4DGR: Neuraminidase

Influenza Subtype 9 Neuraminidase Benzoic Acid Inhibitor Complex. Determined by X-ray diffraction at 1.55 Å resolution. Released 16 May 2012.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Influenza A virus (A/tern/Australia/G70C/1975(H11N9))
Chains: 1
Atoms: 3,859
Mol. weight: 47.72 kDa
Ligands: CA, PO4, 3LV, GLC
Released: 16 May 2012

Explore 4DGR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DGR contains 8 α-helices and 30 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	90-91	2	1
α-helix	92-93	2
β-strand	96-102	7	2
α-helix	105-109	5
β-strand	114	1	3
β-strand	115-124	10	4
β-strand	129-139	11	4
α-helix	143-145	3
β-strand	157-162	6	4
β-strand	168	1	3
α-helix	171	1
β-strand	172-176	5	4
β-strand	179-184	6	5
β-strand	189-195	7	5
β-strand	202-207	6	5
β-strand	210-216	7	5
β-strand	224	1	6
β-strand	233	1	7
β-strand	236	1	7
β-strand	237-244	8	6
β-strand	250-258	9	6
β-strand	261-267	7	6
β-strand	276-283	8	8
β-strand	286-292	7	8
α-helix	300	1
β-strand	301-306	6	8
β-strand	311-316	6	8
α-helix	340-342	3
β-strand	353-354	2	9
β-strand	361-364	4	9
β-strand	372-378	7	9
β-strand	392-403	11	9
β-strand	407-410	4	2
β-strand	417-418	2	1
α-helix	419-420	2
β-strand	421-429	9	2
β-strand	439-449	11	2
α-helix	464-467	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuraminidase	A	protein	389	Influenza A virus (A/tern/Australia/G70C/1975(H11N9))	P03472

Sequence of entity 1 (A), FASTA

>4DGR_1 Neuraminidase (chains A)
IRDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTI
RGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNN
NASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKE
GKILKWEPLAGTAKHIEECSCYGERAEITCTCRDNWQGSNRPVIRIDPVAMTHTSQYICS
PVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVP
NALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWT
SNSIVSMCSSTEFLGQWDWPDGAKIEYFL

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
PO4	Phosphate ion	O4 P	1
3LV	4-[2,2-bis(hydroxymethyl)-5-oxopyrrolidin-1-yl]-3-[(dipropylamino)methyl]benzoi…	C20 H30 N2 O5	1
GLC	alpha-D-glucopyranose	C6 H12 O6	1
BGC	beta-D-glucopyranose	C6 H12 O6	3

Water and common crystallization additives (K) are not listed.

Primary citation

Crystal structure of a new benzoic acid inhibitor of influenza neuraminidase bound with a new tilt induced by overpacking sub-site C6. Venkatramani, L., Johnson, E.S., Kolavi, G. et al. BMC Struct Biol (2012) 12:7-7. DOI 10.1186/1472-6807-12-7 · PubMed

Other PDB entries of the same protein (UniProt P03472), best resolution first:

6HFC 1.29 Å, Influenza A Virus N9 Neuraminidase Native (Tern).
6HCX 1.3 Å, Influenza Virus N9 Neuraminidase A complex with Zanamivir molecule (Tern).
6HG0 1.3 Å, Influenza A Virus N9 Neuraminidase complex with NANA (Tern/Australia).
1F8D 1.4 Å, Native Influenza Neuraminidase in Complex with 9-amino-2-deoxy-2,3-dehydro-N-neuraminic…
1F8E 1.4 Å, Native Influenza Neuraminidase in Complex with 4,9-diamino-2-deoxy-2,3-dehydro-N-acetyl-n…
6D3B 1.4 Å, Influenza virus neuraminidase subtype N9 (TERN) apo form
2QWC 1.6 Å, The X-ray structure of a complex of NEU5AC2EN and a drug resistant variant R292K of tern…
1F8C 1.7 Å, Native Influenza Neuraminidase in Complex with 4-amino-2-deoxy-2,3-dehydro-N-neuraminic…
1MWE 1.7 Å, The X-ray structure of a complex of tern N9 influenza virus neuraminidase complexed with…
2QWA 1.7 Å, The X-ray structure of a drug resistant variant R292K of tern N9 influenza virus…
6HEB 1.75 Å, Influenza A Virus N9 Neuraminidase complex with Oseltamivir (Tern).
1F8B 1.8 Å, Native Influenza Virus Neuraminidase in Complex with NEU5AC2EN

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