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(-) Description

Title :  CRYSTAL STRUCTURE OF AVIAN INFLUENZA VIRUS PAN BOUND TO COMPOUND 6
 
Authors :  R. M. Dubois, P. J. Slavish, T. R. Webb, S. W. White
Date :  14 Mar 12  (Deposition) - 08 Aug 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.47
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 :  Endonuclease Domain, H5N1 Subtype, Viral Protein, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Dubois, P. J. Slavish, B. M. Baughman, M. K. Yun, J. Bao, R. J. Webby T. R. Webb, S. W. White
Structural And Biochemical Basis For Development Of Influenza Virus Inhibitors Targeting The Pa Endonuclease.
Plos Pathog. V. 8 02830 2012
PubMed-ID: 22876176  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002830

(-) Compounds

Molecule 1 - POLYMERASE PROTEIN PA
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET52B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SEE REMARK 999
    Gene: PA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 284218
    Strain: A/VIET NAM/1203/2004
    Synonym: POLYMERASE ACIDIC PROTEIN

 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  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1DBH4Ligand/Ion2,3-DIHYDROXY-BENZOIC ACID
2MN8Ligand/IonMANGANESE (II) ION
3SO48Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1DBH1Ligand/Ion2,3-DIHYDROXY-BENZOIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1DBH1Ligand/Ion2,3-DIHYDROXY-BENZOIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3SO42Ligand/IonSULFATE ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1DBH1Ligand/Ion2,3-DIHYDROXY-BENZOIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3SO42Ligand/IonSULFATE ION
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1DBH1Ligand/Ion2,3-DIHYDROXY-BENZOIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:80 , ASP A:108 , DBH A:305 , HOH A:414BINDING SITE FOR RESIDUE MN A 301
02AC2SOFTWAREHIS A:41 , ASP A:108 , GLU A:119 , ILE A:120 , DBH A:305BINDING SITE FOR RESIDUE MN A 302
03AC3SOFTWAREILE A:30 , GLU A:31 , THR A:32 , ASN A:33 , LYS A:34 , SER A:194BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREGLY A:50B , SER A:50C , ARG A:75 , LYS A:113BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREHIS A:41 , ASP A:108 , GLU A:119 , ILE A:120 , TYR A:130 , LYS A:134 , MN A:301 , MN A:302 , HOH A:402BINDING SITE FOR RESIDUE DBH A 305
06AC6SOFTWAREHIS B:41 , GLU B:80 , ASP B:108 , MN B:302 , DBH B:305 , HOH B:411BINDING SITE FOR RESIDUE MN B 301
07AC7SOFTWAREHIS B:41 , ASP B:108 , GLU B:119 , ILE B:120 , MN B:301 , DBH B:305BINDING SITE FOR RESIDUE MN B 302
08AC8SOFTWAREGLU B:31 , THR B:32 , ASN B:33 , LYS B:34 , SER B:194BINDING SITE FOR RESIDUE SO4 B 303
09AC9SOFTWAREGLY B:50B , SER B:50C , ARG B:75 , LYS B:113BINDING SITE FOR RESIDUE SO4 B 304
10BC1SOFTWAREHIS B:41 , GLU B:80 , ASP B:108 , GLU B:119 , ILE B:120 , LYS B:134 , MN B:301 , MN B:302 , HOH B:402BINDING SITE FOR RESIDUE DBH B 305
11BC2SOFTWAREHIS C:41 , ASP C:108 , GLU C:119 , ILE C:120 , MN C:302 , DBH C:305BINDING SITE FOR RESIDUE MN C 301
12BC3SOFTWAREHIS C:41 , GLU C:80 , ASP C:108 , MN C:301 , DBH C:305 , HOH C:416BINDING SITE FOR RESIDUE MN C 302
13BC4SOFTWAREGLU C:31 , THR C:32 , ASN C:33 , LYS C:34 , SER C:194BINDING SITE FOR RESIDUE SO4 C 303
14BC5SOFTWARESER C:50C , ARG C:75 , LYS C:113BINDING SITE FOR RESIDUE SO4 C 304
15BC6SOFTWAREHIS C:41 , GLU C:80 , ASP C:108 , GLU C:119 , ILE C:120 , LYS C:134 , MN C:301 , MN C:302 , HOH C:401BINDING SITE FOR RESIDUE DBH C 305
16BC7SOFTWAREHIS D:41 , ASP D:108 , GLU D:119 , ILE D:120 , MN D:302 , DBH D:305BINDING SITE FOR RESIDUE MN D 301
17BC8SOFTWAREGLU D:80 , LEU D:106 , ASP D:108 , GLU D:119 , MN D:301 , DBH D:305 , HOH D:413BINDING SITE FOR RESIDUE MN D 302
18BC9SOFTWAREGLU D:31 , THR D:32 , ASN D:33 , LYS D:34 , SER D:194BINDING SITE FOR RESIDUE SO4 D 303
19CC1SOFTWARESER D:50C , ARG D:75 , LYS D:113BINDING SITE FOR RESIDUE SO4 D 304
20CC2SOFTWAREHIS D:41 , GLU D:80 , ASP D:108 , GLU D:119 , ILE D:120 , LYS D:134 , MN D:301 , MN D:302 , HOH D:402BINDING SITE FOR RESIDUE DBH D 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E5L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4E5L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E5L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E5L)

