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(-) Description

Title :  1.1 ANGSTROM RESOLUTION STRUCTURE OF THE COMPLEX BETWEEN THE PROTEIN INHIBITOR, OMTKY3, AND THE SERINE PROTEASE, SUBTILISIN CARLSBERG
 
Authors :  J. R. Horn, S. Ramaswamy, K. P. Murphy
Date :  22 Sep 03  (Deposition) - 11 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  E,I
Keywords :  High Resolution, Serine Protease, Protein Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Horn, S. Ramaswamy, K. P. Murphy
Structure And Energetics Of Protein-Protein Interactions: The Role Of Conformational Heterogeneity In Omtky3 Binding To Serine Proteases
J. Mol. Biol. V. 331 497 2003
PubMed-ID: 12888355  |  Reference-DOI: 10.1016/S0022-2836(03)00783-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUBTILISIN CARLSBERG
    Chains: E
    EC Number: 3.4.21.62
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 1402
 
Molecule 2 - OVOMUCOID
    Chains: I
    Organism Common: TURKEY
    Organism Scientific: MELEAGRIS GALLOPAVO
    Organism Taxid: 9103
    Synonym: OMTKY3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : EI

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA E:37 , HIS E:39 , LEU E:42 , HOH E:4096 , HOH E:4097 , HOH E:4126 , HOH E:4333BINDING SITE FOR RESIDUE CA E 301
2AC2SOFTWAREGLN E:2 , ASP E:41 , LEU E:75 , ASN E:77 , THR E:79 , VAL E:81BINDING SITE FOR RESIDUE CA E 302
3AC3SOFTWAREGLY E:193 , ALA E:194 , LEU E:196 , SER E:260 , HOH E:4174 , HOH E:4286BINDING SITE FOR RESIDUE CA E 303
4AC4SOFTWAREALA E:169 , TYR E:171 , VAL E:174 , HOH E:4021 , HOH E:4084BINDING SITE FOR RESIDUE CA E 305

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1I:8 -I:38
2I:16 -I:35
3I:24 -I:56

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr E:167 -Pro E:168
2Pro E:210 -Thr E:211
3Tyr I:11 -Pro I:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R0R)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KAZAL_1PS00282 Kazal serine protease inhibitors family signature.IOVO_MELGA86-108
145-167		  1-
I:16-38
2SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.SUBT_BACLI133-144  1E:28-39
3SUBTILASE_HISPS00137 Serine proteases, subtilase family, histidine active site.SUBT_BACLI168-178  1E:64-74
4SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.SUBT_BACLI323-333  1E:219-229

(-) Exons   (0, 0)

(no "Exon" information available for 1R0R)

(-) 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 E from PDB  Type:PROTEIN  Length:274
 aligned with SUBT_BACLI | P00780 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:274
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375    
           SUBT_BACLI   106 AQTVPYGIPLIKADKVQAQGFKGANVKVAVLDTGIQASHPDLNVVGGASFVAGEAYNTDGNGHGTHVAGTVAALDNTTGVLGVAPSVSLYAVKVLNSSGSGTYSGIVSGIEWATTNGMDVINMSLGGPSGSTAMKQAVDNAYARGVVVVAAAGNSGSSGNTNTIGYPAKYDSVIAVGAVDSNSNRASFSSVGAELEVMAPGAGVYSTYPTSTYATLNGTSMASPHVAGAAALILSKHPNLSASQVRNRLSSTATYLGSSFYYGKGLINVEAAAQ 379
               SCOP domains d1r0re_ E: Subtilisin                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1r0rE00 E:1-275  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------Peptidase_S8-1r0rE01 E:27-275                                                                                                                                                                                                                            Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.......eeeeee...........eeeeee............hhhhhhhhhhhh..............eeeeee......eehhhhhhhhhhhhhhh...eeee.ee....hhhhhhhhhhhhhh..eeeee......................eeeeee...............eeeeee...eeeee...eeeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------SUBTILASE_AS-----------------------SUBTILASE_H------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r0r E   1 AQTVPYGIPLIKADKVQAQGFKGANVKVAVLDTGIQASHPDLNVVGGASFVAGEAYNTDGNGHGTHVAGTVAALDNTTGVLGVAPSVSLYAVKVLNSSGSGSYSGIVSGIEWATTNGMDVINMSLGGASGSTAMKQAVDNAYARGVVVVAAAGNSGNSGSTNTIGYPAKYDSVIAVGAVDSNSNRASFSSVGAELEVMAPGAGVYSTYPTNTYATLNGTSMASPHVAGAAALILSKHPNLSASQVRNRLSSTATYLGSSFYYGKGLINVEAAAQ 275
                                    10        20        30        40        50    ||  61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
                                                                                 55|                                                                                                                                                                                                                          
                                                                                  57                                                                                                                                                                                                                          


Chain I from PDB  Type:PROTEIN  Length:51
 aligned with IOVO_MELGA | P68390 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:51
                                   144       154       164       174       184 
           IOVO_MELGA   135 VDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC 185
               SCOP domains d1r0ri_ I: Ovomucoid domains                        SCOP domains
               CATH domains 1r0rI00 I:6-56  [code=3.30.60.30, no name defined]  CATH domains
               Pfam domains --Kazal_1-1r0rI01 I:8-56                            Pfam domains
         Sec.struct. author .........eee.....eee....ee.hhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------KAZAL_1  PDB: I:16-38  ------------------ PROSITE
                 Transcript --------------------------------------------------- Transcript
                 1r0r I   6 VDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC  56
                                    15        25        35        45        55
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Kazal (46)
(-)
Clan: no clan defined [family: Peptidase_S8] (104)

(-) Gene Ontology  (12, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (SUBT_BACLI | P00780)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain I   (IOVO_MELGA | P68390)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  1r0r
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 Related Entries

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

UniProtKB/Swiss-Prot
        IOVO_MELGA | P68390: 1cho 1cso 1ct0 1ct2 1ct4 1ds2 1ds3 1hja 1m8b 1m8c 1omt 1omu 1ppf 1sgd 1sge 1sgn 1sgp 1sgq 1sgr 1sgy 1tur 1tus 1yu6 1z7k 2gkr 2gkt 2gkv 2nu0 2nu1 2nu2 2nu3 2nu4 2sgd 2sge 2sgf 2sgp 2sgq 3sgb 3sgq
        SUBT_BACLI | P00780: 1af4 1av7 1avt 1be6 1be8 1bfk 1bfu 1c3l 1cse 1oyv 1sbc 1sca 1scb 1scd 1scn 1sel 1vsb 1yu6 2sec 2wuv 2wuw 3unx 3vsb 4c3u 4c3v

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1R0R)