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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF DELTA-CHYMOTRYPSIN BOUND TO A PEPTIDYL CHLOROMETHYL KETONE INHIBITOR
 
Authors :  A. Mac Sweeney, G. Birrane, M. A. Walsh, T. O'Connell, J. P. G. Malthous
Date :  10 Dec 99  (Deposition) - 03 May 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Biol. Unit 2:  A,B,E  (1x)
Biol. Unit 3:  C,D,F  (1x)
Keywords :  Delta-Chymotrypsin, Peptidic Inhibior, Chloromethyl Ketone, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Mac Sweeney, G. Birrane, M. A. Walsh, T. O'Connell, J. P. Malthouse T. M. Higgins
Crystal Structure Of Delta-Chymotrypsin Bound To A Peptidyl Chloromethyl Ketone Inhibitor.
Acta Crystallogr. , Sect. D V. 56 280 2000
PubMed-ID: 10713514  |  Reference-DOI: 10.1107/S0907444999016583

(-) Compounds

Molecule 1 - THROMBIN LIGHT CHAIN
    ChainsA, C
    EC Number3.4.21.1
    FragmentRESIDUES 1-13
    OrganPANCREAS
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
 
Molecule 2 - THROMBIN HEAVY CHAIN
    ChainsB, D
    EC Number3.4.21.1
    FragmentRESIDUES 16-245
    OrganPANCREAS
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
 
Molecule 3 - PEPTIDIC INHIBITOR
    ChainsE, F
    EngineeredYES
    Other DetailsTHIS SEQUENCE WAS SYNTHETICALLY CONSTRUCTED
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)
Biological Unit 2 (1x)AB  E 
Biological Unit 3 (1x)  CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
10QE2Mod. Amino AcidCHLOROMETHANE
2CL1Ligand/IonCHLORIDE ION
3HPH2Mod. Amino Acid(2S)-2-AMINO-3-PHENYLPROPANE-1,1-DIOL
4PHQ2Mod. Amino AcidBENZYL CHLOROCARBONATE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
10QE1Mod. Amino AcidCHLOROMETHANE
2CL-1Ligand/IonCHLORIDE ION
3HPH1Mod. Amino Acid(2S)-2-AMINO-3-PHENYLPROPANE-1,1-DIOL
4PHQ1Mod. Amino AcidBENZYL CHLOROCARBONATE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
10QE1Mod. Amino AcidCHLOROMETHANE
2CL-1Ligand/IonCHLORIDE ION
3HPH1Mod. Amino Acid(2S)-2-AMINO-3-PHENYLPROPANE-1,1-DIOL
4PHQ1Mod. Amino AcidBENZYL CHLOROCARBONATE
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
10QE1Mod. Amino AcidCHLOROMETHANE
2CL-1Ligand/IonCHLORIDE ION
3HPH1Mod. Amino Acid(2S)-2-AMINO-3-PHENYLPROPANE-1,1-DIOL
4PHQ1Mod. Amino AcidBENZYL CHLOROCARBONATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:90 , HOH B:504 , GLY D:59BINDING SITE FOR RESIDUE CL
2AC2SOFTWAREHIS B:57 , LEU B:97 , THR B:98 , LYS B:175 , SER B:190 , MET B:192 , GLY B:193 , SER B:195 , SER B:214 , TRP B:215 , GLY B:216 , SER B:217 , HOH B:453 , SER D:218 , HOH E:441 , HOH F:294BINDING SITE FOR CHAIN E OF PEPTIDIC INHIBITOR
3AC3SOFTWAREMET B:192 , SER B:218 , HIS D:57 , LEU D:97 , THR D:98 , LYS D:175 , SER D:190 , GLY D:193 , SER D:195 , SER D:214 , TRP D:215 , GLY D:216 , SER D:217 , HOH D:275 , HOH D:290 , HOH D:386 , HOH E:441 , HOH F:294 , HOH F:383BINDING SITE FOR CHAIN F OF PEPTIDIC INHIBITOR

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:1 -B:122
2B:42 -B:58
3B:136 -B:201
4B:168 -B:182
5B:191 -B:220
6C:1 -D:122
7D:42 -D:58
8D:136 -D:201
9D:168 -D:182
10D:191 -D:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DLK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CTRA_BOVIN16-243
 
  2B:16-243
D:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CTRA_BOVIN53-58
 
  2B:53-58
D:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CTRA_BOVIN189-200
 
  2B:189-200
D:189-200
Biological Unit 1 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CTRA_BOVIN16-243
 
  2B:16-243
D:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CTRA_BOVIN53-58
 
  2B:53-58
D:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CTRA_BOVIN189-200
 
  2B:189-200
D:189-200
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CTRA_BOVIN16-243
 
