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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STAPHYLOCOCCAL SERINE PROTEASE SPLA IN COMPLEX WITH A SPECIFIC PHOSPHONATE INHIBITOR
 
Authors :  M. Zdzalik, E. Burchacka, J. S. Niemczyk, K. Pustelny, G. M. Popowicz, B A. Dubin, J. Potempa, M. Sienczyk, G. Dubin, J. Oleksyszyn
Date :  24 Sep 13  (Deposition) - 22 Jan 14  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Chymotrypsin-Like Fold, Serine Endopeptidase, Extracellular Staphylococcal Proteases, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Burchacka, M. Zdzalik, J. S. Niemczyk, K. Pustelny, G. Popowicz, B. Wladyka, A. Dubin, J. Potempa, M. Sienczyk, G. Dubin, J. Oleksyszyn
Development And Binding Characteristics Of Phosphonate Inhibitors Of Spla Protease From Staphylococcus Aureus.
Protein Sci. V. 23 179 2014
PubMed-ID: 24375505  |  Reference-DOI: 10.1002/PRO.2403

(-) Compounds

Molecule 1 - SERINE PROTEASE SPLA
    Chains: A, B, C, D
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Taxid: 1423
    Gene: SPLA, SAOUHSC_01942
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 93061
    Strain: NCTC 8325

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1I1S4Ligand/Ion[(1S)-1-{[(BENZYLOXY)CARBONYL]AMINO}-2-PHENYLETHYL]PHOSPHONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1I1S1Ligand/Ion[(1S)-1-{[(BENZYLOXY)CARBONYL]AMINO}-2-PHENYLETHYL]PHOSPHONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1I1S1Ligand/Ion[(1S)-1-{[(BENZYLOXY)CARBONYL]AMINO}-2-PHENYLETHYL]PHOSPHONIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1I1S1Ligand/Ion[(1S)-1-{[(BENZYLOXY)CARBONYL]AMINO}-2-PHENYLETHYL]PHOSPHONIC ACID
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1I1S1Ligand/Ion[(1S)-1-{[(BENZYLOXY)CARBONYL]AMINO}-2-PHENYLETHYL]PHOSPHONIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:39 , ALA A:149 , GLN A:150 , PRO A:151 , SER A:154 , TYR A:170 , ALA A:171 , GLY A:172 , SER A:173 , GLY A:174 , ASN A:181 , HOH A:443 , HOH A:516 , HOH A:553 , HOH A:598 , LYS C:76BINDING SITE FOR RESIDUE I1S A 301
2AC2SOFTWAREHIS B:39 , ALA B:149 , GLN B:150 , PRO B:151 , SER B:154 , TYR B:170 , ALA B:171 , GLY B:172 , GLY B:174 , LYS B:175 , HOH B:402 , HOH B:411 , HOH B:432 , HOH B:473 , LYS D:76 , GLU D:77 , HOH D:440BINDING SITE FOR RESIDUE I1S B 301
3AC3SOFTWARELYS A:76 , GLU A:77 , HOH A:456 , HOH A:596 , HIS C:39 , ALA C:149 , GLN C:150 , PRO C:151 , SER C:154 , TYR C:170 , ALA C:171 , GLY C:172 , GLY C:174 , LYS C:175 , SER C:178 , HOH C:403 , HOH C:456 , HOH C:464 , HOH C:498BINDING SITE FOR RESIDUE I1S C 301
4AC4SOFTWARELYS B:76 , GLN D:150 , PRO D:151 , SER D:154 , TYR D:170 , ALA D:171 , GLY D:172 , GLY D:174 , LYS D:175 , HOH D:406 , HOH D:411 , HOH D:469 , HOH D:506 , HOH D:550BINDING SITE FOR RESIDUE I1S D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MVN)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:13 -Pro A:14
2Glu B:13 -Pro B:14
3Glu C:13 -Pro C:14
4Glu D:13 -Pro D:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MVN)

