2AEP: Neuraminidase

An epidemiologically significant epitope of a 1998 influenza virus neuraminidase forms a highly hydrated interface in the NA-antibody complex. Determined by X-ray diffraction at 2.1 Å resolution. Released 20 Dec 2005.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Influenza A virus, Mus musculus
Chains: 3
Atoms: 5,812
Mol. weight: 93.74 kDa
Ligands: MAN, CA, NAG, GLC
Released: 20 Dec 2005

Explore 2AEP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2AEP contains 13 α-helices and 50 β-strands across 3 chains. 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: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	90	1
β-strand	91	1	1
α-helix	92-93	2
β-strand	96-102	7	1
α-helix	105-109	5
β-strand	115-124	10	2
β-strand	129-139	11	2
α-helix	143-145	3
β-strand	157-162	6	2
β-strand	172-176	5	2
β-strand	179-184	6	3
β-strand	189-195	7	3
β-strand	202-207	6	3
β-strand	210-216	7	3
β-strand	224	1	4
β-strand	231-233	3	4
β-strand	236-244	9	4
β-strand	250-258	9	4
β-strand	261-267	7	4
β-strand	276-283	8	5
β-strand	286-292	7	5
α-helix	300	1
β-strand	301-305	5	5
β-strand	312-316	5	5
β-strand	353-356	4	6
β-strand	359-364	6	6
β-strand	372-379	8	6
β-strand	391-403	13	6
β-strand	407-413	7	1
β-strand	418-429	12	1
β-strand	439-449	11	1
α-helix	464-466	3

Chain H: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	46-51	6	8
α-helix	52B-53	3
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-96	9	8
β-strand	100-103	5	8
β-strand	107-111	5	8

Chain L: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	9
β-strand	10-13	4	10
β-strand	19-25	7	9
β-strand	33-38	6	10
β-strand	45-50	6	10
β-strand	53-54	2	10
α-helix	55	1
β-strand	62-67	6	9
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	84-90	7	10
α-helix	96	1
β-strand	97-98	2	10
β-strand	102-106	5	10
β-strand	111	1	11
β-strand	140	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
neuraminidase	A	protein	395	Influenza A virus	Q9DL16
FAB heavy chain	H	protein	217	Mus musculus	P84751 (AlphaFold model)
FAB light chain	L	protein	214	Mus musculus	P84750 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2AEP_1 neuraminidase (chains A)
KEICPKLAEYRNWSKPQCKITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFAL
GQGTTLNNRHSNDTVHDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCV
TGHDENATASFIYDGRLVDSIGSWSKKILRTQESECVCINGTCTVVMTDGSASGRADTKI
LFIEEGKIVHISPLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNRPIVDINVKDYSIVS
SYVCSGLVGDTPRKNDSSSSSHCLNPNNEEGGHGVKGWAFDDGNDVWMGRTISEKFRSGY
ETFKVIEGWSKPNSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINRCFYVELIRGRKQET
EVWWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI

Sequence of entity 2 (H), FASTA

>2AEP_2 FAB heavy chain (chains H)
EVKLVESGGGLVQPGGSLSLSCATSGFTFIDYYMSWFRQPPGKALEWLGLIRNKGNGYTM
EYSASLKGRFTISRDNSQSIVYLHMNTLTAEDSATYYCARVDYGTNYDYWGQGTTLTVSS
AKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKI

Sequence of entity 3 (L), FASTA

>2AEP_3 FAB light chain (chains L)
DILMTQSQKFLSTSVGDRVSVTCKASQNVGTNVAWYQKKPGQSPKPLMYSASYRYSGVPD
RFTGSGSGTDFTLTISNVQSEDLAEYFCQQFNRYPLTFGSGTKLELKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
MAN	alpha-D-mannopyranose	C6 H12 O6	1
CA	Calcium ion	Ca	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
GLC	alpha-D-glucopyranose	C6 H12 O6	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

An Epidemiologically Significant Epitope of a 1998 Human Influenza Virus Neuraminidase Forms a Highly Hydrated Interface in the NA-Antibody Complex. Venkatramani, L., Bochkareva, E., Lee, J.T. et al. J Mol Biol (2006) 356:651-663. DOI 10.1016/j.jmb.2005.11.061 · PubMed

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