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(-) Description

Title :  COMPLEX STRUCTURE OF LYSOSTAPHIN SH3B DOMAIN WITH PEPTIDOGLYCAN FRAGMENT
 
Authors :  E. Jagielska, E. Nowak, M. Bochtler, I. Sabala
Date :  30 Jun 16  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,G,H
Biol. Unit 1:  A,H  (1x)
Biol. Unit 2:  B,G  (1x)
Keywords :  Lysostaphin, Peptidoglycan, Complex, Cell Wall Targeting/Binding Domain, Sh3, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Jagielska, E. Nowak, M. Bochtler, I. Sabala
Complex Structure Of Lysostaphin Sh3Doamin With Peptidoglycan Fragment
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LYSOSTAPHIN
    Chains: A, B
    EC Number: 3.4.24.75
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SH3B DOMAIN, UNP RESIDUES 401-493
    Gene: LSS
    Organism Scientific: STAPHYLOCOCCACEAE
    Organism Taxid: 90964
    Synonym: GLYCYL-GLYCINE ENDOPEPTIDASE
 
Molecule 2 - GLY-GLY-GLY-GLY-GLY
    Chains: G, H
    Engineered: YES
    Organism Scientific: STAPHYLOCOCCACEAE
    Organism Taxid: 90964
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABGH
Biological Unit 1 (1x): A  H
Biological Unit 2 (1x):  BG 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:436 , GLN A:437 , HOH A:642 , TRP B:402 , LYS B:454 , ASN B:483 , HOH B:624 , HOH B:672binding site for residue SO4 A 501
2AC2SOFTWAREGLY A:465 , ASN A:466 , SER A:467 , GLN A:469 , HOH A:601 , HOH A:609 , HOH A:640 , HOH A:664binding site for residue SO4 A 502
3AC3SOFTWAREGLU A:414 , ARG A:476 , HOH B:616 , HOH B:713binding site for residue MPD A 503
4AC4SOFTWARETRP A:402 , LYS A:454 , ASN A:483 , HOH A:619 , HOH A:668 , GLN B:437 , HOH B:632 , HOH B:645binding site for residue SO4 B 501
5AC5SOFTWAREARG A:433 , TYR B:411 , HOH B:603 , HOH B:625 , GLY G:1binding site for residue SO4 B 502
6AC6SOFTWARELYS A:403 , TYR A:411 , LYS B:480 , LYS B:493 , HOH B:608 , HOH B:618 , GLY H:1binding site for residue SO4 B 503
7AC7SOFTWAREGLY B:465 , ASN B:466 , SER B:467 , GLN B:469 , HOH B:647binding site for residue SO4 B 504
8AC8SOFTWAREHOH A:607 , GLU B:414 , VAL B:452 , ARG B:476 , ILE B:492binding site for residue MPD B 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LEO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LEO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LEO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LEO)

(-) Exons   (0, 0)

(no "Exon" information available for 5LEO)

(-) 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:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeeeeeeeeee...eeeee........eeeee.....eeeeeeeee..eeeeeee.....eeeeeeeeee....ee....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 5leo A 401 GWKTNKYGTLYKSESASFTPNTDIITRTTGPFRSMPQSGVLKAGQTIHYDEVMKQDGHVWVGYTGNSGQRIYLPVRTWNKSTNTLGVLWGTIK 493
                                   410       420       430       440       450       460       470       480       490   


Chain B from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeeeeeeeeee...eeeee........eeeee.....eeeeeeeee..eeeeeee.....eeeeeeeeee....ee....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 5leo B 401 GWKTNKYGTLYKSESASFTPNTDIITRTTGPFRSMPQSGVLKAGQTIHYDEVMKQDGHVWVGYTGNSGQRIYLPVRTWNKSTNTLGVLWGTIK 493
                                   410       420       430       440       450       460       470       480       490   


Chain G from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5leo G   1 GGGGG   5


Chain H from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5leo H   1 GGGGG   5
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 5LEO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LEO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LEO)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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        LSTP_STASI | P10547: 4lxc 4qp5 4qpb

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