(-) 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:199
                                                                                                                                                                                                                                       
               SCOP domains d4mvna_ A: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......hhh.eeee..eeeeeee..eeeehhhhhhhhhhhh..eee..........ee.eeeeee.......eeeee........hhhhhh.............eeeeee..hhhhh...eeeeeeeeeeee..eeee...........eee.....eeeeeeee.......eeeee.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mvn A   1 EKNVKEITDATKEPYNSVVAFVGGTGVVVGKNTIVTNKHIAKSNDIFKNRVSAHHSSKGKGGGNYDVKDIVEYPGKEDLAIVHVHETSTEGLNFNKNVSYTKFADGAKVKDRISVIGYPKGAQTKYKMFESTGTINHISGTFMEFDAYAQPGNSGSPVLNSKHELIGILYAGSGKDSEKNFGVYFTPQLKEFIQNNIEK 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     ||181       191         
                                                                                                                                                                                                         176|                      
                                                                                                                                                                                                          178                      


Chain B from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains d4mvnb_ B: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhh.eeee..eeeeeee..eeeehhhhhh.......eeee.........eeeeeeeee.......eeeee........hhhhhh.............eeeeee..hhhhhh..eeeeeeeeeeee..eeee...........eee.....eeeeeeee........eeeee.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mvn B   1 EKNVKEITDATKEPYNSVVAFVGGTGVVVGKNTIVTNKHIAKSNDIFKNRVSAHHSSKGGGGNYDVKDIVEYPGKEDLAIVHVHETSTEGLNFNKNVSYTKFADGAKVKDRISVIGYPKGAQTKYKMFESTGTINHISGTFMEFDAYAQPGNSGSPVLNSKHELIGILYAGSGKDESEKNFGVYFTPQLKEFIQNNIEK 200
                                    10        20        30        40        50        61        71        81        91       101       111       121       131       141       151       161       171       181       191         
                                                                                     59|                                                                                                                                           
                                                                                      61                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains d4mvnc_ C: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......hhh.eeee..eeeeeee..eeeehhhhhh.......eeee......eeeeeeeeee.......eeeee........hhhhhh.............eeeeee..hhhhhh..eeeeeeeeeeee..eeee...........eee.....eeeeeee.........eeeee.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mvn C   1 EKNVKEITDATKEPYNSVVAFVGGTGVVVGKNTIVTNKHIAKSNDIFKNRVSAHHSSGGGNYDVKDIVEYPGKEDLAIVHVHETSTEGLNFNKNVSYTKFADGAKVKDRISVIGYPKGAQTKYKMFESTGTINHISGTFMEFDAYAQPGNSGSPVLNSKHELIGILYAGSGKDESEKNFGVYFTPQLKEFIQNNIEK 200
                                    10        20        30        40        50      ||63        73        83        93       103       113       123       133       143       153       163       173       183       193       
                                                                                   57|                                                                                                                                           
                                                                                    61                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains d4mvnd_ D: automated matches                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......hhh.eeee..eeeeeee..eeeehhhhhhhhhhh...eee..........ee.eeeeee.......eeeee........hhhhhh.............eeeeee..hhhhhh..eeeeeeeeeeee..eeee...........eee.....eeeeeee.........eeeee.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mvn D   1 EKNVKEITDATKEPYNSVVAFVGGTGVVVGKNTIVTNKHIAKSNDIFKNRVSAHHSSKGKGGGNYDVKDIVEYPGKEDLAIVHVHETSTEGLNFNKNVSYTKFADGAKVKDRISVIGYPKGAQTKYKMFESTGTINHISGTFMEFDAYAQPGNSGSPVLNSKHELIGILYAGSGKDESEKNFGVYFTPQLKEFIQNNIEK 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SPLA_STAA8 | Q2FXC2: 2w7s 2w7u 3ufa

(-) Related Entries Specified in the PDB File

2w7u APO-PROTEIN
3ufa
3w7s APO-PROTEIN