3TI8 - 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)

Title :   CRYSTAL STRUCTURE OF INFLUENZA A VIRUS NEURAMINIDASE N5 COMPLEXED WITH LANINAMIVIR

Authors :   C. J. Vavricka, Q. Li, Y. Wu, J. Qi, M. Wang, Y. Liu, F. Gao, J. Liu, E. Feng, J. Wang, H. Liu, H. Jiang, G. F. Gao

Date :   20 Aug 11 (Deposition) - 16 Nov 11 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   6-Bladed Beta-Propeller, Calcium Binding, Glycosylation, Antiviral, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. J. Vavricka, Q. Li, Y. Wu, J. Qi, M. Wang, Y. Liu, F. Gao, J. Liu, E. Feng J. He, J. Wang, H. Liu, H. Jiang, G. F. Gao
Structural And Functional Analysis Of Laninamivir And Its Octanoate Prodrug Reveals Group Specific Mechanisms For Influenza Na Inhibition
Plos Pathog. V. 7 02249 2011
PubMed-ID: 22028647 | Reference-DOI: 10.1371/JOURNAL.PPAT.1002249

Molecule 1 - NEURAMINIDASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Plasmid	:	PFASTBAC1
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	UNP RESIDUES 79-473
	Gene	:	NA
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	385582
	Strain	:	A/DUCK/ALBERTA/60/1976 H12N5

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	LNV	2	Ligand/Ion	5-(ACETYLAMINO)-2,6-ANHYDRO-4-CARBAMIMIDAMIDO-3,4,5-TRIDEOXY-7-O-METHYL-D-GLYCERO-D-GALACTO-NON-2-ENONICACID
3	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	LNV	4	Ligand/Ion	5-(ACETYLAMINO)-2,6-ANHYDRO-4-CARBAMIMIDAMIDO-3,4,5-TRIDEOXY-7-O-METHYL-D-GLYCERO-D-GALACTO-NON-2-ENONICACID
3	NAG	8	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (2, 20)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	LNV	4	Ligand/Ion	5-(ACETYLAMINO)-2,6-ANHYDRO-4-CARBAMIMIDAMIDO-3,4,5-TRIDEOXY-7-O-METHYL-D-GLYCERO-D-GALACTO-NON-2-ENONICACID
3	NAG	16	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:1 , HOH A:8 , ASP A:293 , GLY A:297 , ASP A:324 , TYR A:347B	BINDING SITE FOR RESIDUE CA A 601
02	AC2	SOFTWARE	LEU A:91 , ASN A:93 , HOH A:737 , HOH A:907 , HOH A:1054	BINDING SITE FOR RESIDUE NAG A 801
03	AC3	SOFTWARE	ASN A:146 , HOH A:554 , HOH A:731 , HOH A:732 , HOH A:1126	BINDING SITE FOR RESIDUE NAG A 803
04	AC4	SOFTWARE	HOH A:66 , ARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , ARG A:156 , TRP A:178 , ARG A:224 , GLU A:227 , ALA A:246 , GLU A:276 , ARG A:292 , ASN A:294 , TYR A:347B , ARG A:371 , TYR A:406 , HOH A:529 , HOH A:592 , HOH A:637 , HOH A:662 , HOH A:752	BINDING SITE FOR RESIDUE LNV A 901
05	AC5	SOFTWARE	HOH B:6 , HOH B:52 , ASP B:293 , GLY B:297 , ASP B:324 , TYR B:347B	BINDING SITE FOR RESIDUE CA B 601
06	AC6	SOFTWARE	LEU B:91 , ASN B:93 , HOH B:716 , NAG B:802 , HOH B:820 , HOH B:1022	BINDING SITE FOR RESIDUE NAG B 801
07	AC7	SOFTWARE	ASN B:358 , HOH B:560 , HOH B:716 , NAG B:801	BINDING SITE FOR RESIDUE NAG B 802
08	AC8	SOFTWARE	ASN B:146 , HOH B:537 , HOH B:736 , NAG B:804 , HOH B:844 , HOH B:908 , HOH B:1003	BINDING SITE FOR RESIDUE NAG B 803
09	AC9	SOFTWARE	NAG B:803 , HOH B:973	BINDING SITE FOR RESIDUE NAG B 804
10	BC1	SOFTWARE	HOH B:38 , ARG B:118 , GLU B:119 , ASP B:151 , ARG B:152 , ARG B:156 , TRP B:178 , ARG B:224 , GLU B:227 , ALA B:246 , GLU B:276 , GLU B:277 , ARG B:292 , ASN B:294 , TYR B:347B , ARG B:371 , TYR B:406 , HOH B:496 , HOH B:523 , HOH B:630	BINDING SITE FOR RESIDUE LNV B 901

