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(-) Description

Title :  CRYSTAL STRUCTURE OF MTX-II FROM BOTHROPS BRAZILI VENOM COMPLEXED WITH POLYETHYLENE GLYCOL
 
Authors :  C. A. H. Fernandes, E. J. Comparetti, R. J. Borges, M. R. M. Fontes
Date :  03 Apr 13  (Deposition) - 13 Nov 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phospholipase A2, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. H. Fernandes, E. J. Comparetti, R. J. Borges, S. Huancahuire-Vega, L. A. Ponce-Soto, S. Marangoni, A. M. Soares, M. R. M. Fontes
Structural Bases For A Complete Myotoxic Mechanism: Crystal Structures Of Two Non-Catalytic Phospholipases A2-Like From Bothrops Brazili Venom.
Biochim. Biophys. Acta V. 1834 2772 2013
PubMed-ID: 24145104  |  Reference-DOI: 10.1016/J.BBAPAP.2013.10.009

(-) Compounds

Molecule 1 - MTX-II
    Chains: A, B
    Organism Scientific: BOTHROPS BRAZILI
    Organism Taxid: 157546

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
17PE1Ligand/Ion2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
2PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
3PGE1Ligand/IonTRIETHYLENE GLYCOL
4SO45Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:2 , GLY A:6 , PRO A:19 , TYR A:23 , GLY A:24BINDING SITE FOR RESIDUE PGE A 201
2AC2SOFTWARETHR A:82 , ILE A:105 , ARG A:108 , HOH A:307 , HOH A:329 , HOH A:355 , LYS B:36 , HOH B:397BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWAREGLY A:34 , ARG A:35 , LYS A:57 , HOH A:366 , HOH A:372 , HOH A:396BINDING SITE FOR RESIDUE SO4 A 203
4AC4SOFTWARELYS A:116 , ARG A:119BINDING SITE FOR RESIDUE SO4 A 204
5AC5SOFTWARELYS B:7 , LEU B:10 , GLN B:11 , TYR B:75 , TRP B:77 , 7PE B:204BINDING SITE FOR RESIDUE PE4 B 201
6AC6SOFTWAREGLY B:15 , LYS B:16 , ASN B:17 , HOH B:399 , HOH B:427BINDING SITE FOR RESIDUE SO4 B 202
7AC7SOFTWARETHR B:59 , LYS B:115 , ARG B:118 , HOH B:380 , HOH B:403 , HOH B:418BINDING SITE FOR RESIDUE SO4 B 203
8AC8SOFTWAREPRO A:125 , LEU B:2 , GLY B:6 , LEU B:10 , PRO B:18 , TYR B:22 , PE4 B:201 , HOH B:377 , HOH B:413 , HOH B:414 , HOH B:422 , HOH B:428BINDING SITE FOR RESIDUE 7PE B 204

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:28 -A:127
2A:30 -A:46
3A:45 -A:106
4A:51 -A:134
5A:52 -A:99
6A:67 -A:92
7A:85 -A:97
8B:27 -B:126
9B:29 -B:45
10B:44 -B:105
11B:50 -B:133
12B:51 -B:98
13B:61 -B:91
14B:84 -B:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K06)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K06)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K06)

(-) Exons   (0, 0)

(no "Exon" information available for 4K06)

(-) 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:121
                                                                                                                                                         
               SCOP domains d4k06a_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhee...ee........hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k06 A   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 134
                                    10  ||    22        32        42        52||   || 70        80       |91       101       111       121 || || 133 
                                       13|                                   53|  61|                   88|                              123| ||     
                                        16                                    57   67                    90                               125 ||     
                                                                                                                                            127|     
                                                                                                                                             129     


Chain B from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains d4k06b_ B: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhhh...........eee....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k06 B   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  || ||132 
                                       13|                                    53|  61|                   88|                              123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K06)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K06)

(-) Gene Ontology  (5, 9)

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
        PA2B1_BOTJR | Q90249: 2h8i 3cxi 3hzd 3hzw 3i03 3i3h 3i3i 3iq3 4k09 4wtb
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        I6L8L6_9SAUR | I6L8L6: 4dcf 4k09

(-) Related Entries Specified in the PDB File

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