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(-) Description

Title :  CRYSTAL STRUCTURE OF STREPTOMYCES CAESPITOSUS SERMETSTATIN IN COMPLEX WITH S. CAESPITOSUS SNAPALYSIN
 
Authors :  S. Trillo-Muyo, S. Martinez-Rodriguez, J. L. Arolas, F. X. Gomis-Ruth
Date :  09 Nov 12  (Deposition) - 05 Dec 12  (Release) - 27 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Biol. Unit 3:  I,J,K,L  (1x)
Keywords :  Streptomyces Subtilisin Inhibitor Fold, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Trillo-Muyo, S. Martinez-Rodriguez, J. L. Arolas, F. X. Gomis-Rut
Mechanism Of Action Of A Janus-Faced Single-Domain Protein Inhibitor Simultaneously Targeting Two Peptidase Classes
Chem Sci V. 4 791 2013
PubMed: search  |  Reference-DOI: 10.1039/C2SC21712K

(-) Compounds

Molecule 1 - EXTRACELLULAR SMALL NEUTRAL PROTEASE
    Chains: A, C, E, G, I, K
    EC Number: 3.4.24.77
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: MATURE PROTEASE
    Gene: SNPA
    Organism Scientific: STREPTOMYCES CAESPITOSUS
    Organism Taxid: 53502
    Synonym: SCNP, SNAPALYSIN
 
Molecule 2 - NEUTRAL PROTEINASE INHIBITOR SCNPI
    Chains: B, D, F, H, J, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: ORIGAMI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SCNPI
    Organism Scientific: STREPTOMYCES CAESPITOSUS
    Organism Taxid: 53502
    Synonym: SERMETSTATIN

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCD        
Biological Unit 2 (1x):     EFGH    
Biological Unit 3 (1x):         IJKL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:83 , HIS A:87 , ASP A:93 , HOH A:323BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREHIS C:83 , HIS C:87 , ASP C:93 , HOH C:302BINDING SITE FOR RESIDUE ZN C 201
3AC3SOFTWAREGLN C:96 , ALA D:41 , PRO D:42 , ARG D:43 , ALA D:44BINDING SITE FOR RESIDUE GOL D 201
4AC4SOFTWAREHIS E:83 , HIS E:87 , ASP E:93 , HOH E:309BINDING SITE FOR RESIDUE ZN E 201
5AC5SOFTWAREHIS G:83 , HIS G:87 , ASP G:93 , HOH G:311BINDING SITE FOR RESIDUE ZN G 201
6AC6SOFTWAREHIS I:83 , HIS I:87 , ASP I:93 , HOH I:312BINDING SITE FOR RESIDUE ZN I 201
7AC7SOFTWAREGLN D:14 , THR D:20 , THR D:22 , THR J:20 , ASP J:21 , HOH J:621BINDING SITE FOR RESIDUE GOL J 501
8AC8SOFTWAREHIS K:83 , HIS K:87 , ASP K:93 , HOH K:301BINDING SITE FOR RESIDUE ZN K 201

(-) SS Bonds  (18, 18)

Asymmetric Unit
No.Residues
1A:99 -A:112
2B:31 -B:46
3B:69 -B:99
4C:99 -C:112
5D:31 -D:46
6D:69 -D:99
7E:99 -E:112
8F:31 -F:46
9F:69 -F:99
10G:99 -G:112
11H:31 -H:46
12H:69 -H:99
13I:99 -I:112
14J:31 -J:46
15J:69 -J:99
16K:99 -K:112
17L:31 -L:46
18L:69 -L:99

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HX3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HX3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HX3)

(-) Exons   (0, 0)

(no "Exon" information available for 4HX3)

(-) 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:134
                                                                                                                                                                      
               SCOP domains d4hx3a_ A: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhhh....eeeee.....eeeeee......eeee.....eeeeeehhhhhhhhhhhhhhhhhhhhh...........hhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hx3 A  -2 GPMVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYEGNDSRGSYAQTDGHGRGYIFLDYQQNQQYDSTRVTAHETGHVLGLPDHYQGPCSELMSGGGPGPSCTNPYPNAQERSRVNALWANG 132
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128    
                             ||                                                                                                                                   
                            -1|                                                                                                                                   
                              1                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains d4hx3b_ B: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee........eeeeeeeee...ee....hhhhhhhhhhhh..hhhhhhh..............eeeeeeeee..eeeeeeeee.hhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 4hx3 B   1 SAHGPSAMVFTVIQGSGEPTDTVLRATTLSCAYTAEGTHPAPRAACDALNATDGELNRLLAAPDPSLVCPMYFDPVTVTADGVLNGRRVAWKHTFSNTCVMSANLNSNPVYAF 113
                                    10        20        30        40        50        60        70        80        90       100       110   


Chain C from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains d4hx3c_ C: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhhh....eeee......eeeeee......eeee.....eeeeeehhhhhhhhhhhhhhhhhhhhh...........hhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hx3 C  -2 GPMVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYEGNDSRGSYAQTDGHGRGYIFLDYQQNQQYDSTRVTAHETGHVLGLPDHYQGPCSELMSGGGPGPSCTNPYPNAQERSRVNALWANG 132
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128    
                            -1|                                                                                                                                   
                              1                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:109
                                                                                                                                             
