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(-) Description

Title :  RDRP FROM JAPANESESE ENCEPHALITIS VIRUS
 
Authors :  P. Surana, D. T. Nair
Date :  20 Sep 13  (Deposition) - 25 Dec 13  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Rna Dependent Rna Polymerase, Nucleotidyltransferases, Apo, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Surana, V. Satchidanandam, D. T. Nair
Rna-Dependent Rna Polymerase Of Japanese Encephalitis Virus Binds The Initiator Nucleotide Gtp To Form A Mechanisticall Important Pre-Initiation State.
Nucleic Acids Res. V. 42 2758 2014
PubMed-ID: 24293643  |  Reference-DOI: 10.1093/NAR/GKT1106

(-) Compounds

Molecule 1 - RNA DEPENDENT RNA POLYMERASE
    Chains: A, B, C, D
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C41DE3
    Expression System Taxid: 562
    Expression System Vector Type: PGEX6P1
    Fragment: RDRP MODULE OF NS5 (UNP RESIDUES 2799-3422)
    Gene: NS5
    Organism Scientific: JAPANESE ENCEPHALITIS VIRUS
    Organism Taxid: 11072

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:440 , HIS A:444 , CYS A:449 , CYS A:452BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWAREHIS A:717 , CYS A:733 , CYS A:852BINDING SITE FOR RESIDUE ZN A 1002
3AC3SOFTWAREGLU B:440 , HIS B:444 , CYS B:449 , HIS B:450 , CYS B:452BINDING SITE FOR RESIDUE ZN B 1001
4AC4SOFTWAREARG A:859 , HIS B:717 , CYS B:733 , CYS B:852BINDING SITE FOR RESIDUE ZN B 1002
5AC5SOFTWAREGLU C:440 , HIS C:444 , CYS C:449 , HIS C:450 , CYS C:452BINDING SITE FOR RESIDUE ZN C 1001
6AC6SOFTWAREHIS C:717 , CYS C:733 , CYS C:852BINDING SITE FOR RESIDUE ZN C 1002
7AC7SOFTWAREGLU D:440 , HIS D:444BINDING SITE FOR RESIDUE ZN D 1001
8AC8SOFTWAREHIS D:717 , CYS D:733 , CYS D:852BINDING SITE FOR RESIDUE ZN D 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MTP)

