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(-) Description

Title :  REFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C COMPLEX AT 2.1-ANGSTROMS RESOLUTION
 
Authors :  D. Yamamoto, K. Matsumoto, H. Ohishi, T. Ishida, M. Inoue, K. Kitamura,
Date :  14 May 91  (Deposition) - 15 Apr 93  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Sulfhydryl Proteinase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Yamamoto, K. Matsumoto, H. Ohishi, T. Ishida, M. Inoue, K. Kitamura H. Mizuno
Refined X-Ray Structure Of Papain. E-64-C Complex At 2. 1-A Resolution.
J. Biol. Chem. V. 266 14771 1991
PubMed-ID: 1860874
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PAPAIN
    Chains: A
    EC Number: 3.4.22.2
    Engineered: YES
    Organism Common: PAPAYA
    Organism Scientific: CARICA PAPAYA
    Organism Taxid: 3649

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1E6C1Ligand/IonN-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE
2MOH14Ligand/IonMETHANOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:19 , GLY A:23 , SER A:24 , CYS A:25 , TYR A:61 , ASN A:64 , GLY A:65 , GLY A:66 , VAL A:157 , ASP A:158 , MOH A:216 , HOH A:232 , HOH A:404BINDING SITE FOR RESIDUE E6C A 213
02AC2SOFTWAREARG A:41 , THR A:42 , HOH A:283BINDING SITE FOR RESIDUE MOH A 214
03AC3SOFTWAREGLY A:23BINDING SITE FOR RESIDUE MOH A 215
04AC4SOFTWAREVAL A:110 , ARG A:111 , E6C A:213BINDING SITE FOR RESIDUE MOH A 216
05AC5SOFTWAREGLY A:20 , HOH A:231 , HOH A:232BINDING SITE FOR RESIDUE MOH A 218
06AC6SOFTWAREARG A:8BINDING SITE FOR RESIDUE MOH A 219
07AC7SOFTWAREARG A:41 , LYS A:211BINDING SITE FOR RESIDUE MOH A 220
08AC8SOFTWAREILE A:148 , ASN A:169 , LYS A:190BINDING SITE FOR RESIDUE MOH A 221
09AC9SOFTWARELEU A:45BINDING SITE FOR RESIDUE MOH A 222
10BC1SOFTWARETYR A:78 , HOH A:259BINDING SITE FOR RESIDUE MOH A 223
11BC2SOFTWAREASN A:127 , HOH A:230 , HOH A:292BINDING SITE FOR RESIDUE MOH A 224
12BC3SOFTWARELYS A:100 , TRP A:177 , THR A:179 , GLY A:180BINDING SITE FOR RESIDUE MOH A 225
13BC4SOFTWAREVAL A:133BINDING SITE FOR RESIDUE MOH A 226

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:63
2A:56 -A:95
3A:153 -A:200

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:151 -Pro A:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PE6)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.PAPA1_CARPA152-163  1A:19-30
2THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.PAPA1_CARPA290-300  1A:157-167
3THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.PAPA1_CARPA303-322  1A:170-189

(-) Exons   (0, 0)

(no "Exon" information available for 1PE6)

(-) 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 A from PDB  Type:PROTEIN  Length:212
 aligned with PAPA1_CARPA | P00784 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:212
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343  
          PAPA1_CARPA   134 IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 345
               SCOP domains d1pe6a_ A: Papain                                                                                                                                                                                                    SCOP domains
               CATH domains 1pe6A00 A:1-212 Cysteine proteinases                                                                                                                                                                                 CATH domains
               Pfam domains Peptidase_C1-1pe6A01 A:1-210                                                                                                                                                                                      -- Pfam domains
         Sec.struct. author ....eee................hhhhhhhhhhhhhhhhhhh.......hhhhhhhh.........hhhhhhhhhhhh.............................eeeeee...hhhhhhhhhhh..eeeee...hhhhh...............eeeeeeeeee..eeeeee.........eeeeeee..............eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE--THIOL_PROTEASE_ASN  ----------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pe6 A   1 IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
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  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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_CA (169)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PAPA1_CARPA | P00784)
molecular function
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    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:0097655    serpin family protein binding    Interacting selectively and non-covalently with any member of the serpin protein family (serine protease inhibitors or classified inhibitor family I4). Serpins are a broadly distributed family of protease inhibitors that use a conformational change to inhibit target enzymes. They are central in controlling many important proteolytic cascades. The majority of serpins inhibit serine proteases, but serpins that inhibit caspases and papain-like cysteine proteases have also been identified. Rarely, serpins perform a non-inhibitory function; for example, several human serpins function as hormone transporters and certain serpins function as molecular chaperones or tumor suppressors.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  3.4.22.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        PAPA1_CARPA | P00784: 1bp4 1bqi 1cvz 1eff 1khp 1khq 1pad 1pip 1pop 1ppd 1ppn 1ppp 1stf 2cio 2pad 3e1z 3ima 3lfy 3tnx 3usv 4kp9 4pad 4qrg 4qrv 4qrx 5pad 6pad 9pap

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1PE6)