Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  X-RAY STRUCTURAL AND BIOLOGICAL EVALUATION OF A SERIES OF POTENT AND HIGHLY SELECTIVE INHIBITORS OF HUMAN CORONAVIRUS PAPAIN-LIKE PROTEASES
 
Authors :  Y. M. Baez-Santos, A. Mesecar
Date :  28 Jan 14  (Deposition) - 23 Apr 14  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cov, Coronavirus, Hcov, Human Coronavirus, Sars, Severe Acute Respiratory Syndrome, Mers, Middle East Respiratory Syndrome, Plpro, Papain-Like Protease; Inhibitor, Complex, Dub, Deubiquitinating Enzyme, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. M. Baez-Santos, S. J. Barraza, M. W. Wilson, M. P. Agius, A. M. Mielech, N. M. Davis, S. C. Baker, S. D. Larsen, A. D. Mesecar
X-Ray Structural And Biological Evaluation Of A Series Of Potent And Highly Selective Inhibitors Of Human Coronavirus Papain-Like Proteases.
J. Med. Chem. V. 57 2393 2014
PubMed-ID: 24568342  |  Reference-DOI: 10.1021/JM401712T

(-) Compounds

Molecule 1 - PAPAIN-LIKE PROTEASE
    Chains: A, B
    EC Number: 3.4.19.12, 3.4.22.69
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: SARS CORONAVIRUS
    Organism Taxid: 228330
    Strain: URBANI
    Synonym: NON-STRUCTURAL PROTEIN 3, NSP3, PL2-PRO, PL-PRO, SARS CORONAVIRUS MAIN PROTEINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
1DMS3Ligand/IonDIMETHYL SULFOXIDE
2GOL1Ligand/IonGLYCEROL
3OCS2Mod. Amino AcidCYSTEINESULFONIC ACID
4S882Ligand/IonN-[(3-FLUOROPHENYL)METHYL]-1-[(1R)-1-NAPHTHALEN-1-YLETHYL]PIPERIDINE-4-CARBOXAMIDE
5ZN2Ligand/IonZINC ION
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
1DMS2Ligand/IonDIMETHYL SULFOXIDE
2GOL1Ligand/IonGLYCEROL
3OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
4S881Ligand/IonN-[(3-FLUOROPHENYL)METHYL]-1-[(1R)-1-NAPHTHALEN-1-YLETHYL]PIPERIDINE-4-CARBOXAMIDE
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2GOL-1Ligand/IonGLYCEROL
3OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
4S881Ligand/IonN-[(3-FLUOROPHENYL)METHYL]-1-[(1R)-1-NAPHTHALEN-1-YLETHYL]PIPERIDINE-4-CARBOXAMIDE
5ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:190 , CYS A:193 , CYS A:225 , CYS A:227binding site for residue ZN A 901
2AC2SOFTWARELEU A:163 , GLY A:164 , ASP A:165 , PRO A:249 , TYR A:265 , TYR A:269 , GLN A:270 , TYR A:274 , THR A:302 , DMS A:903 , MET B:209 , GLY B:210 , PRO B:248 , TYR B:269binding site for residue S88 A 902
3AC3SOFTWARELYS A:158 , LEU A:163 , TYR A:269 , S88 A:902 , HOH A:1057 , MET B:209binding site for residue DMS A 903
4AC4SOFTWAREGLN A:233 , VAL B:160 , GLU B:162binding site for residue GOL A 904
5AC5SOFTWAREGLU A:125 , ASN A:178 , SER A:240 , SER A:241 , HOH A:1046binding site for residue DMS A 905
6AC6SOFTWARECYS B:190 , CYS B:193 , CYS B:225 , CYS B:227binding site for residue ZN B 901
7AC7SOFTWAREMET A:209 , GLY A:210 , PRO A:248 , TYR A:269 , GLY B:164 , ASP B:165 , PRO B:249 , TYR B:265 , TYR B:269 , TYR B:274 , THR B:302binding site for residue S88 B 902
8AC8SOFTWAREGLY A:82 , SER A:86 , THR B:199 , HOH B:1022binding site for residue DMS B 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OW0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4OW0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OW0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OW0)

(-) Exons   (0, 0)

(no "Exon" information available for 4OW0)

(-) 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:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee......eeeeee....hhhhhh.ee....hhhhh.........eeee...hhhhhhhhhhhhh....hhhhhhhhhhhhhh.....ee..ee.......hhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhh........hhhhhhhhhhh.......eeeeeee.....eeeeeeehhhhheee...hhhhhhhheeee.....eeeeeeeeee..eeeeeeeeeeeeee.....eeeeeee....eeeeeeee...eeeee..eeeee.eeeeeeeeeeee..eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ow0 A   4 KTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTFFVLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNcYLSSVLLALQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLESAKRVLNVVCKHCGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPCVCGRDATQYLVQQESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSEYKGPVTDVFYKETSYTTTI 315
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313  
                                                                                                                                      112-OCS                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh....hhhhhhhhhhhhhh.....ee..ee.......hhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhh.....eeeeeeee...eeeeeeeehhhhheee...hhhhhhhheee.......eeeeeeeee..eeeeeeeeeeeeee.....eeeeeee....eeeeeeee...eeeee..eeeee.eeeeeeeeeeee..eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ow0 B  57 FVLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNcYLSSVLLALQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLESAKRVLNVVCKHCGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPCVCGRDATQYLVQQESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSEYKGPVTDVFYKETSYTTTIK 316
                                    66        76        86        96       106     | 116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316
                                                                                 112-OCS
   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 4OW0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OW0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OW0)

(-) Gene Ontology  (36, 36)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    DMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OCS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    S88  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ow0)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ow0
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  R1A_CVHSA | P0C6U8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.19.12
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  3.4.22.69
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  R1A_CVHSA | P0C6U8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        R1A_CVHSA | P0C6U8: 1o5s 1p76 1p9t 1pa5 1puk 1q1x 1q2w 1qz8 1uj1 1uk2 1uk3 1uk4 1uw7 1wof 1ysy 1z1i 1z1j 2a5a 2a5i 2a5k 2acf 2ahm 2aj5 2alv 2amd 2amq 2bx3 2bx4 2c3s 2d2d 2duc 2fav 2fe8 2fyg 2g1f 2g9t 2ga6 2gdt 2gri 2gt7 2gt8 2gtb 2gx4 2gz7 2gz8 2gz9 2h2z 2hob 2hsx 2idy 2jzd 2jze 2jzf 2k87 2kaf 2kqv 2kqw 2kys 2liz 2op9 2ozk 2pwx 2q6g 2qc2 2qcy 2qiq 2rhb 2rnk 2w2g 2wct 2z3c 2z3d 2z3e 2z94 2z9g 2z9j 2z9k 2z9l 2zu4 2zu5 3atw 3avz 3aw0 3aw1 3d62 3e91 3e9s 3ea7 3ea8 3ea9 3eaj 3ee7 3f9e 3f9f 3f9g 3f9h 3fzd 3iwm 3m3s 3m3t 3m3v 3mj5 3r24 3sn8 3sna 3snb 3snc 3snd 3sne 3szn 3tit 3tiu 3tns 3tnt 3v3m 3vb3 3vb4 3vb5 3vb6 3vb7 4hi3 4m0w 4mds 4mm3 4ovz 5f22

(-) Related Entries Specified in the PDB File

4ovz