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(-) Description

Title :  CRYSTAL STRUCTURE OF PAPAIN MODIFY BY ACHIRAL RU(II)COMPLEX
 
Authors :  M. V. Cherrier, N. Madern, P. Amara, M. Salmain, J. C. Fontecilla-Camps
Date :  13 May 13  (Deposition) - 25 Jun 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Artificial Metalloenzyme, Hydrolase, Achiral Ru(Ii) Complex, Hydroxylations (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. V. Cherrier, N. Madern, P. Amara, M. Salmain, J. C. Fontecilla-Camp
X-Ray Structural Evidence For Unusual Radical Oh-Based Tyrosine Hydroxylations In An Achiral Ru(Ii)-Papain Complex
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PAPAIN
    Chains: A
    EC Number: 3.4.22.2
    Organism Common: MAMON
    Organism Scientific: CARICA PAPAYA
    Organism Taxid: 3649
    Synonym: PAPAYA PROTEINASE I, PPI
 
Molecule 2 - PAPAIN
    Chains: B
    EC Number: 3.4.22.2
    Organism Common: MAMON
    Organism Scientific: CARICA PAPAYA
    Organism Taxid: 3649
    Synonym: PAPAYA PROTEINASE I, PPI

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 17)

Asymmetric/Biological Unit (9, 17)
No.NameCountTypeFull Name
1ACT9Ligand/IonACETATE ION
2BU11Ligand/Ion1,4-BUTANEDIOL
3CL1Ligand/IonCHLORIDE ION
4NA1Ligand/IonSODIUM ION
5OMX1Mod. Amino Acid(BETAR)-BETA-HYDROXY-L-TYROSINE
6SO41Ligand/IonSULFATE ION
7TXY1Mod. Amino Acid3-[(5S)-4,5-DIHYDROXYCYCLOHEXA-1,3-DIEN-1-YL]-L-ALANINE
8YXX1Ligand/IonCHLORO(1-{5-[DI(PYRIDIN-2-YL-KAPPAN)AMINO]PENTYL}PYRROLIDINE-2,5-DIONE)RUTHENIUM
9YXZ1Ligand/IonCHLORO[N,N-DI(PYRIDIN-2-YL-KAPPAN)PENTANE-1,5-DIAMINE]RUTHENIUM

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:19 , GLY A:23 , SER A:24 , CYS A:25 , ASP A:158 , HIS A:159 , YXZ A:305BINDING SITE FOR RESIDUE BU1 A 301
02AC2SOFTWAREARG A:93 , TYR A:94 , ASN A:169 , LYS A:190BINDING SITE FOR RESIDUE CL A 302
03AC3SOFTWAREASN A:18 , GLY A:20 , HOH A:508BINDING SITE FOR RESIDUE ACT A 303
04AC4SOFTWARETXY A:67 , VAL A:157 , HOH A:513 , HOH A:561BINDING SITE FOR RESIDUE ACT A 304
05AC5SOFTWAREOMX A:61 , GLY A:65 , GLY A:66 , TXY A:67 , BU1 A:301 , PRO B:115 , TYR B:116 , NA B:309BINDING SITE FOR RESIDUE YXZ A 305
06AC6SOFTWARETYR A:82 , ASN A:84 , HOH A:552BINDING SITE FOR RESIDUE ACT A 306
07AC7SOFTWAREPRO A:115 , TYR A:116 , CYS B:25 , TRP B:26 , TYR B:61 , GLY B:65 , GLY B:66 , TYR B:67 , ASP B:158 , ACT B:308 , HOH B:517BINDING SITE FOR RESIDUE YXX B 301
08AC8SOFTWAREGLN A:73 , GLY A:109 , VAL A:110 , ARG A:111 , GLY B:109 , VAL B:110 , ARG B:111 , HOH B:545BINDING SITE FOR RESIDUE SO4 B 302
09AC9SOFTWARETYR B:197 , NA B:309BINDING SITE FOR RESIDUE ACT B 303
10BC1SOFTWAREVAL B:157 , HOH B:488 , HOH B:497 , HOH B:558BINDING SITE FOR RESIDUE ACT B 304
11BC2SOFTWAREALA A:137 , GLY A:138 , LYS A:139 , TYR B:103 , ALA B:104 , HOH B:459BINDING SITE FOR RESIDUE ACT B 305
12BC3SOFTWAREHOH B:560BINDING SITE FOR RESIDUE ACT B 306
13BC4SOFTWAREARG B:145 , HOH B:561BINDING SITE FOR RESIDUE ACT B 307
14BC5SOFTWAREARG B:8 , TYR B:61 , GLU B:183 , ARG B:188 , YXX B:301 , HOH B:454BINDING SITE FOR RESIDUE ACT B 308
15BC6SOFTWAREYXZ A:305 , ACT B:303BINDING SITE FOR RESIDUE NA B 309

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:63
2A:56 -A:95
3A:153 -A:200
4B:22 -B:63
5B:56 -B:95
6B:153 -B:200

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:151 -Pro A:152
2Gly B:151 -Pro B:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KP9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KP9)

(-) Exons   (0, 0)

(no "Exon" information available for 4KP9)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh...............................hhhhhh.......eeee....hhhhhhhhhhhh.eeeee...hhhhhhh...ee.........eeeeeeeee..eeeee...........eeeee.......hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kp9 A   1 IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSyGCNGGyYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 212
                                    10        20        30        40        50        60|     | 69        79        89        99       109       119       129       139       149       159       169       179       189       199       209   
                                                                                       61-OMX |                                                                                                                                                  
                                                                                             67-TXY                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhh...hhhhh.........hhhhhh.......eeeee...hhhhhhhhhh...eeeee...hhhhhhh...ee.........eeeeeeeee..eeeee...........eeeee.......hhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kp9 B   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)
  - → 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  (0, 0)

(no "SCOP Domain" information available for 4KP9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KP9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KP9)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:151 - Pro A:152   [ RasMol ]  
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  PAPA1_CARPA | P00784
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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 1pe6 1pip 1pop 1ppd 1ppn 1ppp 1stf 2cio 2pad 3e1z 3ima 3lfy 3tnx 3usv 4pad 4qrg 4qrv 4qrx 5pad 6pad 9pap

(-) Related Entries Specified in the PDB File

1ppp