3UPF - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MURINE NOROVIRUS RNA-DEPENDENT RNA POLYMERASE BOUND TO NF023

Authors :   M. Milani, E. Mastrangelo, M. Bolognesi

Date :   18 Nov 11 (Deposition) - 02 May 12 (Release) - 23 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: A,B,C  (2x)

Keywords :   Murine Norovirus, Rna-Dependent Rna Polymerase, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Mastrangelo, M. Pezzullo, D. Tarantino, R. Petazzi, F. Germani, D. Kramer, I. Robel, J. Rohayem, M. Bolognesi, M. Milani
Structure-Based Inhibition Of Norovirus Rna-Dependent Rna Polymerases.
J. Mol. Biol. V. 419 198 2012
PubMed-ID: 22446684 | Reference-DOI: 10.1016/J.JMB.2012.03.008

Molecule 1 - RNA-DEPENDENT RNA POLYMERASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 1174-1684
	Organism Scientific	:	MURINE NOROVIRUS 1
	Organism Taxid	:	223997

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	0BU	3	Ligand/Ion	8-({3-[({3-[(4,6,8-TRISULFONAPHTHALEN-1-YL)CARBAMOYL]PHENYL}CARBAMOYL)AMINO]BENZOYL}AMINO)NAPHTHALENE-1,3,5-TRISULFONIC ACID
2	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	0BU	1	Ligand/Ion	8-({3-[({3-[(4,6,8-TRISULFONAPHTHALEN-1-YL)CARBAMOYL]PHENYL}CARBAMOYL)AMINO]BENZOYL}AMINO)NAPHTHALENE-1,3,5-TRISULFONIC ACID
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	0BU	1	Ligand/Ion	8-({3-[({3-[(4,6,8-TRISULFONAPHTHALEN-1-YL)CARBAMOYL]PHENYL}CARBAMOYL)AMINO]BENZOYL}AMINO)NAPHTHALENE-1,3,5-TRISULFONIC ACID
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 5)

No.	Name	Count	Type	Full Name
1	0BU	1	Ligand/Ion	8-({3-[({3-[(4,6,8-TRISULFONAPHTHALEN-1-YL)CARBAMOYL]PHENYL}CARBAMOYL)AMINO]BENZOYL}AMINO)NAPHTHALENE-1,3,5-TRISULFONIC ACID
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 20)

No.	Name	Count	Type	Full Name
1	0BU	6	Ligand/Ion	8-({3-[({3-[(4,6,8-TRISULFONAPHTHALEN-1-YL)CARBAMOYL]PHENYL}CARBAMOYL)AMINO]BENZOYL}AMINO)NAPHTHALENE-1,3,5-TRISULFONIC ACID
2	SO4	14	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:42 , ASP A:65 , GLN A:66 , PRO A:69 , GLU A:168 , VAL A:170 , LYS A:171 , LYS A:174 , LYS A:180 , ARG A:182 , ARG A:245 , ARG A:392 , ARG A:413 , SO4 A:516 , HOH A:687	BINDING SITE FOR RESIDUE 0BU A 600
02	AC2	SOFTWARE	THR A:244 , ARG A:245 , HOH A:560 , 0BU A:600	BINDING SITE FOR RESIDUE SO4 A 516
03	AC3	SOFTWARE	TRP B:42 , ASP B:65 , GLN B:66 , LYS B:68 , PRO B:69 , GLU B:168 , VAL B:170 , LYS B:171 , LYS B:174 , LYS B:178 , LYS B:180 , ARG B:182 , ARG B:245 , ARG B:392 , ARG B:413 , SO4 B:517 , HOH B:608	BINDING SITE FOR RESIDUE 0BU B 600
04	AC4	SOFTWARE	VAL B:322 , ARG B:326 , ASP B:328	BINDING SITE FOR RESIDUE SO4 B 516
05	AC5	SOFTWARE	TYR B:243 , THR B:244 , ARG B:245 , 0BU B:600 , HOH B:608	BINDING SITE FOR RESIDUE SO4 B 517
06	AC6	SOFTWARE	TRP C:42 , ASP C:65 , GLN C:66 , LYS C:68 , PRO C:69 , GLU C:168 , VAL C:170 , LYS C:171 , LYS C:174 , LYS C:178 , LYS C:180 , ARG C:182 , ARG C:245 , ARG C:392 , SO4 C:516 , HOH C:743	BINDING SITE FOR RESIDUE 0BU C 600
07	AC7	SOFTWARE	TYR C:243 , THR C:244 , ARG C:245 , HOH C:520 , 0BU C:600	BINDING SITE FOR RESIDUE SO4 C 516
08	AC8	SOFTWARE	GLY C:7 , ALA C:10 , ARG C:64 , HOH C:633	BINDING SITE FOR RESIDUE SO4 C 517
09	AC9	SOFTWARE	VAL C:322 , ARG C:326	BINDING SITE FOR RESIDUE SO4 C 518
10	BC1	SOFTWARE	THR C:25 , GLY C:48 , SER C:49 , SER C:58 , LEU C:59 , HOH C:610 , HOH C:695	BINDING SITE FOR RESIDUE SO4 C 519

(no "SS Bond" information available for 3UPF)

Asymmetric Unit

No.	Residues
1	Tyr A:121	-	Pro A:122
2	Tyr B:121	-	Pro B:122
3	Tyr C:121	-	Pro C:122