  1B:16-243
-
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CTRA_BOVIN53-58
 
  1B:53-58
-
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CTRA_BOVIN189-200
 
  1B:189-200
-
Biological Unit 3 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CTRA_BOVIN16-243
 
  1-
D:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CTRA_BOVIN53-58
 
  1-
D:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CTRA_BOVIN189-200
 
  1-
D:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 1DLK)

(-) 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:13
 aligned with CTRA_BOVIN | P00766 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:13
                                    10   
           CTRA_BOVIN     1 CGVPAIQPVLSGL  13
               SCOP domains d1dlk.1 A:,B: SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                PROSITE (1) ------------- PROSITE (1)
                PROSITE (2) ------------- PROSITE (2)
                 Transcript ------------- Transcript
                 1dlk A   1 CGVPAIQPVLSGL  13
                                    10   

Chain B from PDB  Type:PROTEIN  Length:230
 aligned with CTRA_BOVIN | P00766 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:230
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245
           CTRA_BOVIN    16 IVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRYTNANTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN 245
               SCOP domains d1dlk.1 A:,B: (alpha,gamma)-chymotrypsin(ogen)                                                                                                                                                                                         SCOP domains
               CATH domains 1dlkB01     1dlkB02 B:28-120,B:233-243 Trypsin-like serine proteases                                     1dlkB01 B:16-27,B:121-232 Trypsin-like serine proteases                                                         1dlkB02    -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeee....eeeehhhhh.....eeee............eeeeeeeeee.............eeeee..........................eeeeee...............eeeeeeeehhhhhhhhhhhhh...eeeee.............eeeeee..eeeeeeeeee.........eeeeeehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 16-243                                                                                                                                                                                          -- PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dlk B  16 IVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRYTNANTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN 245
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245

Chain C from PDB  Type:PROTEIN  Length:13
 aligned with CTRA_BOVIN | P00766 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:13
                                    10   
           CTRA_BOVIN     1 CGVPAIQPVLSGL  13
               SCOP domains d1dlk.2 C:,D: SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                PROSITE (1) ------------- PROSITE (1)
                PROSITE (2) ------------- PROSITE (2)
                 Transcript ------------- Transcript
                 1dlk C   1 CGVPAIQPVLSGL  13
                                    10   

Chain D from PDB  Type:PROTEIN  Length:230
 aligned with CTRA_BOVIN | P00766 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:230
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245
           CTRA_BOVIN    16 IVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRYTNANTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN 245
               SCOP domains d1dlk.2 C:,D: (alpha,gamma)-chymotrypsin(ogen)                                                                                                                                                                                         SCOP domains
               CATH domains 1dlkD01     1dlkD02 D:28-120,D:233-243 Trypsin-like serine proteases                                     1dlkD01 D:16-27,D:121-232 Trypsin-like serine proteases                                                         1dlkD02    -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeeeee..eeeehhhhh.....eeee............eeeeeeeeee.............eeeee..........................eeeeee...............eeeeee..hhhhhhhhhhhhh...eeeee.............eeeeee..eeeeeeeeee.........eeeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: D:16-243 UniProt: 16-243                                                                                                                                                                                          -- PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dlk D  16 IVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRYTNANTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN 245
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245

Chain E 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
                 1dlk E   1 xGGxx   5
                            |  ||
                            1-PHQ
                               4-HPH
                                5-0QE

Chain F 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
                 1dlk F   1 xGGxx   5
                            |  ||
                            |  ||
                            1-PHQ
                               4-HPH
                                5-0QE

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a1dlkB02B:28-120,B:233-243
1b1dlkD02D:28-120,D:233-243
1c1dlkB01B:16-27,B:121-232
1d1dlkD01D:16-27,D:121-232

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DLK)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CTRA_BOVIN | P00766)
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: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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0007586    digestion    The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CTRA_BOVIN | P007661ab9 1acb 1afq 1ca0 1cbw 1cgi 1cgj 1chg 1cho 1ex3 1gcd 1gct 1gg6 1ggd 1gha 1ghb 1gl0 1gl1 1gmc 1gmd 1gmh 1hja 1k2i 1mtn 1n8o 1oxg 1p2m 1p2n 1p2o 1p2q 1t7c 1t8l 1t8m 1t8n 1t8o 1vgc 1yph 2cga 2cha 2gch 2gct 2gmt 2p8o 2vgc 2y6t 3bg4 3gch 3gct 3ru4 3t62 3vgc 4cha 4gch 4q2k 4vgc 5cha 5gch 5j4q 5j4s 6cha 6gch 7gch 8gch

(-) Related Entries Specified in the PDB File

1gch REFINED CRYSTAL STRUCTURE OF GAMMA-CHYMOTRYPSIN AT 1.9 ANGSTROMS RESOLUTION