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(-) Description

Title :  CRYSTAL STRUCTURE OF A DIMERIC MYOTOXIC COMPONENT OF THE VIPERA AMMODYTES MERIDIONALIS VENOM REVEALS DETERMINANTS OF MYOTOXICITY AND MEMBRANE DAMAGING ACTIVITY
 
Authors :  D. Georgieva, M. Coronado, D. Oberthuer, F. Buck, D. Duhalov, R. K. Arni C. Betzel
Date :  04 Dec 11  (Deposition) - 25 Apr 12  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.97
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 :  Toxin, Snake Venom, Ser49 Myotoxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Georgieva, M. Coronado, D. Oberthur, F. Buck, D. Duhalov, R. K. Arni C. Betzel
Crystal Structure Of A Dimeric Ser49 Pla(2)-Like Myotoxic Component Of The Vipera Ammodytes Meridionalis Venomics Reveals Determinants Of Myotoxicity And Membrane Damaging Activity.
Mol Biosyst V. 8 1405 2012
PubMed-ID: 22362132  |  Reference-DOI: 10.1039/C2MB05490F

(-) Compounds

Molecule 1 - AMMODYTIN L(1) ISOFORM
    Chains: A, B, C, D, E, F, G, H
    Organism Scientific: VIPERA AMMODYTES MERIDIONALIS
    Organism Taxid: 73841

 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, 19)

Asymmetric Unit (1, 19)
No.NameCountTypeFull Name
1SO419Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 6 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 7 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 8 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:39 , ARG A:42 , LYS E:105 , LYS E:108BINDING SITE FOR RESIDUE SO4 A 123
02AC2SOFTWARETYR A:21 , CYS A:28 , GLY A:29BINDING SITE FOR RESIDUE SO4 A 124
03AC3SOFTWARELYS A:15 , ASN A:16 , THR A:19 , SER A:20 , HOH A:127 , ALA E:91BINDING SITE FOR RESIDUE SO4 A 125
04AC4SOFTWARECYS A:75 , GLU A:87 , LYS E:7BINDING SITE FOR RESIDUE SO4 A 126
05AC5SOFTWARELYS B:121 , HOH B:128 , ARG H:112BINDING SITE FOR RESIDUE SO4 B 123
06AC6SOFTWAREARG B:42 , LYS H:105BINDING SITE FOR RESIDUE SO4 B 124
07AC7SOFTWARELEU C:18BINDING SITE FOR RESIDUE SO4 C 123
08AC8SOFTWARELYS C:35 , LYS F:97 , LYS G:114BINDING SITE FOR RESIDUE SO4 C 124
09AC9SOFTWARELYS D:15 , ASN D:16 , THR D:19 , SER D:20 , HOH D:131 , ALA F:91BINDING SITE FOR RESIDUE SO4 D 123
10BC1SOFTWAREALA D:39 , ARG D:42 , LYS F:108BINDING SITE FOR RESIDUE SO4 D 124
11BC2SOFTWARELYS A:105 , LYS A:108 , HOH A:134 , ALA E:39 , ARG E:42 , HOH E:134BINDING SITE FOR RESIDUE SO4 E 123
12BC3SOFTWARESER F:119BINDING SITE FOR RESIDUE SO4 F 123
13BC4SOFTWARELYS D:7 , GLN D:10 , CYS F:75 , GLU F:87 , LYS F:90BINDING SITE FOR RESIDUE SO4 F 124
14BC5SOFTWARELYS D:105 , ARG F:42BINDING SITE FOR RESIDUE SO4 F 125
15BC6SOFTWARELYS C:108 , ALA G:39 , ARG G:42BINDING SITE FOR RESIDUE SO4 G 123
16BC7SOFTWAREHOH G:130BINDING SITE FOR RESIDUE SO4 G 124
17BC8SOFTWAREALA C:91 , ASN G:16 , THR G:19 , SER G:20BINDING SITE FOR RESIDUE SO4 G 125
18BC9SOFTWAREGLY H:29 , LEU H:30 , HOH H:129BINDING SITE FOR RESIDUE SO4 H 123
19CC1SOFTWARELYS H:37 , TYR H:107 , TYR H:110BINDING SITE FOR RESIDUE SO4 H 124

(-) SS Bonds  (56, 56)

