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(-) Description

Title :  CATALYTICALLY INACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH SUBSTRATE
 
Authors :  J. Phan, A. Zdanov, A. G. Evdokimov, J. E. Tropea, H. K. Peters Iii, R. B. M. Li, A. Wlodawer, D. S. Waugh
Date :  28 May 02  (Deposition) - 27 Nov 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A,B,C,D  (4x)
Biol. Unit 4:  A,B,C,D  (2x)
Biol. Unit 5:  A,B,C,D  (1x)
Keywords :  Beta Barrel, Protein-Peptide Complex, Chymotrypsin-Like Cystein Protease, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Phan, A. Zdanov, A. G. Evdokimov, J. E. Tropea, H. K. Peters Iii, R. B. Kapust, M. Li, A. Wlodawer, D. S. Waugh
Structural Basis For The Substrate Specificity Of Tobacco Etch Virus Protease.
J. Biol. Chem. V. 277 50564 2002
PubMed-ID: 12377789  |  Reference-DOI: 10.1074/JBC.M207224200

(-) Compounds

Molecule 1 - CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPRK529
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificTOBACCO ETCH VIRUS
    Organism Taxid12227
 
Molecule 2 - OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
    ChainsC, D
    EngineeredYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D
Biological Unit 3 (4x)ABCD
Biological Unit 4 (2x)ABCD
Biological Unit 5 (1x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 56)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2MSE48Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (2, 28)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (2, 14)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:9 , ASP A:10 , TYR A:11 , ASN A:12 , SER A:15 , SER B:120 , MSE B:121 , HOH B:460BINDING SITE FOR RESIDUE GOL A 401
2AC2SOFTWARESER A:120 , MSE A:121 , ARG B:9 , ASP B:10 , TYR B:11 , ASN B:12 , SER B:15 , SER B:123 , HOH B:408BINDING SITE FOR RESIDUE GOL B 402

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:130 -A:130

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LVB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1LVB)

(-) 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:214
 aligned with POLG_TEV | P04517 from UniProtKB/Swiss-Prot  Length:3054

    Alignment length:214
                                  2054      2064      2074      2084      2094      2104      2114      2124      2134      2144      2154      2164      2174      2184      2194      2204      2214      2224      2234      2244      2254    
            POLG_TEV   2045 PRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDMIIIRMPKDFPPFPQKLKFREPQREERICLVTTNFQTKSMSSMVSDTSCTFPSSDGIFWKHWIQTKDGQCGSPLVSTRDGFIVGIHSASNFTNTNNYFTSVPKNFMELLTNQEAQQWVSGWRLNADSVLWGGHKVFMSKP 2258
               SCOP domains d1lvba_ A: TEV protease (nucleat inclusion protein A, NIA)                                                                                                                                                             SCOP domains
               CATH domains 1lvbA01   1lvbA02 A:18-98,A:182-206 Trypsin-like serine proteases                          1lvbA01 A:8-17,A:99-181,A:207-221 Trypsin-like serine proteases                    1lvbA02 A:18-98,A:182-2061lvbA01         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.eeeeeeee..eeeeeeeeee..eeeehhhhhh...eeeeeee..eeeee.hhhhheeee......eeee......................eeeeeeee...eeeeee......eee....eeee...........eeee.....eeeeeeeee.....eeeee...hhhhhhhhhhhh...........eeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lvb A    8 PRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDmIIIRmPKDFPPFPQKLKFREPQREERICLVTTNFQTKSmSSmVSDTSCTFPSSDGIFWKHWIQTKDGQAGSPLVSTRDGFIVGIHSASNFTNTNNYFTSVPKNFmELLTNQEAQQWVSGWRLNADSVLWGGHKVFmSKP  221
                                    17        27        37        47        57        67        77    |   87        97       107       117   |  |127       137       147       157       167       177       187       197       207       217|   
                                                                                                     82-MSE|                               121-MSE                                                           187-MSE                        218-MSE
                                                                                                          87-MSE                              124-MSE                                                                                             

