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

(-) Description

Title :  POLIOVIRUS POLYMERASE - C290V LOOP MUTANT
 
Authors :  A. J. Sholders, O. B. Peersen
Date :  14 Nov 13  (Deposition) - 22 Jan 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Polymerase, Rna Dependent Rna Polymerase, Rdrp, Virus, Viral Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. J. Sholders, O. B. Peersen
Distinct Conformations Of A Putative Translocation Element In Poliovirus Polymerase.
J. Mol. Biol. V. 426 1407 2014
PubMed-ID: 24424421  |  Reference-DOI: 10.1016/J.JMB.2013.12.031

(-) Compounds

Molecule 1 - RNA-DIRECTED RNA POLYMERASE 3D-POL
    ChainsA
    EC Number2.7.7.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKK
    Expression System StrainBL21(DE3) PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificHUMAN POLIOVIRUS 1
    Organism Taxid12081
    StrainMAHONEY
    SynonymP3D-POL, GENOME POLYPROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2ACY5Ligand/IonACETIC ACID
3CAS3Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
4NA1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:28 , ILE A:401 , TRP A:403 , THR A:404 , THR A:410 , HIS A:413 , HOH A:1154BINDING SITE FOR RESIDUE ACY A 901
2AC2SOFTWARETYR A:334 , HIS A:336 , PRO A:440 , ARG A:443 , HOH A:1164BINDING SITE FOR RESIDUE ACY A 903
3AC3SOFTWAREARG A:379BINDING SITE FOR RESIDUE ACY A 904
4AC4SOFTWAREMET A:189BINDING SITE FOR RESIDUE ACY A 905
5AC5SOFTWARESER A:219 , PHE A:461BINDING SITE FOR RESIDUE 1PE A 906
6AC6SOFTWAREPHE A:378BINDING SITE FOR RESIDUE 1PE A 907
7AC7SOFTWARELEU A:268 , ASN A:269 , SER A:271 , GLY A:284 , GLY A:285 , HOH A:1073BINDING SITE FOR RESIDUE NA A 908

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:118 -Pro A:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NLP)

(-) 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:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4nlpa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhh............ee...........ee............hhhhhhhh..........hhhhhhhhhhhhhhhhh........hhhhhhhh...............hhhhh..hhhhh.......hhhhhhhhhhhh....eeeee...eehhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.hhhhhh..eee.eee.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhheeeeee..eeeeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhheeeee..eeeeee....hhhhhhhhhhh....eee.hhh................eeee.......eeee.hhhhhhhhhhee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nlp A   1 GEIQWMRPSKEVGYPIINAPSKTKLEPSAFHYVFEGVKEPAVLTKNDPRLKTDFEEAIFSKYVGNKITEVDEYMKEAVDHYAGQLMSLDINTEQMcLEDAMYGTDGLEALDLSTSAGYPYVAMGKKKRDILNKQTRDTKEMQKLLDTYGINLPLVTYVKDELRSKTKVEQGKSRLIEASSLNDSVAMRMAFGNLYAAFHKNPGVITGSAVGcDPDLFWSKIPVLMEEKLFAFDYTGYDASLSPAWFEALKMVLEKIGFGDRVDYIDYLNHSHHLYKNKTYcVKGGMPSGVSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAYGDDVIASYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCLLAWHNGEEEYNKFLAKIRSVPIGRALDLPEYSTLYDRWLDSF 461
                                    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 
                                                                                                                          96-CAS                                                                                                             212-CAS                                                              281-CAS                                                                                                                                                                                

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (48, 48)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CAS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
 
  Cis Peptide Bonds
    Tyr A:118 - Pro A:119   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4nlp
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  POLG_POL1M | P03300
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.48
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  POLG_POL1M | P03300
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_POL1M | P033001al2 1ar6 1ar7 1ar8 1ar9 1asj 1dgi 1fpt 1hxs 1l1n 1ng7 1nn8 1po1 1po2 1pov 1ra6 1ra7 1raj 1rdr 1tql 1vbd 1xyr 2bbl 2bbp 2ijd 2ijf 2ily 2ilz 2im0 2im1 2im2 2im3 2plv 3epc 3iyb 3iyc 3j3o 3j3p 3j48 3j8f 3j9f 3jbc 3jbd 3jbe 3jbf 3jbg 3ol7 4dcd 4k4s 4k4t 4k4u 4k4v 4k4w 4nlo 4nlq 4nlr 4nls 4nlt 4nlu 4nlv 4nlw 4nlx 4nly 4r0e 5ktz 5ku0 5ku2 5kwl

(-) Related Entries Specified in the PDB File

4nlo 4nlq 4nlr 4nls 4nlt 4nlu 4nlv 4nlw 4nlx 4nly