Asymmetric Unit
No.Residues
1A:26 -A:115
2A:28 -A:44
3A:43 -A:95
4A:49 -A:122
5A:50 -A:88
6A:57 -A:81
7A:75 -A:86
8B:26 -B:115
9B:28 -B:44
10B:43 -B:95
11B:49 -B:122
12B:50 -B:88
13B:57 -B:81
14B:75 -B:86
15C:26 -C:115
16C:28 -C:44
17C:43 -C:95
18C:49 -C:122
19C:50 -C:88
20C:57 -C:81
21C:75 -C:86
22D:26 -D:115
23D:28 -D:44
24D:43 -D:95
25D:49 -D:122
26D:50 -D:88
27D:57 -D:81
28D:75 -D:86
29E:26 -E:115
30E:28 -E:44
31E:43 -E:95
32E:49 -E:122
33E:50 -E:88
34E:57 -E:81
35E:75 -E:86
36F:26 -F:115
37F:28 -F:44
38F:43 -F:95
39F:49 -F:122
40F:50 -F:88
41F:57 -F:81
42F:75 -F:86
43G:26 -G:115
44G:28 -G:44
45G:43 -G:95
46G:49 -G:122
47G:50 -G:88
48G:57 -G:81
49G:75 -G:86
50H:26 -H:115
51H:28 -H:44
52H:43 -H:95
53H:49 -H:122
54H:50 -H:88
55H:57 -H:81
56H:75 -H:86

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser B:119 -Glu B:120
2Glu H:69 -Gly H:70

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UX7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UX7)

(-) Exons   (0, 0)

(no "Exon" information available for 3UX7)

(-) 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:122
 aligned with I1SB18_VIPAE | I1SB18 from UniProtKB/TrEMBL  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
         I1SB18_VIPAE     1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
               SCOP domains d3ux7a_ A: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhhhhhhh.......eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ux7 A   1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with I1SB18_VIPAE | I1SB18 from UniProtKB/TrEMBL  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
         I1SB18_VIPAE     1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
               SCOP domains d3ux7b_ B: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhhh.......eee....eee...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ux7 B   1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain C from PDB  Type:PROTEIN  Length:122
 aligned with I1SB18_VIPAE | I1SB18 from UniProtKB/TrEMBL  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
         I1SB18_VIPAE     1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
               SCOP domains d3ux7c_ C: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhhh.......eee....eee...hhhhhhhhhhhhhhhhhhhhh....hhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ux7 C   1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain D from PDB  Type:PROTEIN  Length:122
 aligned with I1SB18_VIPAE | I1SB18 from UniProtKB/TrEMBL  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
         I1SB18_VIPAE     1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
               SCOP domains d3ux7d_ D: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhh.......eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ux7 D   1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain E from PDB  Type:PROTEIN  Length:122
 aligned with I1SB18_VIPAE | I1SB18 from UniProtKB/TrEMBL  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
         I1SB18_VIPAE     1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
               SCOP domains d3ux7e_ E: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhhh.......eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ux7 E   1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain F from PDB  Type:PROTEIN  Length:122
 aligned with I1SB18_VIPAE | I1SB18 from UniProtKB/TrEMBL  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
         I1SB18_VIPAE     1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
               SCOP domains d3ux7f_ F: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhhh........eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ux7 F   1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain G from PDB  Type:PROTEIN  Length:122
 aligned with I1SB18_VIPAE | I1SB18 from UniProtKB/TrEMBL  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
         I1SB18_VIPAE     1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
               SCOP domains d3ux7g_ G: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhh...........eee....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ux7 G   1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain H from PDB  Type:PROTEIN  Length:122
 aligned with I1SB18_VIPAE | I1SB18 from UniProtKB/TrEMBL  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
         I1SB18_VIPAE     1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
               SCOP domains d3ux7h_ H: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhhh.......eee....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ux7 H   1 SVIEFGKMIQEETDKNPLTSYSFYGCHCGLGNGGKPKDATDRCCFVHSCCYASLSDCSPATNRYSYHKEGGAIVCGSSTPCKGQICECDKAAAICFKENLKTYNKKYKVYLRFKCKGVSEKC 122
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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  (1, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UX7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UX7)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (I1SB18_VIPAE | I1SB18)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004623    phospholipase A2 activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
biological process
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
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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  3ux7
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
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 Related Entries

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