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(-) Description

Title :  CRYSTAL STRUCTURES OF GLUTARYL 7-AMINOCEPHALOSPORANIC ACID ACYLASE: INSIGHT INTO AUTOPROTEOLYTIC ACTIVATION
 
Authors :  J. K. Kim, I. S. Yang, S. Rhee, Z. Dauter, Y. S. Lee, S. S. Park, K. H. Kim
Date :  11 Mar 03  (Deposition) - 11 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Glutaryl 7-Aminocephalosporanic Acid, N-Terminal Nucleophile (Ntn) Hydrolases, Glutaryl 7- Aminocephalosporanic Acid Acylase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. K. Kim, I. S. Yang, S. Rhee, Z. Dauter, Y. S. Lee, S. S. Park, K. H. Kim
Crystal Structures Of Glutaryl 7-Aminocephalosporanic Acid Acylase: Insight Into Autoproteolytic Activation
Biochemistry V. 42 4084 2003
PubMed-ID: 12680762  |  Reference-DOI: 10.1021/BI027181X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTARYL 7-AMINOCEPHALOSPORANIC ACID ACYLASE
    ChainsA, C
    EC Number3.5.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET23A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentALPHA SUBUNIT, RESIDUES 1-160
    Organism ScientificPSEUDOMONAS SP. SY-77-1
    Organism Taxid269086
    StrainGK16
 
Molecule 2 - GLUTARYL ACYLASE
    ChainsB, D
    EC Number3.5.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET23A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentBETA SUBUNIT, RESIDUES 1-522
    Organism ScientificPSEUDOMONAS SP. SY-77-1
    Organism Taxid269086
    StrainGK16
    SynonymGLUTARYL 7-AMINOCEPHALOSPORANIC ACID ACYLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 26)

Asymmetric Unit (2, 26)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 13)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 13)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:318 , SER B:1 , PRO B:22 , TYR B:33 , ARG B:57 , PHE B:58 , ASN B:68 , THR B:69 , VAL B:70 , PHE B:177 , HOH B:2389BINDING SITE FOR RESIDUE EDO B 2001
2AC2SOFTWARESER D:1 , ARG D:57 , PHE D:58 , ASN D:68 , THR D:69 , PHE D:177 , HOH D:2458BINDING SITE FOR RESIDUE EDO D 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OR0)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Leu A:130 -Pro A:131
2Trp B:252 -Pro B:253
3Thr B:378 -Pro B:379
4Thr B:465 -Pro B:466
5Leu C:130 -Pro C:131
6Trp D:252 -Pro D:253
7Thr D:378 -Pro D:379
8Thr D:465 -Pro D:466

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OR0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OR0)

(-) Exons   (0, 0)

(no "Exon" information available for 1OR0)

(-) 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:153
 aligned with G7AC_PSEU7 | P07662 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:153
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186   
           G7AC_PSEU7    37 APIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPEVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEG 189
               SCOP domains d1or0.1 A:,B: Cephalosporin acylase                                                                                                                       SCOP domains
               CATH domains 1or0A00 A:8-160 Penicillin Amidohydrolase, domain 1                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1or0 A   8 APIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPDVRQVLPVSGADVVAHAHRLmNFLYVASPGRTLGEG 160
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157   
                                                                                                                                                                   145-MSE           

Chain B from PDB  Type:PROTEIN  Length:521
 aligned with G7AC_PSEU7 | P07662 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:521
                                   208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718 
           G7AC_PSEU7   199 SNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERPQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNFK 719
               SCOP domains d1or0.1 A:,B: Cephalosporin acylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1or0B01 B:1-75,B:142-267,B:451-508                                         1or0B03 B:76-141  [code=2.30.120.10, no name defined]             1or0B01 B:1-75,B:142-267,B:451-508 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                 --1or0B02 B:270-450  [code=1.10.1400.10, no name defined]                                                                                                                              1or0B01 B:1-75,B:142-267,B:451-508                        ------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhh.....eeeee.eee..hhhh.eeeeeee....eeeeeee.......eee...eeeeee......eeeee..ee..eeee..eee.....eeeeeee.....eeeeeee........eee.....eeeeee......hhhhhhhhhhh..hhhhhhhhhh.......eeeeee....eeeee..........hhhhhhh.ee..hhhhh.....hhhhh.eee.....eee...............hhhhh..........hhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhhhh.........eee...........eee.hhhhhhhhhhhhhhhhhhhhh....hhhhhheeee..eeee....hhhhh....eee..........eeeee.eeeeee.....eeeeee...............hhhhhh....ee...hhhhhhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1or0 B   1 SNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRmGITNTVNGmVGATNYRLTLQDGGYLYDGQVRPFERPQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGmLEQYFDmITADSFDDYEAALARmQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLmSENDDLTLERFmALQLSHRAVmADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRmILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAmIEFSTPVRAYGLmSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNFK 521
                                    10        20        30        40        50        60   |    70  |     80        90       100       110       120       130       140       150     | 160       170 |     180       190       200       210       220       230       240       250       260       270       280 |     290   |   300   |   310       320       330       340       350       360       370       380       390       400       410     | 420       430       440       450       460       470  |    480       490       500       510       520 
                                                                                          64-MSE   73-MSE                                                                     149-MSE  |             172-MSE                                                                                                       282-MSE     294-MSE   304-MSE                                                                                                         416-MSE                                     460-MSE      473-MSE                                            
                                                                                                                                                                                     156-MSE                                                                                                                                                                                                                                                                                                                                                                         

