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(-) Description

Title :  CRYSTAL STRUCTURE OF NATRIN, A SNAKE VENOM CRISP FROM TAIWAN COBRA (NAJA ATRA)
 
Authors :  Y. -L. Wang, K. -X. Goh, S. -C. Lee, W. -N. Huang, W. -G. Wu, C. -J. Chen
Date :  21 Oct 04  (Deposition) - 13 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Natrin, Crisp, Serine Protease, Ion Channel Blocking, Naja Atra, Cobra, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. -L. Wang, K. -X. Goh, S. -C. Lee, W. -N. Huang, W. -G. Wu, C. -J. Chen
Structures Of Snake Venom Crisp Reveal An Action Mechanism Involving Serine Protease And Ion Channel Blocking Domains
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NATRIN 1
    Chains: A, B
    Organism Common: CHINESE COBRA
    Organism Scientific: NAJA ATRA
    Organism Taxid: 8656
    Synonym: CYSTEINE-RICH VENOM PROTEIN 1, NA-CRVP1, CRISP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1XTA)

(-) Sites  (0, 0)

(no "Site" information available for 1XTA)

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:56 -A:134
2A:73 -A:148
3A:129 -A:145
4A:167 -A:174
5A:170 -A:179
6A:183 -A:216
7A:192 -A:210
8A:201 -A:214
9B:56 -B:134
10B:73 -B:148
11B:129 -B:145
12B:167 -B:174
13B:170 -B:179
14B:183 -B:216
15B:192 -B:210
16B:201 -B:214

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser A:30 -Pro A:31
2Ser A:107 -Pro A:108
3Cys A:148 -Pro A:149
4Ser B:30 -Pro B:31
5Ser B:107 -Pro B:108
6Cys B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XTA)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRISP_1PS01009 CRISP family signature 1.CRVP1_NAJAT132-142
 		  2A:114-124
B:114-124
2CRISP_2PS01010 CRISP family signature 2.CRVP1_NAJAT160-171
 		  2A:142-153
B:142-153
3SHKTPS51670 ShKT domain profile.CRVP1_NAJAT201-234
 		  2A:183-216
B:183-216

(-) Exons   (0, 0)

(no "Exon" information available for 1XTA)

(-) Sequences/Alignments

Asymmetric/Biological 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:220
 aligned with CRVP1_NAJAT | Q7T1K6 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:220
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239
          CRVP1_NAJAT    20 VDFNSESTRRKKKQKEIVDLHNSLRRRVSPTASNMLKMEWYPEAASNAERWANTCSLNHSPDNLRVLEGIQCGESIYMSSNARTWTEIIHLWHDEYKNFVYGVGANPPGSVTGHYTQIVWYQTYRAGCAVSYCPSSAWSYFYVCQYCPSGNFQGKTATPYKLGPPCGDCPSACDNGLCTNPCTIYNKLTNCDSLLKQSSCQDDWIKSNCPASCFCRNKII 239
               SCOP domains d1xtaa1 A:2-164 automated matches                                                                                                                                  d1xtaa2 A:165-221 automated matches                       SCOP domains
               CATH domains 1xtaA01 A:2-180 Pathogenesis-related Protein p14a                                                                                                                                  ----------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..hhhhhhhhhhhhhhhhhh...........eehhhhhhhhhhhhh.......hhhh.ee..ee.eeeeeee....hhhhhhhhhhhhhh.ee...ee......hhhhhhhh.....eeeeeeee.......eeeeeeee.........................ee..ee...........hhhhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------CRISP_1    -----------------CRISP_2     -----------------------------SHKT  PDB: A:183-216              ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xta A   2 VDFNSESTRRKKKQKEIVDLHNSLRRRVSPTASNMLKMEWYPEAASNAERWANTCSLNHSPDNLRVLEGIQCGESIYMSSNARTWTEIIHLWHDEYKNFVYGVGASPPGSVTGHYTQIVWYQTYRAGCAVSYCPSSAWSYFYVCQYCPSGNFQGKTATPYKLGPPCGDCPSACDNGLCTNPCTIYNKLTNCDSLLKQSSCQDDWIKSNCPASCFCRNKII 221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221


Chain B from PDB  Type:PROTEIN  Length:219
 aligned with CRVP1_NAJAT | Q7T1K6 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:219
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
          CRVP1_NAJAT    21 DFNSESTRRKKKQKEIVDLHNSLRRRVSPTASNMLKMEWYPEAASNAERWANTCSLNHSPDNLRVLEGIQCGESIYMSSNARTWTEIIHLWHDEYKNFVYGVGANPPGSVTGHYTQIVWYQTYRAGCAVSYCPSSAWSYFYVCQYCPSGNFQGKTATPYKLGPPCGDCPSACDNGLCTNPCTIYNKLTNCDSLLKQSSCQDDWIKSNCPASCFCRNKII 239
               SCOP domains d1xtab1 B:3-164 automated matches                                                                                                                                 d1xtab2 B:165-221 automated matches                       SCOP domains
               CATH domains 1xtaB01 B:3-180 Pathogenesis-related Protein p14a                                                                                                                                 ----------------------------------------- CATH domains
           Pfam domains (1) ----------------CAP-1xtaB03 B:19-147                                                                                                             -------------------Crisp-1xtaB01 B:167-221                                 Pfam domains (1)
           Pfam domains (2) ----------------CAP-1xtaB04 B:19-147                                                                                                             -------------------Crisp-1xtaB02 B:167-221                                 Pfam domains (2)
         Sec.struct. author .hhhhh..hhhhhhhhhhhhhhhhhh...........eehhhhhhhhhhhhh.......hhhh.ee..ee.eeeeeee....hhhhhhhhhhhhhh.ee...ee......hhhhhhhh.....eeeeeeee.......eeeeeeee.........................ee..ee............hhhhh......hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------CRISP_1    -----------------CRISP_2     -----------------------------SHKT  PDB: B:183-216              ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xta B   3 DFNSESTRRKKKQKEIVDLHNSLRRRVSPTASNMLKMEWYPEAASNAERWANTCSLNHSPDNLRVLEGIQCGESIYMSSNARTWTEIIHLWHDEYKNFVYGVGASPPGSVTGHYTQIVWYQTYRAGCAVSYCPSSAWSYFYVCQYCPSGNFQGKTATPYKLGPPCGDCPSACDNGLCTNPCTIYNKLTNCDSLLKQSSCQDDWIKSNCPASCFCRNKII 221
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: ShK-like (4)
(-)
Clan: no clan defined [family: CAP] (7)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CRVP1_NAJAT | Q7T1K6)
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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  Cis Peptide Bonds
    Cys A:148 - Pro A:149   [ RasMol ]  
    Cys B:148 - Pro B:149   [ RasMol ]  
    Ser A:107 - Pro A:108   [ RasMol ]  
    Ser A:30 - Pro A:31   [ RasMol ]  
    Ser B:107 - Pro B:108   [ RasMol ]  
    Ser B:30 - Pro B:31   [ RasMol ]  
 

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  CRVP1_NAJAT | Q7T1K6
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 Related Entries

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

UniProtKB/Swiss-Prot
        CRVP1_NAJAT | Q7T1K6: 1xx5 2giz 3mz8

(-) Related Entries Specified in the PDB File

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