Asymmetric Unit

No.	Residues
1	A:92	-	A:417
2	A:124	-	A:129
3	A:183	-	A:230
4	A:232	-	A:237
5	A:278	-	A:291
6	A:280	-	A:289
7	A:318	-	A:337
8	A:421	-	A:447
9	B:92	-	B:417
10	B:124	-	B:129
11	B:183	-	B:230
12	B:232	-	B:237
13	B:278	-	B:291
14	B:280	-	B:289
15	B:318	-	B:337
16	B:421	-	B:447

Asymmetric Unit

No.	Residues
1	Thr A:325	-	Pro A:326
2	Lys A:430	-	Pro A:431
3	Leu A:464	-	Pro A:465
4	Thr B:325	-	Pro B:326
5	Lys B:430	-	Pro B:431
6	Leu B:464	-	Pro B:465

(no "SAP(SNP)/Variant" information available for 3TI8)

(no "PROSITE Motif" information available for 3TI8)

(no "Exon" information available for 3TI8)

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:394
 aligned with A1ILL9_I76A2 | A1ILL9 from UniProtKB/TrEMBL  Length:473

    Alignment length:394
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468    
        A1ILL9_I76A2     79 PEFLNNTEPLCNVSGFAIVSKDNGIRIGSRGHVFVIREPFVACGPTECRTFFLTQGALLNDKHSNNTVKDRSPYRALMSVPLGSSPNAYQAKFESVAWSATACHDGKKWLAVGISGADDDAYAVIHYGGMPTDVVRSWRKQILRTQESSCVCMNGNCYWVMTDGPANSQASYKIFKSHEGMVTNEREVSFQGGHIEECSCYPNLGKVECVCRDNWNGMNRPILIFDEDLDYEVGYLCAGIPTDTPRVQDSSFTGSCTNAVGGSGTNNYGVKGFGFRQGNSVWAGRTVSISSRSGFEILLIEDGWIRTSKTIVKKVEVLNNKNWSGYSGAFTIPITMTSKQCLVPCFWLEMIRGKPEERTSIWTSSSSTVFCGVSSEVPGWSWDDGAILPFDIDK  472
               SCOP domains d3ti8a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhh.....eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeee.......eeeeeeee..eeeeeeee.......eeeeeeee..eeeeeee........eeeee.....eeeee............hhhhh.....................eeee..eeeeee.......eeeeeeee..........eeeeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee.........eeeeeeeeeee................hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ti8 A   82 PEFLNNTEPLCNVSGFAIVSKDNGIRIGSRGHVFVIREPFVACGPTECRTFFLTQGALLNDKHSNNTVKDRSPYRALMSVPLGSSPNAYQAKFESVAWSATACHDGKKWLAVGISGADDDAYAVIHYGGMPTDVVRSWRKQILRTQESSCVCMNGNCYWVMTDGPANSQASYKIFKSHEGMVTNEREVSFQGGHIEECSCYPNLGKVECVCRDNWNGMNRPILIFDEDLDYEVGYLCAGIPTDTPRVQDSSFTGSCTNAVGGSGTNNYGVKGFGFRQGNSVWAGRTVSISSRSGFEILLIEDGWIRTSKTIVKKVEVLNNKNWSGYSGAFTIPITMTSKQCLVPCFWLEMIRGKPEERTSIWTSSSSTVFCGVSSEVPGWSWDDGAILPFDIDK  470
                                    91       101       111       121       131       141       151       161   |   170       180       190       200       210       220       230       240       250       260       270       280       290       300     ||311       321       331       341      |349       359       369       379     ||390       400       410   ||||416       426       436       446       456       466    
                                                                                                            164A                                                                                                                                           306|                                    347A|                                   385|                       413A|||                                                         
                                                                                                                                                                                                                                                            308                                     347B                                    387                        413B||                                                         
                                                                                                                                                                                                                                                                                                                                                                        413C|                                                         
                                                                                                                                                                                                                                                                                                                                                                         413D

Chain B from PDB  Type:PROTEIN  Length:394
 aligned with A1ILL9_I76A2 | A1ILL9 from UniProtKB/TrEMBL  Length:473