(no "SAP(SNP)/Variant" information available for 3UPF)

(no "PROSITE Motif" information available for 3UPF)

(no "Exon" information available for 3UPF)

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:476
 aligned with Q80J95_9CALI | Q80J95 from UniProtKB/TrEMBL  Length:1687

    Alignment length:487
                                  1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431      1441      1451      1461      1471      1481      1491      1501      1511      1521      1531      1541      1551      1561      1571      1581      1591      1601      1611      1621      1631      1641      1651      1661       
        Q80J95_9CALI   1182 LPRPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRSVLRWVRFG 1668
               SCOP domains d3upfa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee..eeeeee.........eeeee...........ee.............hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhh............hhhhhh.....hhhhhhhhhhhhhhhhh......eeeeee...eehhhhh.......eeee.hhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh...eee...........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeee...eeeee......-..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhh...........-...........ee..eeeeee..eeeee.hhhhhhhhhheeeeeee..........--..-.hhhhhhhhhh.hhhhhhhhhhhhhh...------...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3upf A    2 LPRPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPS-CPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEE-PLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGH--RP-QLMALLGEAAMHGEKYYRTVASRVSKEAA------VVPRHRSVLRWVRFG  488
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        |-|      311       321       331       341       351       361       371    | |381       391       401       411       421       431 |  || 441       451       461     |   -  |    481       
                                                                                                                                                                                                                                                                                                                                    300 |                                                                       376 |                                                    433  || |                         467    474              
                                                                                                                                                                                                                                                                                                                                      302                                                                         378                                                       436| |                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             437 |                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               439

Chain B from PDB  Type:PROTEIN  Length:483
 aligned with Q80J95_9CALI | Q80J95 from UniProtKB/TrEMBL  Length:1687

    Alignment length:487
                                  1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431      1441      1451      1461      1471      1481      1491      1501      1511      1521      1531      1541      1551      1561      1571      1581      1591      1601      1611      1621      1631      1641      1651      1661       
        Q80J95_9CALI   1182 LPRPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRSVLRWVRFG 1668
               SCOP domains d3upfb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee..eeeeee.........eeeee...........ee.............hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhh............hhhhhh.....hhhhhhhhhhhhhhhhh......eeeeee...ee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeee...eeeee........-.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhh.......................ee..eeeeee..eeeee.hhhhhhhhhheeeeeee............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...---...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3upf B    2 LPRPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGC-CTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSG---VVPRHRSVLRWVRFG  488
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301| |    311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461        |-  |    481       
                                                                                                                                                                                                                                                                                                                                      302 |                                                                                                                                                                   470 474              
                                                                                                                                                                                                                                                                                                                                        304

Chain C from PDB  Type:PROTEIN  Length:471
 aligned with Q80J95_9CALI | Q80J95 from UniProtKB/TrEMBL  Length:1687

    Alignment length:484
                                  1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314      1324      1334      1344      1354      1364      1374      1384      1394      1404      1414      1424      1434      1444      1454      1464      1474      1484      1494      1504      1514      1524      1534      1544      1554      1564      1574      1584      1594      1604      1614      1624      1634      1644      1654      1664    
        Q80J95_9CALI   1185 PSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRSVLRWVRFG 1668
               SCOP domains d3upfc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..eeeeee.........eeeee...........ee.............hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhh............hhhhhh.....hhhhhhhhhhhhhhhhh.......eeeee...ee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeee...eeeee........--.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhh.......................ee..eeeeee..eeeee.hhhhhhhhhheeeeeee.........--.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh---------..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3upf C    5 PSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGC--TTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPG--QRPSQLMALLGEAAMHGEKYYRTVASRVSKE---------VPRHRSVLRWVRFG  488
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       | -|      314       324       334       344       354       364       374       384       394       404       414       424       | -|      444       454       464|        -|      484    
                                                                                                                                                                                                                                                                                                                                   302  |                                                                                                                            432  |                           465       475             
                                                                                                                                                                                                                                                                                                                                      305                                                                                                                               435

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: DNA/RNA polymerases (850)

Superfamily: DNA/RNA polymerases (850)

Family: RNA-dependent RNA-polymerase (253)

Protein domain: automated matches (100)

Murine norovirus 1 [TaxId: 223997] (6)

1a	d3upfa_	A:
1b	d3upfb_	B:
1c	d3upfc_	C:

(no "CATH Domain" information available for 3UPF)

(no "Pfam Domain" information available for 3UPF)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q80J95_9CALI | Q80J95)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003724	RNA helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
	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: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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0017111	nucleoside-triphosphatase activity	Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
	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: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:0044419	interspecies interaction between organisms	Any process in which an organism has an effect on an organism of a different species.
	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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Tyr A:121 - Pro A:122	[ RasMol ]
		Tyr B:121 - Pro B:122	[ RasMol ]
		Tyr C:121 - Pro C:122	[ RasMol ]

Biological Units
	Complete Structure
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		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

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Access by PDB/NDB ID
	3upf
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
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Access by UniProt ID/Accession number
	Q80J95_9CALI \| Q80J95
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		Interatomic Contacts of Structural Units	:	CSU
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	Q80J95_9CALI \| Q80J95
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (18, 18)

Visualization

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Still Images

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Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File