDUE NA D 304
05AC5SOFTWARELYS A:62 , VAL B:21 , LYS B:22 , TYR B:86 , ILE B:89 , TYR B:108 , HOH B:774BINDING SITE FOR RESIDUE FMT B 305
06AC6SOFTWAREVAL A:21 , LYS A:22 , TYR A:86 , ILE A:89 , TYR A:108BINDING SITE FOR RESIDUE FMT A 306
07AC7SOFTWARESER B:184 , LYS B:187 , SER C:103 , VAL C:104 , ILE C:105 , GLY C:106BINDING SITE FOR RESIDUE FMT C 307
08AC8SOFTWARESER A:184 , LYS A:187 , SER D:103 , VAL D:104 , ILE D:105 , GLY D:106BINDING SITE FOR RESIDUE FMT D 308
09AC9SOFTWAREGLU A:88 , VAL A:104 , GLN B:74 , SER B:128 , TYR B:131 , NA B:302 , HOH B:718BINDING SITE FOR RESIDUE FMT B 309
10BC1SOFTWAREALA A:51 , HIS A:52 , SER D:189 , THR D:193BINDING SITE FOR RESIDUE FMT A 310
11BC2SOFTWARETRP A:78 , ALA A:122 , SER A:123BINDING SITE FOR RESIDUE GOL A 311

(-) SS Bonds  (32, 32)

Asymmetric Unit
No.Residues
1A:48 -A:126
2A:65 -A:138
3A:121 -A:135
4A:157 -A:164
5A:160 -A:169
6A:173 -A:206
7A:182 -A:200
8A:191 -A:204
9B:48 -B:126
10B:65 -B:138
11B:121 -B:135
12B:157 -B:164
13B:160 -B:169
14B:173 -B:206
15B:182 -B:200
16B:191 -B:204
17C:48 -C:126
18C:65 -C:138
19C:121 -C:135
20C:157 -C:164
21C:160 -C:169
22C:173 -C:206
23C:182 -C:200
24C:191 -C:204
25D:48 -D:126
26D:65 -D:138
27D:121 -D:135
28D:157 -D:164
29D:160 -D:169
30D:173 -D:206
31D:182 -D:200
32D:191 -D:204

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Lys A:22 -Pro A:23
2Lys A:99 -Pro A:100
3Cys A:138 -Pro A:139
4Lys B:22 -Pro B:23
5Lys B:99 -Pro B:100
6Cys B:138 -Pro B:139
7Lys C:22 -Pro C:23
8Lys C:99 -Pro C:100
9Cys C:138 -Pro C:139
10Lys D:22 -Pro D:23
11Lys D:99 -Pro D:100
12Cys D:138 -Pro D:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DDA)

(-) PROSITE Motifs  (3, 12)

Asymmetric Unit (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRISP_1PS01009 CRISP family signature 1.CRVP_PSEAU133-143
 
 
 
  4A:106-116
B:106-116
C:106-116
D:106-116
2CRISP_2PS01010 CRISP family signature 2.CRVP_PSEAU159-170
 
 
 
  4A:132-143
B:132-143
C:132-143
D:132-143
3SHKTPS51670 ShKT domain profile.CRVP_PSEAU200-233
 
 
 
  4A:173-206
B:173-206
C:173-206
D:173-206
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRISP_1PS01009 CRISP family signature 1.CRVP_PSEAU133-143
 
 
 
  1A:106-116
-
-
-
2CRISP_2PS01010 CRISP family signature 2.CRVP_PSEAU159-170
 
 
 
  1A:132-143
-
-
-
3SHKTPS51670 ShKT domain profile.CRVP_PSEAU200-233
 
 
 
  1A:173-206
-
-
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRISP_1PS01009 CRISP family signature 1.CRVP_PSEAU133-143
 
 
 
  1-
B:106-116
-
-
2CRISP_2PS01010 CRISP family signature 2.CRVP_PSEAU159-170
 
 
 
  1-
B:132-143
-
-
3SHKTPS51670 ShKT domain profile.CRVP_PSEAU200-233
 
 
 
  1-
B:173-206
-
-
Biological Unit 3 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRISP_1PS01009 CRISP family signature 1.CRVP_PSEAU133-143
 
 
 
  1-
-
C:106-116
-
2CRISP_2PS01010 CRISP family signature 2.CRVP_PSEAU159-170
 
 
 
  1-
-
C:132-143
-
3SHKTPS51670 ShKT domain profile.CRVP_PSEAU200-233
 
 
 
  1-
-
C:173-206
-
Biological Unit 4 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRISP_1PS01009 CRISP family signature 1.CRVP_PSEAU133-143
 
 
 
  1-
-
-
D:106-116
2CRISP_2PS01010 CRISP family signature 2.CRVP_PSEAU159-170
 
 
 
  1-
-
-
D:132-143
3SHKTPS51670 ShKT domain profile.CRVP_PSEAU200-233
 
 
 
