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(-) Description

Title :  CRYSTAL STRUCTURE OF CATHEPSIN C IN COMPLEX WITH DIPEPTIDE SUBSTRATES
 
Authors :  B. Zhao, A. Smallwood, N. Concha
Date :  13 Jan 14  (Deposition) - 25 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.52
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Beta Barrel, Dipeptidyl Aminopeptidase I, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. K. Rubach, G. Cui, J. L. Schneck, A. N. Taylor, B. Zhao, A. Smallwood, N. Nevins, D. Wisnoski, S. H. Thrall, T. D. Meek
The Amino-Acid Substituents Of Dipeptide Substrates Of Cathepsin C Can Determine The Rate-Limiting Steps Of Catalysis.
Biochemistry V. 51 7551 2012
PubMed-ID: 22928782  |  Reference-DOI: 10.1021/BI300719B

(-) Compounds

Molecule 1 - DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
    Chains: A
    EC Number: 3.4.14.1
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Gene: CPPI, CTSC
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CATHEPSIN C, CATHEPSIN J, DIPEPTIDYL PEPTIDASE I, DPP-I, DPPI, DIPEPTIDYL TRANSFERASE
 
Molecule 2 - DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
    Chains: B
    EC Number: 3.4.14.1
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Gene: CTSC, CPPI
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CATHEPSIN C, CATHEPSIN J, DIPEPTIDYL PEPTIDASE I, DPP-I, DPPI, DIPEPTIDYL TRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 11)

Asymmetric Unit (6, 11)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3GLY1Mod. Amino AcidGLYCINE
4LYS1Mod. Amino AcidLYSINE
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO41Ligand/IonSULFATE ION
Biological Unit 1 (5, 20)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO8Ligand/Ion1,2-ETHANEDIOL
3GLY2Mod. Amino AcidGLYCINE
4LYS2Mod. Amino AcidLYSINE
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO42Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:1 , CYS A:234 , GLY A:276 , GLY A:277 , PHE A:278 , LYS A:502 , HOH A:768 , ASN B:380 , HIS B:381 , ALA B:382BINDING SITE FOR RESIDUE GLY A 501
02AC2SOFTWAREASP A:1 , GLN A:228 , GLY A:232 , CYS A:234 , GLU A:275 , GLY A:501 , HOH A:862 , ASN B:380BINDING SITE FOR RESIDUE LYS A 502
03AC3SOFTWAREEDO A:510 , HOH A:697 , HOH A:797 , HOH A:798BINDING SITE FOR RESIDUE SO4 A 503
04AC4SOFTWARELEU A:207 , THR A:209 , ASN A:252 , NAG A:505BINDING SITE FOR RESIDUE NAG A 504
05AC5SOFTWARENAG A:504BINDING SITE FOR RESIDUE NAG A 505
06AC6SOFTWAREASN A:5 , ASN A:65 , HOH A:667 , PHE B:376BINDING SITE FOR RESIDUE NAG A 506
07AC7SOFTWAREPHE A:278 , PRO A:279 , TYR A:280 , TYR A:323BINDING SITE FOR RESIDUE CL A 507
08AC8SOFTWAREGLN A:36 , GLN A:228 , ALA A:229 , CYS A:231 , TRP B:405BINDING SITE FOR RESIDUE EDO A 508
09AC9SOFTWARECYS A:267 , GLN A:269 , PHE A:290 , HOH A:801 , HOH A:847BINDING SITE FOR RESIDUE EDO A 509
10BC1SOFTWAREVAL A:265 , SER A:266 , SER A:268 , GLY A:273 , SO4 A:503 , HOH A:724BINDING SITE FOR RESIDUE EDO A 510
11BC2SOFTWAREHIS A:59 , PHE A:60 , THR A:61 , VAL A:71 , TYR A:280 , HOH A:673 , HOH A:762BINDING SITE FOR RESIDUE EDO A 511

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:6 -A:94
2A:30 -A:112
3A:231 -A:274
4A:267 -A:307
5A:297 -A:313

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:46 -Leu A:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OEM)

(-) 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:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhheeeeeeeeeeee....hhhhh..eeeeeeeeee...eee.....eeeeeee...eeeeee..eeeeeeeeeeee..eeeeeeeee..eeeee.....eeeeeeee......ee....................hhhhhhhhhhhhhhhhhhh........hhhhhhhhh...hhhhh.hhhhhhhhhhhhh...hhhhh...................eeeeee........hhhhhhhhhhhhh.eeeee..hhhhhh....ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4oem A   1 DTPANCTYLDLLGTWVFQVGSSGSQRDVNCSVMGPQEKKVVVYLQKLDTAYDDLGNSGHFTIIYNQGFEIVLNDYKWFAFFKYKEEGSKVTTYCNETMTGWVHDVLGRNWACFTGKKVHLPTSWDWRNVHGINFVSPVRNQASCGSCYSFASMGMLEARIRILTNNSQTPILSPQEVVSCSQYAQGCEGGFPYLIAGKYAQDFGLVEEACFPYTGTDSPCKMKEDCFRYYSSEYHYVGGFYGGCNEALMKLELVHHGPMAVAFEVYDDFLHYKKGIYHHTGK 502
                                    10        20        30        40        50        60        70        80        90       100       110       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367| 
                                                                                                                                               118|                                                                                                                                                              367| 
                                                                                                                                                206                                                                                                                                                               501 


Chain B from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee......eeeeee...........eeeee...hhhhh....eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4oem B 373 FNPFELTNHAVLLVGYGTDSASGMDYWIVKNSWGTGWGENGYFRIRRGTDECAIESIAVAATPIPKLE 440
                                   382       392       402       412       422       432
   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 4OEM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

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    Lys A:46 - Leu A:47   [ RasMol ]  
 
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 Related Entries

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        CATC_HUMAN | P53634: 1k3b 2djf 2djg 3pdf 4cdc 4cdd 4cde 4cdf 4oel

(-) Related Entries Specified in the PDB File

4oel