               SCOP domains d4hx3d_ D: automated matches                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee........eeeeeeeee...eee...hhhhhhhhhhhh..hhhhhh...........eeeeeeeee..eeeeeeeee.hhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 4hx3 D   1 SAHGPSAMVFTVIQGSGEPTDTVLRATTLSCAYTAEGTHPAPRAACDALNATDGELNRLLAALVCPMYFDPVTVTADGVLNGRRVAWKHTFSNTCVMSANLNSNPVYAF 113
                                    10        20        30        40        50        60 ||     74        84        94       104         
                                                                                        62|                                              
                                                                                         67                                              


Chain E from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains d4hx3e_ E: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhhh....eeeee.....eeeeee......eeee.....eeeeee.hhhhhhhhhhhhhhhhhhhh...........hhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hx3 E   1 MVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYEGNDSRGSYAQTDGHGRGYIFLDYQQNQQYDSTRVTAHETGHVLGLPDHYQGPCSELMSGGGPGPSCTNPYPNAQERSRVNALWANG 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain F from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains d4hx3f_ F: automated matches                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee........eeeeeeeee...ee....hhhhhhhhhhhh..hhhhhhh..............eeeeeeeee..eeeeeeeee.hhhhhhhhh..hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 4hx3 F   2 AHGPSAMVFTVIQGSGEPTDTVLRATTLSCAYTAEGTHPAPRAACDALNATDGELNRLLAAPDPSLVCPMYFDPVTVTADGVLNGRRVAWKHTFSNTCVMSANLNSNPVYAF 113
                                    11        21        31        41        51        61        71        81        91       101       111  


Chain G from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains d4hx3g_ G: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhhhh....eeeee.....eeeeee......eeee.....eeeeee.hhhhhhhhhhhhhhhhhhhh...........hhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hx3 G  -1 PMVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYEGNDSRGSYAQTDGHGRGYIFLDYQQNQQYDSTRVTAHETGHVLGLPDHYQGPCSELMSGGGPGPSCTNPYPNAQERSRVNALWANG 132
                            ||       9        19        29        39        49        59        69        79        89        99       109       119       129   
                           -1|                                                                                                                                   
                             1                                                                                                                                   


Chain H from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d4hx3h_ H: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeee........eeeeeeeee...ee....hhhhhhhhhhhh..hhhhhh.........eeeeeeeee..eeeeeeeee.hhhhhhhhh..hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 4hx3 H  -1 GSAHGPSAMVFTVIQGSGEPTDTVLRATTLSCAYTAEGTHPAPRAACDALNATDGELNRLLLVCPMYFDPVTVTADGVLNGRRVAWKHTFSNTCVMSANLNSNPVYAF 113
                            ||       9        19        29        39        49        59||      75        85        95       105        
                           -1|                                                         60|                                              
                             1                                                          67                                              


Chain I from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains d4hx3i_ I: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhhh....eeeee.....eeeeee......eeee.....eeeeee.hhhhhhhhhhhhhhhhhhhh...........hhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hx3 I  -2 GPMVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYEGNDSRGSYAQTDGHGRGYIFLDYQQNQQYDSTRVTAHETGHVLGLPDHYQGPCSELMSGGGPGPSCTNPYPNAQERSRVNALWANG 132
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128    
                            -1|                                                                                                                                   
                              1                                                                                                                                   


Chain J from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains d4hx3j_ J: automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee........eeeeeeeee...ee....hhhhhhhhhhhh..hhhhhh.............eeeeeeeee..eeeeeeeee.hhhhhhhhh..hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4hx3 J   1 SAHGPSAMVFTVIQGSGEPTDTVLRATTLSCAYTAEGTHPAPRAACDALNATDGELNRLLAAPDPVCPMYFDPVTVTADGVLNGRRVAWKHTFSNTCVMSANLNSNPVYAF 113
                                    10        20        30        40        50        60    ||  72        82        92       102       112 
                                                                                           65|                                             
                                                                                            68                                             


Chain K from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains d4hx3k_ K: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhhh....eeeee.....eeeeee......eeee.....eeeeee.hhhhhhhhhhhhhhhhhhhh...........hhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hx3 K  -1 PMVTVTYDPSNAPSFQQEIANAAQIWNSSVRNVQLRAGGNADFSYYEGNDSRGSYAQTDGHGRGYIFLDYQQNQQYDSTRVTAHETGHVLGLPDHYQGPCSELMSGGGPGPSCTNPYPNAQERSRVNALWANG 132
                            ||       9        19        29        39        49        59        69        79        89        99       109       119       129   
                           -1|                                                                                                                                   
                             1                                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains d4hx3l_ L: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee........eeeeeeeee...ee....hhhhhhhhhhhh..hhhhhh...............eeeeeeeee..eeeeeeeee.hhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 4hx3 L   1 SAHGPSAMVFTVIQGSGEPTDTVLRATTLSCAYTAEGTHPAPRAACDALNATDGELNRLLAAPDPSLVCPMYFDPVTVTADGVLNGRRVAWKHTFSNTCVMSANLNSNPVYAF 113
                                    10        20        30        40        50        60        70        80        90       100       110
   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  (2, 12)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HX3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HX3)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

4hwx CRYSTAL STRUCTURE OF SERMETSTATIN
4hx2