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(-) Description

Title :  CRYSTAL STRUCTURE OF MYOTOXIN II FROM BOTHROPS MOOJENI COMPLEXED TO SURAMIN
 
Authors :  G. H. M. Salvador, M. R. M. Fontes
Date :  19 Mar 15  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bothrops Moojeni, Myotoxin Ii, Lys49-Pla2, Suramin, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. H. M. Salvador, M. R. M. Fontes
Structural And Functional Evidence For Membrane Docking And Disruption Sites On Phospholipase A2-Like Proteins Revealed By Complexation With The Inhibitor Suramin
Acta Crystallogr. , Sect. D V. 71 2066 2015
PubMed: search  |  Reference-DOI: 10.1107/S1399004715014443

(-) Compounds

Molecule 1 - BASIC PHOSPHOLIPASE A2 HOMOLOG 2
    Chains: B, A
    Organism Common: LANCE-HEADED VIPER
    Organism Scientific: BOTHROPS MOOJENI
    Organism Taxid: 98334
    Synonym: SVPLA2 HOMOLOG,M-VI,MJTX-II,MYOTOXIN II

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
3SO47Ligand/IonSULFATE ION
4SVR2Ligand/Ion8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS B:20 , LYS B:115 , ARG B:118 , SO4 B:202binding site for residue SO4 B 201
02AC2SOFTWARELYS B:16 , ASN B:17 , LYS B:20 , SO4 B:201 , HOH B:301 , HOH B:351binding site for residue SO4 B 202
03AC3SOFTWARELYS A:7 , LEU A:10 , GLN A:11 , GLY A:15 , TYR A:75 , TRP A:77 , LYS B:7 , LEU B:10 , GLN B:11 , GLY B:15 , TYR B:75 , TRP B:77binding site for residue PE4 B 203
04AC4SOFTWARETYR A:121 , LYS A:123 , PRO A:125 , LEU B:2 , ILE B:9 , CYS B:29 , GLY B:30 , HIS B:48binding site for residue 1PE B 204
05AC5SOFTWAREGLY B:33 , ARG B:34 , LYS B:53 , HOH B:302binding site for residue SO4 B 205
06AC6SOFTWARELYS A:38 , LYS A:116 , TYR A:117 , LYS B:116 , TYR B:117binding site for residue SO4 B 206
07AC7SOFTWAREPHE A:3 , LYS A:7 , LEU A:10 , ASN A:17 , PRO A:18 , CYS A:27 , LYS A:38 , ARG A:72 , PHE A:126 , CYS A:127 , LYS A:128 , SO4 A:202 , SVR A:205 , HOH A:380 , ASN B:114 , LYS B:115 , LYS B:116 , TYR B:119 , TYR B:121 , LEU B:122 , PHE B:126 , HOH B:305 , HOH B:311 , HOH B:316 , HOH B:320 , HOH B:338 , HOH B:347 , HOH B:352 , HOH B:356 , HOH B:361binding site for residue SVR B 207
08AC8SOFTWARELYS A:16 , LYS A:20 , LYS A:115 , ARG A:118binding site for residue SO4 A 201
09AC9SOFTWARELYS A:16 , ASN A:17 , LYS A:20 , HOH A:301 , SVR B:207binding site for residue SO4 A 202
10AD1SOFTWAREILE A:9 , PRO A:18 , TYR A:22 , ASN A:28 , GLY A:30 , CYS A:45 , HIS A:48 , LYS A:49binding site for residue 1PE A 203
11AD2SOFTWAREARG A:34 , LYS A:53 , HOH A:372binding site for residue SO4 A 204
12AD3SOFTWAREASN A:114 , LYS A:115 , LYS A:116 , TYR A:119 , TYR A:121 , LEU A:122 , PHE A:126 , HOH A:305 , HOH A:316 , HOH A:321 , HOH A:348 , HOH A:353 , HOH A:355 , HOH A:357 , HOH A:363 , HOH A:368 , HOH A:369 , PHE B:3 , GLY B:6 , LYS B:7 , LEU B:10 , ASN B:17 , PRO B:18 , CYS B:27 , LYS B:36 , LYS B:38 , ARG B:72 , PHE B:126 , CYS B:127 , LYS B:128 , SVR B:207 , HOH B:323 , HOH B:351binding site for residue SVR A 205

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:27 -A:127
2A:29 -A:45
3A:44 -A:105
4A:50 -A:133
5A:51 -A:98
6A:61 -A:90
7A:84 -A:96
8B:27 -B:127
9B:29 -B:45
10B:44 -B:105
11B:50 -B:133
12B:51 -B:98
13B:61 -B:90
14B:84 -B:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YV5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YV5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YV5)

(-) Exons   (0, 0)

(no "Exon" information available for 4YV5)

(-) 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:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhhh...........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yv5 A   1 SLFELGKMILQETGKNPAKSYGVYGCNCGVGGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNSCLKELCECDKAVAICLRENLDTYNKKYRYNYLKPFCKKADPC 133
                                    10  ||    21        31        41        51 ||   ||69        79        89||     100       110       120  ||   131  
                                       13|                                    53|  61|                     90|                            123|        
                                        15                                     57   67                      92                             125        


Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yv5 B   1 SLFELGKMILQETGKNPAKSYGVYGCNCGVGGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNSCLKELCECDKAVAICLRENLDTYNKKYRYNYLKPFCKKADPC 133
                                    10  ||    21        31        41        51 ||   ||69        79        89||     100       110       120  ||   131  
                                       13|                                    53|  61|                     90|                            123|        
                                        15                                     57   67                      92                             125
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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 4YV5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YV5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YV5)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PA2H2_BOTMO | Q9I834: 1xxs 4kf3

(-) Related Entries Specified in the PDB File

4kf3 SAME PROTEIN IN NATIVE FORM.