Chain C from PDB  Type:PROTEIN  Length:152
 aligned with G7AC_PSEU7 | P07662 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:152
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187  
           G7AC_PSEU7    38 PIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPEVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEG 189
               SCOP domains d1or0.2 C:,D: Cephalosporin acylase                                                                                                                      SCOP domains
               CATH domains 1or0C00 C:9-160 Penicillin Amidohydrolase, domain 1                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1or0 C   9 PIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPDVRQVLPVSGADVVAHAHRLmNFLYVASPGRTLGEG 160
                                    18        28        38        48        58        68        78        88        98       108       118       128       138      |148       158  
                                                                                                                                                                  145-MSE           

Chain D from PDB  Type:PROTEIN  Length:521
 aligned with G7AC_PSEU7 | P07662 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:521
                                   208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718 
           G7AC_PSEU7   199 SNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERPQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNFK 719
               SCOP domains d1or0.2 C:,D: Cephalosporin acylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1or0D01 D:1-75,D:142-267,D:451-508                                         1or0D03 D:76-141  [code=2.30.120.10, no name defined]             1or0D01 D:1-75,D:142-267,D:451-508 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                 --1or0D02 D:270-450  [code=1.10.1400.10, no name defined]                                                                                                                              1or0D01 D:1-75,D:142-267,D:451-508                        ------------- CATH domains
           Pfam domains (1) Penicil_amidase-1or0D01 D:1-514                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   ------- Pfam domains (1)
           Pfam domains (2) Penicil_amidase-1or0D02 D:1-514                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   ------- Pfam domains (2)
           Pfam domains (3) Penicil_amidase-1or0D03 D:1-514                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   ------- Pfam domains (3)
           Pfam domains (4) Penicil_amidase-1or0D04 D:1-514                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   ------- Pfam domains (4)
         Sec.struct. author .eeeee.hhhh.....eeeee.eee..hhhh.eeeeeee....eeeeeee.......eee...eeeeee......eeeee..ee..eeee..eee.....eeeeeee.....eeeeeee........eee.....eeeeee......hhhhhhhhhhh..hhhhhhhhhh.......eeeeee....eeeee..........hhhhhhh.ee..hhhhh.....hhhhh.eee.....eee...............hhhhh..........hhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhh.........eee...........eee.hhhhhhhhhhhhhhhhhhhhh....hhhhhheeee..eeee....hhhhh....eee..........eeeee.eeeeee.....eeeeee...............hhhhhh....ee...hhhhhhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1or0 D   1 SNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRmGITNTVNGmVGATNYRLTLQDGGYLYDGQVRPFERPQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGmLEQYFDmITADSFDDYEAALARmQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLmSENDDLTLERFmALQLSHRAVmADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRmILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAmIEFSTPVRAYGLmSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNFK 521
                                    10        20        30        40        50        60   |    70  |     80        90       100       110       120       130       140       150     | 160       170 |     180       190       200       210       220       230       240       250       260       270       280 |     290   |   300   |   310       320       330       340       350       360       370       380       390       400       410     | 420       430       440       450       460       470  |    480       490       500       510       520 
                                                                                          64-MSE   73-MSE                                                                     149-MSE  |             172-MSE                                                                                                       282-MSE     294-MSE   304-MSE                                                                                                         416-MSE                                     460-MSE      473-MSE                                            
                                                                                                                                                                                     156-MSE                                                                                                                                                                                                                                                                                                                                                                         

   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, 2)

Asymmetric Unit

(-) CATH Domains  (4, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: NTN (93)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (G7AC_PSEU7 | P07662)
molecular function
    GO:0033968    glutaryl-7-aminocephalosporanic-acid acylase activity    Catalysis of the reaction: (7R)-7-(4-carboxybutanamido)cephalosporanate + H2O = (7R)-7-aminocephalosporanate + glutarate.
    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:0016811    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        G7AC_PSEU7 | P076621gk0 1gk1 2adv 2ae3 2ae4 2ae5 3s8r

(-) Related Entries Specified in the PDB File

1oqz 1OQZ CONTAINS THE SAME PROTEIN COMPLEXED WITH 4 CHAINS