  1-
-
-
D:173-206

(-) Exons   (0, 0)

(no "Exon" information available for 2DDA)

(-) 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:208
 aligned with CRVP_PSEAU | Q8AVA4 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:208
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
           CRVP_PSEAU    31 KNYQKEIVDKHNALRRSVKPTARNMLQMKWNSRAAQNAKRWANRCTFAHSPPNKRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSYLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNKLCTNPCKRNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 238
               SCOP domains d2ddaa1 A:4-154 automated matches                                                                                                                      d2ddaa2 A:155-211 automated matches                       SCOP domains
               CATH domains 2ddaA01 A:4-170 Pathogenesis-related Protein p14a                                                                                                                      ----------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...........eehhhhhhhhhhhhh.......hhhh.ee..ee.eeeeeee....hhhhhhhhhhhhhh.ee...ee......hhhhhhhh.....eeeeeeeeee..eeeeeeeee.........................ee..ee...........hhhhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------CRISP_1    ---------------CRISP_2     -----------------------------SHKT  PDB: A:173-206              ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dda A   4 KNYQKEIVDKHNALRRSVKPTARNMLQMKWNSRAAQNAKRWANRCTFAHSPPNKRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSYLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNKLCTNPCKRNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 211
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        

Chain B from PDB  Type:PROTEIN  Length:208
 aligned with CRVP_PSEAU | Q8AVA4 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:208
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
           CRVP_PSEAU    31 KNYQKEIVDKHNALRRSVKPTARNMLQMKWNSRAAQNAKRWANRCTFAHSPPNKRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSYLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNKLCTNPCKRNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 238
               SCOP domains d2ddab1 B:4-154 automated matches                                                                                                                      d2ddab2 B:155-211 automated matches                       SCOP domains
               CATH domains 2ddaB01 B:4-170 Pathogenesis-related Protein p14a                                                                                                                      ----------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh............eehhhhhhhhhhhhhh......hhhh.ee..ee.eeeeeee....hhhhhhhhhhhhhh.ee...ee......hhhhhhhh.....eeeeeeeeee..eeeeeeeee.........................ee..ee...........hhhhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------CRISP_1    ---------------CRISP_2     -----------------------------SHKT  PDB: B:173-206              ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dda B   4 KNYQKEIVDKHNALRRSVKPTARNMLQMKWNSRAAQNAKRWANRCTFAHSPPNKRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSYLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNKLCTNPCKRNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 211
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        

Chain C from PDB  Type:PROTEIN  Length:208
 aligned with CRVP_PSEAU | Q8AVA4 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:208
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
           CRVP_PSEAU    31 KNYQKEIVDKHNALRRSVKPTARNMLQMKWNSRAAQNAKRWANRCTFAHSPPNKRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSYLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNKLCTNPCKRNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 238
               SCOP domains d2ddac1 C:4-154 automated matches                                                                                                                      d2ddac2 C:155-211 automated matches                       SCOP domains
               CATH domains 2ddaC01 C:4-170 Pathogenesis-related Protein p14a                                                                                                                      ----------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...........eehhhhhhhhhhhhh.......hhhh.ee..ee.eeeeeee....hhhhhhhhhhhhhh.ee...ee......hhhhhhhh.....eeeeeeeeee..eeeeeeeee..........................................hhhhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------CRISP_1    ---------------CRISP_2     -----------------------------SHKT  PDB: C:173-206              ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dda C   4 KNYQKEIVDKHNALRRSVKPTARNMLQMKWNSRAAQNAKRWANRCTFAHSPPNKRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSYLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNKLCTNPCKRNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 211
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        

Chain D from PDB  Type:PROTEIN  Length:208
 aligned with CRVP_PSEAU | Q8AVA4 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:208
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
           CRVP_PSEAU    31 KNYQKEIVDKHNALRRSVKPTARNMLQMKWNSRAAQNAKRWANRCTFAHSPPNKRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSYLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNKLCTNPCKRNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 238
               SCOP domains d2ddad1 D:4-154 automated matches                                                                                                                      d2ddad2 D:155-211 automated matches                       SCOP domains
               CATH domains 2ddaD01 D:4-170 Pathogenesis-related Protein p14a                                                                                                                      ----------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh............eehhhhhhhhhhhhh.......hhhh.ee..ee.eeeeeee....hhhhhhhhhhhhhh.ee...ee......hhhhhhhh.....eeeeeeeeee..eeeeeeeee..........................................hhhhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------CRISP_1    ---------------CRISP_2     -----------------------------SHKT  PDB: D:173-206              ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dda D   4 KNYQKEIVDKHNALRRSVKPTARNMLQMKWNSRAAQNAKRWANRCTFAHSPPNKRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSYLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNKLCTNPCKRNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII 211
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        

   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  (2, 8)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DDA)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CRVP_PSEAU | Q8AVA4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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2ddb PSEUDECIN FROM PSEUDECHIS PORPHYRIACUS