1NCA: Influenza a subtype N9 neuraminidase

Refined crystal structure of the influenza virus N9 neuraminidase-NC41 FAB complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 31 Jan 1994.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Influenza A virus, Mus musculus
Chains: 3
Atoms: 6,577
Mol. weight: 92.74 kDa
Ligands: CA, NAG
Released: 31 Jan 1994

Explore 1NCA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NCA contains 22 α-helices and 73 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 H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	14
α-helix	7-9	3
β-strand	10-12	3	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	34-40	7	15
β-strand	44-51	8	15
β-strand	57-59	3	15
α-helix	61-63	3
β-strand	64	1	14
β-strand	67-72	6	14
α-helix	73-75	3
β-strand	77-82	6	14
α-helix	84-86	3
β-strand	88-95	8	15
β-strand	100C-103	4	15
β-strand	107-111	5	15
α-helix	114-116	3
β-strand	117	1	16
β-strand	120-124	5	17
β-strand	137-147	11	17
β-strand	148	1	16
β-strand	153-157	4	18
β-strand	166	1	18
β-strand	171-173	3	17
α-helix	174-176	3
β-strand	177-179	3	17
β-strand	184-194	11	17
β-strand	206-212	6	18
β-strand	217-222	6	18

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	9
β-strand	10-13	4	10
β-strand	19-25	7	9
β-strand	33-38	6	10
β-strand	44-49	6	10
β-strand	53-54	2	10
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	98	1	10
β-strand	102-106	5	10
α-helix	108-110	3
β-strand	111	1	11
β-strand	114-118	5	12
α-helix	122-126	5
β-strand	129-139	11	12
β-strand	140	1	11
β-strand	144-150	7	13
β-strand	153-155	3	13
β-strand	159-163	5	12
α-helix	164-167	4
β-strand	173-182	10	12
α-helix	183-186	4
β-strand	192-198	7	13
α-helix	204	1
β-strand	205-209	5	13

Chain N: 8 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	91	1	1
α-helix	92-93	2
β-strand	96-102	7	2
α-helix	105-108	4
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
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	224-225	2	6
β-strand	233	1	6
β-strand	236-244	9	6
β-strand	250-258	9	6
β-strand	261-267	7	6
β-strand	279-283	5	7
β-strand	286-290	5	7
α-helix	300	1
β-strand	301-306	6	7
β-strand	311-316	6	7
α-helix	328-330	3
α-helix	340-341	2
β-strand	353-354	2	8
α-helix	357-359	3
β-strand	361-364	4	8
β-strand	372-378	7	8
β-strand	392-403	11	8
β-strand	407-411	5	2
β-strand	418	1	1
β-strand	420-429	10	2
β-strand	439-449	11	2
α-helix	464-467	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Influenza a subtype N9 neuraminidase	N	protein	389	Influenza A virus	P03472
IGG2A-kappa NC41 FAB (light chain)	L	protein	214	Mus musculus
IGG2A-kappa NC41 FAB (heavy chain)	H	protein	221	Mus musculus	P01865 (AlphaFold model)

Sequence of entity 1 (N), FASTA

>1NCA_1 INFLUENZA A SUBTYPE N9 NEURAMINIDASE (chains N)
IRDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTI
RGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNN
NASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKE
GKILKWEPLAGTAKHIEECSCYGERAEITCTCRDNWQGSNRPVIRIDPVAMTHTSQYICS
PVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVP
NALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWT
SNSIVSMCSSTEFLGQWDWPDGAKIEYFL

Sequence of entity 2 (L), FASTA

>1NCA_2 IGG2A-KAPPA NC41 FAB (LIGHT CHAIN) (chains L)
DIVMTQSPKFMSTSVGDRVTITCKASQDVSTAVVWYQQKPGQSPKLLIYWASTRHIGVPD
RFAGSGSGTDYTLTISSVQAEDLALYYCQQHYSPPWTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (H), FASTA

>1NCA_3 IGG2A-KAPPA NC41 FAB (HEAVY CHAIN) (chains H)
QIQLVQSGPELKKPGETVKISCKASGYTFTNYGMNWVKQAPGKGLKWMGWINTNTGEPTY
GEEFKGRFAFSLETSASTANLQINNLKNEDTATFFCARGEDNFGSLSDYWGQGTTVTVSS
AKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex. Tulip, W.R., Varghese, J.N., Laver, W.G. et al. J Mol Biol (1992) 227:122-148. DOI 10.1016/0022-2836(92)90687-F · 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
4DGR 1.55 Å, Influenza Subtype 9 Neuraminidase Benzoic Acid Inhibitor Complex
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).

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