(-) Exons   (0, 0)

(no "Exon" information available for 4E5L)

(-) 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:179
 aligned with Q5EP34_9INFA | Q5EP34 from UniProtKB/TrEMBL  Length:716

    Alignment length:198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        
        Q5EP34_9INFA      1 MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSDFHFIDERSESIIVESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEETHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGE  198
               SCOP domains d4e5la_ A: PA N-terminal domain                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh--------------h..-----...eee....hhhhhhhhhhhhhhhhh.........eee....eeeeeeee..hhhhhhhhhhhhhh....eeeeee....eee.hhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4e5l A    1 MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSD--------------GGS-----KHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEETHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERAA 196B
                                    10        20        30        40        50         -    |||  -  |     80        90       100       110       120       130       140       150       160       170       180       190      ||
                                                                            50            50A||    73                                                                                                                        196A|
                                                                                           50B|                                                                                                                               196B
                                                                                            50C                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:178
 aligned with Q5EP34_9INFA | Q5EP34 from UniProtKB/TrEMBL  Length:716

    Alignment length:197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
        Q5EP34_9INFA      1 MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSDFHFIDERSESIIVESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEETHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERG  197
               SCOP domains d4e5lb_ B: PA N-terminal domain                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh--------------h..-----...eee....hhhhhhhhhhhhhhhhh.........eee....eeeeeeee..hhhhhhhhhhhhhh....eeeeee....eee.hhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4e5l B    1 MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSD--------------GGS-----KHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEETHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERA 196A
                                    10        20        30        40        50         -    |||  -  |     80        90       100       110       120       130       140       150       160       170       180       190      |
                                                                            50            50A||    73                                                                                                                        196A
                                                                                           50B|                                                                                                                                  
                                                                                            50C                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:181
 aligned with Q5EP34_9INFA | Q5EP34 from UniProtKB/TrEMBL  Length:716

    Alignment length:200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
        Q5EP34_9INFA      1 MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSDFHFIDERSESIIVESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEETHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEET  200
               SCOP domains d4e5lc_ C: PA N-terminal domain                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh--------------...-----...eee....hhhhhhhhhhhhhhhhh.........eee....eeeeeeee..hhhhhhhhhhhhhh....eeeeee....eee.hhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4e5l C    1 MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSD--------------GGS-----KHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEETHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERAAAE 196D
                                    10        20        30        40        50         -    |||  -  |     80        90       100       110       120       130       140       150       160       170       180       190      196D
                                                                            50            50A||    73                                                                                                                        196A|||
                                                                                           50B|                                                                                                                               196B||
                                                                                            50C                                                                                                                                196C|
                                                                                                                                                                                                                                196D


Chain D from PDB  Type:PROTEIN  Length:181
 aligned with Q5EP34_9INFA | Q5EP34 from UniProtKB/TrEMBL  Length:716

    Alignment length:200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
        Q5EP34_9INFA      1 MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSDFHFIDERSESIIVESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEETHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEET  200
               SCOP domains d4e5ld_ D: PA N-terminal domain                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh--------------h..-----...eee....hhhhhhhhhhhhhhhhh.........eee....eeeeeeee..hhhhhhhhhhhhhh....eeeeee....eee.hhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4e5l D    1 MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSD--------------GGS-----KHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEETHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERAAAE 196D
                                    10        20        30        40        50         -    |||  -  |     80        90       100       110       120       130       140       150       160       170       180       190      196D
                                                                            50            50A||    73                                                                                                                        196A|||
                                                                                           50B|                                                                                                                               196B||
                                                                                            50C                                                                                                                                196C|
                                                                                                                                                                                                                                196D
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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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E5L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E5L)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5EP34_9INFA | Q5EP34)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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.

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  4e5l
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 Related Entries

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

UniProtKB/TrEMBL
        Q5EP34_9INFA | Q5EP34: 4e5e 4e5f 4e5g 4e5h 4e5i 4e5j

(-) Related Entries Specified in the PDB File

4e5e 4e5f 4e5g 4e5h 4e5i 4e5j