(-) 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:591
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...............eeeeeee.......hhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhh......eeeeeee.............eeeee.hhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee...eeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhh..eeee..eeee...hhhhhhhhhhhhhh.................hhhhh.....eeeeee.....eeeeee.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........................hhhhhhhhhhh.............hhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mtp A 276 QEKIKKRIQKLKEEFATTWHKDPEHPYRTWTYHGSYEVKATGLVNGVVKLMSKPWDAIANVTTMAMTDTTPFGQQRVFKEKVDTKAPEPPAGVREVLNETTNWLWAHLSREKRPRLCTKEEFIKKVNAREAVNDPRFWEMVDEERENHLRGECHTCIYNMMGKREKKPGEFGKAKGSRAIWFMWLGARYLEFEALGFLNEDHWLSRENSGGGVEGSGVQKLGYILRDIAGKQGGKMYADDTAGWDTRITRTDLENEAKVLELLDGEHRMLARAIIELTYRHKVVKVMRPAAEGKTVMDVISREDQRGSGQVVTYALNTFTNIAVQLVRLMEAEGVIGPQHLEQLPRKNKIAVRTWLFENGEERVTRMAISGDDCVVKPLDDRFATALHFLNAMSKVRKDIQEWKPSHGWHDWQQVPFCSNHFQEIVMKDGRSIVVPCRGQDELIGRARISPGANVKDTACLAKAYAQMWLLLYFHRRDLRLMANAICSAVPVDWVPTGRTSWSIHSKGEWMTTEDMLQVWNRVWIEENEWMMDKTPIASWTDVPYVGKREDIWCGSLIGTRSRATWAENIYAAINQVRAVIGKENYVDYMT 889
                                   285       295       305       315 ||    329       339       349       359       369       379       389       399      |426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746  ||   758       768       778       788       798       808       818       828       838       848       858       868       878       888 
                                                                   317|                                                                                 406|                                                                                                                                                                                                                                                                                                                                  749|                                                                                                                                         
                                                                    322                                                                                  424                                                                                                                                                                                                                                                                                                                                   752                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:591
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...............eeeeeee.......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.............eeeeeehhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee...eeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhh..eeee..eeee...hhhhhhhhhhhhhh.................hhhhh.....eeeeee.....eeeeee.hhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........................hhhhhhhhhhh.............hhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mtp B 276 QEKIKKRIQKLKEEFATTWHKDPEHPYRTWTYHGSYEVKATGLVNGVVKLMSKPWDAIANVTTMAMTDTTPFGQQRVFKEKVDTKAPEPPAGVREVLNETTNWLWAHLSREKRPRLCTKEEFIKKVNAREAVNDPRFWEMVDEERENHLRGECHTCIYNMMGKREKKPGEFGKAKGSRAIWFMWLGARYLEFEALGFLNEDHWLSRENSGGGVEGSGVQKLGYILRDIAGKQGGKMYADDTAGWDTRITRTDLENEAKVLELLDGEHRMLARAIIELTYRHKVVKVMRPAAEGKTVMDVISREDQRGSGQVVTYALNTFTNIAVQLVRLMEAEGVIGPQHLEQLPRKNKIAVRTWLFENGEERVTRMAISGDDCVVKPLDDRFATALHFLNAMSKVRKDIQEWKPSHGWHDWQQVPFCSNHFQEIVMKDGRSIVVPCRGQDELIGRARISPGANVKDTACLAKAYAQMWLLLYFHRRDLRLMANAICSAVPVDWVPTGRTSWSIHSKGEWMTTEDMLQVWNRVWIEENEWMMDKTPIASWTDVPYVGKREDIWCGSLIGTRSRATWAENIYAAINQVRAVIGKENYVDYMT 889
                                   285       295       305       315 ||    329       339       349       359       369       379       389       399      |426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746  ||   758       768       778       788       798       808       818       828       838       848       858       868       878       888 
                                                                   317|                                                                                 406|                                                                                                                                                                                                                                                                                                                                  749|                                                                                                                                         
                                                                    322                                                                                  424                                                                                                                                                                                                                                                                                                                                   752                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:585
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...............eeeeeee.......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh......hhhhhhhhhhhhhhhhhh......eeeeeee.......eeeeeehhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...eeeeeeeee...eeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhh..eeee..eeee...hhhhhh.hhhhhhh.................hhhhh.....eeeeee.....eeeeee.hhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........................hhhhhhhhhhh.............hhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mtp C 276 QEKIKKRIQKLKEEFATTWHKDPEHPYRTWTYHGSYEVKATGLVNGVVKLMSKPWDAIANVTTMAMTDTTPFGQQRVFKEKVDTKAPEPPAGVREVLNETTNWLWAHLSREKRPRLCTKEEFIKKVNAREAVNDPRFWEMVDEERENHLRGECHTCIYNMMGKRFGKAKGSRAIWFMWLGARYLEFEALGFLNEDHWLSRENSGGGVEGSGVQKLGYILRDIAGKQGGKMYADDTAGWDTRITRTDLENEAKVLELLDGEHRMLARAIIELTYRHKVVKVMRPAAEGKTVMDVISREDQRGSGQVVTYALNTFTNIAVQLVRLMEAEGVIGPQHLEQLPRKNKIAVRTWLFENGEERVTRMAISGDDCVVKPLDDRFATALHFLNAMSKVRKDIQEWKPSHGWHDWQQVPFCSNHFQEIVMKDGRSIVVPCRGQDELIGRARISPGANVKDTACLAKAYAQMWLLLYFHRRDLRLMANAICSAVPVDWVPTGRTSWSIHSKGEWMTTEDMLQVWNRVWIEENEWMMDKTPIASWTDVPYVGKREDIWCGSLIGTRSRATWAENIYAAINQVRAVIGKENYVDYMT 889
                                   285       295       305       315 ||    329       339       349       359       369       379       389       399      |426       436       446       456   ||  472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742      |754       764       774       784       794       804       814       824       834       844       854       864       874       884     
                                                                   317|                                                                                 406|                                 460|                                                                                                                                                                                                                                                                                       749|                                                                                                                                         
                                                                    322                                                                                  424                                  467                                                                                                                                                                                                                                                                                        752                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:546
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.............................hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee...eee..hhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhh..eeee..eeee...hhhhhhhhhhhhhh.................hhhhh.....eeeeee.....eeeeee.hhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........................hhhhhhhhhhh.............hhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mtp D 276 QEKIKKRIQKLKEEFATTWHKDPEHPYRTWTYHGSYEVKATGLVNGVVKLMSKPWDAIANVTTMAMTDTTPFGQQRVFKEKVDTKAPEPPAGVREVLNETTNWLWAHLSREKRPRLCTKEEFIKKVNAREAVNDPRFWEMVDEERENHLRGWLGARYLEFEALGFLNEDHWLSRENSGGGVEGSGVQKLGYILRDIAGKQGGKMYADDTAGWDTRITRTDLENEAKVLELLDGEHRMLARAIIELTYRHKVVKVMRPAAEGKTVQVVTYALNTFTNIAVQLVRLMEAEGVIGPQHLEQLPRKNKIAVRTWLFENGEERVTRMAISGDDCVVKPLDDRFATALHFLNAMSKVRKDIQEWKPSHGWHDWQQVPFCSNHFQEIVMKDGRSIVVPCRGQDELIGRARISPGANVKDTACLAKAYAQMWLLLYFHRRDLRLMANAICSAVPVDWVPTGRTSWSIHSKGEWMTTEDMLQVWNRVWIEENEWMMDKTPIASWTDVPYVGKREDIWCGSLIGTRSRATWAENIYAAINQVRAVIGKENYVDYMT 889
                                   285       295       305       315 ||    329       339       349       359       369       379       389       399      |426       436       446||     488       498       508       518       528       538       548       558       568       578       588   ||  611       621       631       641       651       661       671       681       691       701       711       721       731       741       753       763       773       783       793       803       813       823       833       843       853       863       873       883      
                                                                   317|                                                                                 406|                    447|                                                                                                             592|                                                                                                                                            749|                                                                                                                                         
                                                                    322                                                                                  424                     480                                                                                                              606                                                                                                                                             752
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  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 4MTP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (62, 107)

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  POLG_JAEV1 | P27395
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 Related Entries

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

UniProtKB/Swiss-Prot
        G3LHD9_9FLAV | G3LHD9: 4hdg 4hdh
        POLG_JAEV1 | P27395: 2z83 3p54 4hdg 4hdh 4k6m

(-) Related Entries Specified in the PDB File

4hdg THE SAME PROTEIN COMPLEXED WITH GTP
4hdh THE SAME PROTEIN COMPLEXED WITH ATP