Chain B from PDB  Type:PROTEIN  Length:214
 aligned with POLG_TEV | P04517 from UniProtKB/Swiss-Prot  Length:3054

    Alignment length:214
                                  2054      2064      2074      2084      2094      2104      2114      2124      2134      2144      2154      2164      2174      2184      2194      2204      2214      2224      2234      2244      2254    
            POLG_TEV   2045 PRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDMIIIRMPKDFPPFPQKLKFREPQREERICLVTTNFQTKSMSSMVSDTSCTFPSSDGIFWKHWIQTKDGQCGSPLVSTRDGFIVGIHSASNFTNTNNYFTSVPKNFMELLTNQEAQQWVSGWRLNADSVLWGGHKVFMSKP 2258
               SCOP domains d1lvbb_ B: TEV protease (nucleat inclusion protein A, NIA)                                                                                                                                                             SCOP domains
               CATH domains 1lvbB01   1lvbB02 B:18-98,B:182-206 Trypsin-like serine proteases                          1lvbB01 B:8-17,B:99-181,B:207-221 Trypsin-like serine proteases                    1lvbB02 B:18-98,B:182-2061lvbB01         CATH domains
           Pfam domains (1) Peptidase_C4-1lvbB01 B:8-221                                                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) Peptidase_C4-1lvbB02 B:8-221                                                                                                                                                                                           Pfam domains (2)
         Sec.struct. author ...hhhhhh.eeeeeeee..eeeeeeeeee..eeeehhhhhh...eeeeeee..eeeee.hhhhheeee......eeee.....................eeeeeeeee...eeeeee...eeeee.....eeee...........eeee.....eeeeeeeee.....eeeee...hhhhhhhhhhhh...........eeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lvb B    8 PRDYNPISSTICHLTNESDGHTTSLYGIGFGPFIITNKHLFRRNNGTLLVQSLHGVFKVKNTTTLQQHLIDGRDmIIIRmPKDFPPFPQKLKFREPQREERICLVTTNFQTKSmSSmVSDTSCTFPSSDGIFWKHWIQTKDGQAGSPLVSTRDGFIVGIHSASNFTNTNNYFTSVPKNFmELLTNQEAQQWVSGWRLNADSVLWGGHKVFmSKP  221
                                    17        27        37        47        57        67        77    |   87        97       107       117   |  |127       137       147       157       167       177       187       197       207       217|   
                                                                                                     82-MSE|                               121-MSE                                                           187-MSE                        218-MSE
                                                                                                          87-MSE                              124-MSE                                                                                             

Chain C from PDB  Type:PROTEIN  Length:10
 aligned with POLG_TEV | P04517 from UniProtKB/Swiss-Prot  Length:3054

    Alignment length:10
                                  2794
            POLG_TEV   2785 TENLYFQSGT 2794
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ...eee.... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                1lvb C  301 TENLYFQSGT  310
                                   310

Chain D from PDB  Type:PROTEIN  Length:10
 aligned with POLG_TEV | P04517 from UniProtKB/Swiss-Prot  Length:3054

    Alignment length:10
                                  2794
            POLG_TEV   2785 TENLYFQSGT 2794
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ...eee.... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                1lvb D  301 TENLYFQSGT  310
                                   310

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a1lvbA02A:18-98,A:182-206
1b1lvbA01A:8-17,A:99-181,A:207-221
1c1lvbB01B:8-17,B:99-181,B:207-221
1d1lvbB02B:18-98,B:182-206

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (POLG_TEV | P04517)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008026    ATP-dependent helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-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: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:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0016818    hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides    Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0018144    RNA-protein covalent cross-linking    The formation of a covalent cross-link between RNA and a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
cellular component
    GO:0019029    helical viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form a protein helix with the genetic material contained within. Tobacco mosaic virus has such a capsid structure.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_TEV | P045171lvm 1q31

(-) Related Entries Specified in the PDB File

1lvm CATALYTICALLY ACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH PRODUCT