    Alignment length:394
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468    
        A1ILL9_I76A2     79 PEFLNNTEPLCNVSGFAIVSKDNGIRIGSRGHVFVIREPFVACGPTECRTFFLTQGALLNDKHSNNTVKDRSPYRALMSVPLGSSPNAYQAKFESVAWSATACHDGKKWLAVGISGADDDAYAVIHYGGMPTDVVRSWRKQILRTQESSCVCMNGNCYWVMTDGPANSQASYKIFKSHEGMVTNEREVSFQGGHIEECSCYPNLGKVECVCRDNWNGMNRPILIFDEDLDYEVGYLCAGIPTDTPRVQDSSFTGSCTNAVGGSGTNNYGVKGFGFRQGNSVWAGRTVSISSRSGFEILLIEDGWIRTSKTIVKKVEVLNNKNWSGYSGAFTIPITMTSKQCLVPCFWLEMIRGKPEERTSIWTSSSSTVFCGVSSEVPGWSWDDGAILPFDIDK  472
               SCOP domains d3ti8b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhh.....eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeee.......eeeeeeee..eeeeeeee.......eeeeeeee..eeeeeee........eeeee.....eeeee............hhhhh.....................eeee..eeeeee.......eeeeeeee..........eeeeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee.........eeeeeeeeeee................hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ti8 B   82 PEFLNNTEPLCNVSGFAIVSKDNGIRIGSRGHVFVIREPFVACGPTECRTFFLTQGALLNDKHSNNTVKDRSPYRALMSVPLGSSPNAYQAKFESVAWSATACHDGKKWLAVGISGADDDAYAVIHYGGMPTDVVRSWRKQILRTQESSCVCMNGNCYWVMTDGPANSQASYKIFKSHEGMVTNEREVSFQGGHIEECSCYPNLGKVECVCRDNWNGMNRPILIFDEDLDYEVGYLCAGIPTDTPRVQDSSFTGSCTNAVGGSGTNNYGVKGFGFRQGNSVWAGRTVSISSRSGFEILLIEDGWIRTSKTIVKKVEVLNNKNWSGYSGAFTIPITMTSKQCLVPCFWLEMIRGKPEERTSIWTSSSSTVFCGVSSEVPGWSWDDGAILPFDIDK  470
                                    91       101       111       121       131       141       151       161   |   170       180       190       200       210       220       230       240       250       260       270       280       290       300     ||311       321       331       341      |349       359       369       379     ||390       400       410   ||||416       426       436       446       456       466    
                                                                                                            164A                                                                                                                                           306|                                    347A|                                   385|                       413A|||                                                         
                                                                                                                                                                                                                                                            308                                     347B                                    387                        413B||                                                         
                                                                                                                                                                                                                                                                                                                                                                        413C|                                                         
                                                                                                                                                                                                                                                                                                                                                                         413D

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: All beta proteins (24004)

Fold: 6-bladed beta-propeller (327)

Superfamily: Sialidases (238)

Family: automated matches (54)

Protein domain: automated matches (54)

Influenza A virus [TaxId: 385582] (3)

1a	d3ti8a_	A:
1b	d3ti8b_	B:

(no "CATH Domain" information available for 3TI8)

(no "Pfam Domain" information available for 3TI8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (A1ILL9_I76A2 | A1ILL9)

molecular function
	GO:0052794	exo-alpha-(2->3)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->3)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0052795	exo-alpha-(2->6)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->6)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0052796	exo-alpha-(2->8)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->8)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0004308	exo-alpha-sialidase activity	Catalysis of the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
	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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Asymmetric Unit
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	Cis Peptide Bonds
		Leu A:464 - Pro A:465	[ RasMol ]
		Leu B:464 - Pro B:465	[ RasMol ]
		Lys A:430 - Pro A:431	[ RasMol ]
		Lys B:430 - Pro B:431	[ RasMol ]
		Thr A:325 - Pro A:326	[ RasMol ]
		Thr B:325 - Pro B:326	[ RasMol ]

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	3ti8
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	A1ILL9_I76A2 \| A1ILL9	:	3sal 3san

3sal	INFLUENZA A VIRUS NEURAMINIDASE N5 HAS AN EXTENDED 150- CAVITY
3san	INFLUENZA A VIRUS NEURAMINIDASE N5 HAS AN EXTENDED 150- CAVITY
3ti3
3ti4
3ti5
3ti6
3tia
3tib
3tic

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (16, 16)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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